Starting phenix.real_space_refine on Sat Jun 28 10:10:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdn_17615/06_2025/8pdn_17615.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdn_17615/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8pdn_17615/06_2025/8pdn_17615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdn_17615/06_2025/8pdn_17615.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdn_17615/06_2025/8pdn_17615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdn_17615/06_2025/8pdn_17615.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 19.35, per 1000 atoms: 0.58 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: 9.10 Conformation dependent library (CDL) restraints added in 4.6 seconds 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7560 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 24 sheets defined 69.9% alpha, 2.4% beta 0 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 12.49 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: 13.25 Time building geometry restraints manager: 10.73 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: 0.29 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'b' selection = chain 'e' selection = chain 'd' selection = chain 'g' selection = chain 'f' selection = chain 'i' selection = chain 'h' selection = chain 'k' selection = chain 'j' selection = chain 'l' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'b' selection = chain 'e' selection = chain 'd' selection = chain 'g' selection = chain 'f' selection = chain 'i' selection = chain 'h' selection = chain 'k' selection = chain 'j' selection = chain 'l' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.570 Check model and map are aligned: 0.270 Set scattering table: 0.310 Process input model: 85.260 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.310 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (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 TRP 0.005 0.001 TRP E 123 HIS 0.004 0.001 HIS L 275 PHE 0.014 0.002 PHE K 169 TYR 0.032 0.003 TYR G 53 ARG 0.008 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.11155 ( 1969) hydrogen bonds : angle 5.77744 ( 5799) covalent geometry : bond 0.00672 (33888) covalent geometry : angle 0.66180 (46104) 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0091 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 : 0.005 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 : 0.288 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.4412 (mtm) cc_final: 0.3660 (mtp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2060 time to fit residues: 12.3058 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 : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 8.9990 chunk 300 optimal weight: 10.0000 chunk 166 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 310 optimal weight: 7.9990 chunk 120 optimal weight: 0.0050 chunk 188 optimal weight: 0.0070 chunk 231 optimal weight: 7.9990 chunk 359 optimal weight: 0.3980 overall best weight: 1.0414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 256 GLN F 303 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.069100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.068161 restraints weight = 1485.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.068753 restraints weight = 296.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.068931 restraints weight = 110.385| |-----------------------------------------------------------------------------| r_work (final): 0.3257 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.082364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.067994 restraints weight = 11018.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.070120 restraints weight = 7327.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.071691 restraints weight = 5333.080| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.337 33890 Z= 0.261 Angle : 0.552 6.487 46104 Z= 0.295 Chirality : 0.039 0.131 5436 Planarity : 0.006 0.081 5580 Dihedral : 12.059 73.759 5760 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.50 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.14), residues: 4020 helix: 1.37 (0.10), residues: 2820 sheet: -1.40 (0.32), residues: 180 loop : -0.66 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 261 HIS 0.002 0.001 HIS B 56 PHE 0.011 0.002 PHE I 169 TYR 0.016 0.002 TYR E 252 ARG 0.019 0.001 ARG D 78 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 1969) hydrogen bonds : angle 4.24693 ( 5799) covalent geometry : bond 0.00259 (33888) covalent geometry : angle 0.55182 (46104) Misc. bond : bond 0.29548 ( 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0068 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 : 0.005 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 : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 TYR cc_start: 0.8537 (m-10) cc_final: 0.7614 (t80) REVERT: F 90 VAL cc_start: 0.8870 (m) cc_final: 0.8505 (t) REVERT: F 134 THR cc_start: 0.8247 (m) cc_final: 0.7968 (p) REVERT: F 170 THR cc_start: 0.9116 (p) cc_final: 0.8795 (t) REVERT: F 303 HIS cc_start: 0.8284 (m-70) cc_final: 0.7761 (m-70) outliers start: 1 outliers final: 1 residues processed: 120 average time/residue: 0.1943 time to fit residues: 26.6032 Evaluate side-chains 71 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 257 optimal weight: 0.6980 chunk 328 optimal weight: 3.9990 chunk 87 optimal weight: 0.0270 chunk 369 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 346 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 366 optimal weight: 4.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.065625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.064978 restraints weight = 2044.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.065192 restraints weight = 358.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.065319 restraints weight = 90.183| |-----------------------------------------------------------------------------| r_work (final): 0.3269 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.080199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.066376 restraints weight = 11707.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.068258 restraints weight = 7818.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.069652 restraints weight = 5756.605| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.498 33890 Z= 1.196 Angle : 0.985 30.197 46104 Z= 0.555 Chirality : 0.045 0.164 5436 Planarity : 0.009 0.102 5580 Dihedral : 12.456 75.065 5760 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 26.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.35 % Allowed : 4.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 4020 helix: 0.68 (0.10), residues: 2772 sheet: -1.87 (0.27), residues: 228 loop : -1.06 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 261 HIS 0.004 0.002 HIS E 303 PHE 0.012 0.002 PHE G 244 TYR 0.020 0.002 TYR L 23 ARG 0.019 0.002 ARG L 339 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 1969) hydrogen bonds : angle 4.55505 ( 5799) covalent geometry : bond 0.02241 (33888) covalent geometry : angle 0.98454 (46104) Misc. bond : bond 0.31634 ( 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0066 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 : 0.005 Evaluate side-chains 88 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 TYR cc_start: 0.8643 (m-10) cc_final: 0.7648 (t80) REVERT: F 14 LYS cc_start: 0.8790 (mttt) cc_final: 0.8433 (mmtt) REVERT: F 145 ASN cc_start: 0.8127 (m110) cc_final: 0.7879 (m110) REVERT: F 149 ASN cc_start: 0.8123 (p0) cc_final: 0.7621 (m110) REVERT: F 239 LYS cc_start: 0.8296 (mttm) cc_final: 0.7930 (tptt) REVERT: F 272 MET cc_start: 0.7798 (mpp) cc_final: 0.7458 (mpp) outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.1628 time to fit residues: 16.5957 Evaluate side-chains 54 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 54 optimal weight: 6.9990 chunk 120 optimal weight: 0.4980 chunk 211 optimal weight: 0.0030 chunk 258 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 chunk 368 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 117 HIS F 275 HIS F 303 HIS ** F 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.079246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.077379 restraints weight = 1383.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.078195 restraints weight = 533.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.078710 restraints weight = 244.053| |-----------------------------------------------------------------------------| r_work (final): 0.3273 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.081532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.067929 restraints weight = 11983.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.069852 restraints weight = 8109.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.071273 restraints weight = 5979.190| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.6592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.503 33890 Z= 1.190 Angle : 0.898 28.999 46104 Z= 0.513 Chirality : 0.044 0.187 5436 Planarity : 0.007 0.094 5580 Dihedral : 12.110 73.888 5760 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 4.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 4020 helix: 0.52 (0.09), residues: 2844 sheet: -2.00 (0.27), residues: 228 loop : -0.56 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 261 HIS 0.006 0.001 HIS H 303 PHE 0.009 0.001 PHE C 244 TYR 0.020 0.002 TYR E 252 ARG 0.024 0.001 ARG D 339 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 1969) hydrogen bonds : angle 4.26944 ( 5799) covalent geometry : bond 0.02219 (33888) covalent geometry : angle 0.89788 (46104) Misc. bond : bond 0.31525 ( 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0063 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 : 0.005 Evaluate side-chains 73 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 TYR cc_start: 0.8654 (m-10) cc_final: 0.7539 (t80) REVERT: F 14 LYS cc_start: 0.8699 (mttt) cc_final: 0.8423 (mmtt) REVERT: F 149 ASN cc_start: 0.7937 (p0) cc_final: 0.7665 (p0) REVERT: F 162 LEU cc_start: 0.9638 (mt) cc_final: 0.9355 (mt) REVERT: F 216 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8772 (tm-30) REVERT: F 239 LYS cc_start: 0.8259 (mttm) cc_final: 0.7948 (tptt) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1350 time to fit residues: 11.8400 Evaluate side-chains 48 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 239 optimal weight: 7.9990 chunk 375 optimal weight: 0.0030 chunk 333 optimal weight: 8.9990 chunk 383 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 299 optimal weight: 2.9990 chunk 86 optimal weight: 0.0980 chunk 164 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.075762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.073812 restraints weight = 1353.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.074493 restraints weight = 494.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.074946 restraints weight = 256.475| |-----------------------------------------------------------------------------| r_work (final): 0.3246 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.081185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.068211 restraints weight = 12109.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.070157 restraints weight = 8237.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.071562 restraints weight = 6030.443| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.6919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.520 33890 Z= 1.187 Angle : 0.888 29.791 46104 Z= 0.512 Chirality : 0.042 0.155 5436 Planarity : 0.006 0.097 5580 Dihedral : 11.887 73.532 5760 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.35 % Allowed : 5.57 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 4020 helix: 0.55 (0.10), residues: 2844 sheet: -2.15 (0.28), residues: 228 loop : -0.61 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 123 HIS 0.006 0.002 HIS G 15 PHE 0.009 0.001 PHE A 244 TYR 0.023 0.002 TYR C 252 ARG 0.029 0.001 ARG K 339 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 1969) hydrogen bonds : angle 4.38210 ( 5799) covalent geometry : bond 0.02227 (33888) covalent geometry : angle 0.88772 (46104) Misc. bond : bond 0.27548 ( 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0073 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 : 0.005 Evaluate side-chains 72 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 14 LYS cc_start: 0.8770 (mttt) cc_final: 0.8384 (mmtp) REVERT: F 149 ASN cc_start: 0.7882 (p0) cc_final: 0.7576 (p0) REVERT: F 162 LEU cc_start: 0.9661 (mt) cc_final: 0.9387 (mt) REVERT: F 171 LYS cc_start: 0.8861 (mmpt) cc_final: 0.8452 (mmmt) REVERT: F 216 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8678 (tm-30) REVERT: F 239 LYS cc_start: 0.8242 (mttm) cc_final: 0.7868 (tptt) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1377 time to fit residues: 12.1553 Evaluate side-chains 49 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 266 optimal weight: 9.9990 chunk 338 optimal weight: 2.9990 chunk 324 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 259 optimal weight: 1.9990 chunk 124 optimal weight: 0.0050 chunk 36 optimal weight: 7.9990 chunk 366 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 117 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.074937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.073067 restraints weight = 1414.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.073803 restraints weight = 527.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.074181 restraints weight = 268.616| |-----------------------------------------------------------------------------| r_work (final): 0.3286 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.079071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.066438 restraints weight = 11779.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.068343 restraints weight = 7577.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.069771 restraints weight = 5490.529| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.7301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.515 33890 Z= 1.182 Angle : 0.857 29.364 46104 Z= 0.508 Chirality : 0.042 0.177 5436 Planarity : 0.006 0.051 5580 Dihedral : 11.921 73.426 5760 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.13), residues: 4020 helix: 0.62 (0.10), residues: 2844 sheet: -2.28 (0.27), residues: 228 loop : -0.51 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 261 HIS 0.005 0.001 HIS L 303 PHE 0.011 0.001 PHE I 244 TYR 0.022 0.002 TYR C 252 ARG 0.018 0.001 ARG K 339 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 1969) hydrogen bonds : angle 4.44283 ( 5799) covalent geometry : bond 0.02218 (33888) covalent geometry : angle 0.85737 (46104) Misc. bond : bond 0.27254 ( 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0064 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 : 0.005 Evaluate side-chains 66 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 14 LYS cc_start: 0.8751 (mttt) cc_final: 0.8434 (mmtp) REVERT: F 162 LEU cc_start: 0.9665 (mt) cc_final: 0.9406 (mt) REVERT: F 216 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8667 (tm-30) REVERT: F 239 LYS cc_start: 0.8272 (mttm) cc_final: 0.7838 (tptt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1328 time to fit residues: 10.6937 Evaluate side-chains 46 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 110 optimal weight: 2.9990 chunk 341 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 243 optimal weight: 6.9990 chunk 206 optimal weight: 0.9980 chunk 215 optimal weight: 0.0570 chunk 325 optimal weight: 5.9990 chunk 63 optimal weight: 0.3980 chunk 98 optimal weight: 0.2980 chunk 37 optimal weight: 0.0010 chunk 268 optimal weight: 0.9990 overall best weight: 0.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 81 GLN F 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.073198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.071216 restraints weight = 1684.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.071937 restraints weight = 544.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072371 restraints weight = 256.334| |-----------------------------------------------------------------------------| r_work (final): 0.3240 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.080831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.068010 restraints weight = 12090.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.070160 restraints weight = 7719.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.071383 restraints weight = 5442.728| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.7643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.518 33890 Z= 1.186 Angle : 0.914 29.479 46104 Z= 0.518 Chirality : 0.042 0.127 5436 Planarity : 0.007 0.112 5580 Dihedral : 11.879 73.429 5760 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.70 % Allowed : 2.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 4020 helix: 0.52 (0.10), residues: 2832 sheet: -2.18 (0.30), residues: 228 loop : -0.51 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 123 HIS 0.004 0.001 HIS F 303 PHE 0.009 0.001 PHE K 244 TYR 0.022 0.002 TYR G 252 ARG 0.033 0.002 ARG K 339 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 1969) hydrogen bonds : angle 4.34304 ( 5799) covalent geometry : bond 0.02227 (33888) covalent geometry : angle 0.91391 (46104) Misc. bond : bond 0.27478 ( 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0077 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 : 0.005 Evaluate side-chains 68 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.311 Fit side-chains REVERT: F 14 LYS cc_start: 0.8730 (mttt) cc_final: 0.8365 (mmtp) REVERT: F 48 CYS cc_start: 0.9441 (m) cc_final: 0.9039 (m) REVERT: F 162 LEU cc_start: 0.9643 (mt) cc_final: 0.9361 (mt) REVERT: F 171 LYS cc_start: 0.8601 (mmpt) cc_final: 0.8121 (mmmt) REVERT: F 216 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8784 (tm-30) REVERT: F 231 LEU cc_start: 0.8861 (tp) cc_final: 0.8630 (tp) REVERT: F 239 LYS cc_start: 0.8310 (mttm) cc_final: 0.7876 (tptt) REVERT: F 272 MET cc_start: 0.7783 (mpp) cc_final: 0.7439 (mmm) outliers start: 2 outliers final: 0 residues processed: 68 average time/residue: 0.1664 time to fit residues: 13.3328 Evaluate side-chains 46 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 344 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 286 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 385 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 389 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 161 optimal weight: 0.0970 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 81 GLN F 117 HIS ** F 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.071126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.070041 restraints weight = 1445.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.070625 restraints weight = 461.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.070868 restraints weight = 180.858| |-----------------------------------------------------------------------------| r_work (final): 0.3248 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.080550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.067804 restraints weight = 12004.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.069858 restraints weight = 7844.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.071340 restraints weight = 5603.242| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.8102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.516 33890 Z= 1.185 Angle : 0.912 29.516 46104 Z= 0.517 Chirality : 0.043 0.132 5436 Planarity : 0.006 0.070 5580 Dihedral : 11.782 73.414 5760 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 4020 helix: 0.50 (0.10), residues: 2772 sheet: -2.20 (0.31), residues: 228 loop : -0.37 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 261 HIS 0.003 0.001 HIS L 220 PHE 0.014 0.002 PHE H 244 TYR 0.019 0.002 TYR F 59 ARG 0.026 0.002 ARG K 339 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 1969) hydrogen bonds : angle 4.43759 ( 5799) covalent geometry : bond 0.02228 (33888) covalent geometry : angle 0.91206 (46104) Misc. bond : bond 0.27732 ( 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0066 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 : 0.005 Evaluate side-chains 61 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.325 Fit side-chains REVERT: F 14 LYS cc_start: 0.8755 (mttt) cc_final: 0.8445 (mmtp) REVERT: F 44 ILE cc_start: 0.9379 (tp) cc_final: 0.9118 (tt) REVERT: F 162 LEU cc_start: 0.9626 (mt) cc_final: 0.9379 (mt) REVERT: F 171 LYS cc_start: 0.8398 (mmpt) cc_final: 0.7970 (mmmt) REVERT: F 216 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8863 (tm-30) REVERT: F 239 LYS cc_start: 0.8494 (mttm) cc_final: 0.7870 (tptt) REVERT: F 272 MET cc_start: 0.7909 (mpp) cc_final: 0.7623 (mmm) REVERT: F 295 MET cc_start: 0.7970 (mmp) cc_final: 0.7733 (mmm) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.1822 time to fit residues: 12.9760 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 : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 15 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 170 optimal weight: 0.7980 chunk 356 optimal weight: 0.5980 chunk 349 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 195 optimal weight: 0.8980 chunk 294 optimal weight: 0.0770 chunk 16 optimal weight: 1.9990 chunk 173 optimal weight: 0.4980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle 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 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.073571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.071725 restraints weight = 1431.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.072588 restraints weight = 545.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.072917 restraints weight = 243.356| |-----------------------------------------------------------------------------| r_work (final): 0.3281 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.081722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.069110 restraints weight = 12139.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.071065 restraints weight = 8015.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.072471 restraints weight = 5786.949| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.8319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.514 33890 Z= 1.184 Angle : 0.914 29.524 46104 Z= 0.515 Chirality : 0.043 0.139 5436 Planarity : 0.005 0.062 5580 Dihedral : 11.869 73.398 5760 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 23.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.13), residues: 4020 helix: 0.60 (0.10), residues: 2748 sheet: -2.23 (0.32), residues: 228 loop : -0.17 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 261 HIS 0.005 0.001 HIS H 303 PHE 0.013 0.001 PHE K 244 TYR 0.018 0.002 TYR G 252 ARG 0.024 0.001 ARG K 339 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 1969) hydrogen bonds : angle 4.41488 ( 5799) covalent geometry : bond 0.02222 (33888) covalent geometry : angle 0.91416 (46104) Misc. bond : bond 0.27683 ( 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0064 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 : 0.005 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 : 0.316 Fit side-chains revert: symmetry clash REVERT: F 14 LYS cc_start: 0.8812 (mttt) cc_final: 0.8563 (mmtm) REVERT: F 52 LEU cc_start: 0.5964 (mm) cc_final: 0.5603 (mm) REVERT: F 161 LEU cc_start: 0.9435 (pp) cc_final: 0.8888 (pp) REVERT: F 162 LEU cc_start: 0.9668 (mt) cc_final: 0.9434 (mt) REVERT: F 171 LYS cc_start: 0.8305 (mmpt) cc_final: 0.7839 (mmmt) REVERT: F 216 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8719 (tm-30) REVERT: F 239 LYS cc_start: 0.8468 (mttm) cc_final: 0.7797 (tptt) REVERT: F 272 MET cc_start: 0.7842 (mpp) cc_final: 0.7276 (mmm) REVERT: F 304 LEU cc_start: 0.8927 (mp) cc_final: 0.8329 (mp) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.1445 time to fit residues: 11.4810 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 : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 271 optimal weight: 8.9990 chunk 336 optimal weight: 0.5980 chunk 162 optimal weight: 0.9990 chunk 0 optimal weight: 10.9990 chunk 278 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 126 optimal weight: 0.0020 chunk 347 optimal weight: 0.0980 chunk 131 optimal weight: 0.0980 chunk 345 optimal weight: 0.6980 chunk 279 optimal weight: 0.3980 overall best weight: 0.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 HIS ** F 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.071977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.070268 restraints weight = 1566.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.071038 restraints weight = 555.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.071432 restraints weight = 263.109| |-----------------------------------------------------------------------------| r_work (final): 0.3220 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.082042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.068720 restraints weight = 11959.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.070702 restraints weight = 8067.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.071953 restraints weight = 5960.479| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.8767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.516 33890 Z= 1.186 Angle : 0.945 29.606 46104 Z= 0.529 Chirality : 0.042 0.178 5436 Planarity : 0.005 0.052 5580 Dihedral : 11.678 73.449 5760 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.13), residues: 4020 helix: 0.62 (0.10), residues: 2748 sheet: -2.26 (0.32), residues: 228 loop : 0.02 (0.21), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 261 HIS 0.005 0.001 HIS H 303 PHE 0.020 0.002 PHE F 248 TYR 0.013 0.002 TYR F 59 ARG 0.023 0.001 ARG K 339 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 1969) hydrogen bonds : angle 4.69453 ( 5799) covalent geometry : bond 0.02229 (33888) covalent geometry : angle 0.94530 (46104) Misc. bond : bond 0.27870 ( 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 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0066 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 : 0.005 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 : 0.290 Fit side-chains revert: symmetry clash REVERT: F 14 LYS cc_start: 0.8805 (mttt) cc_final: 0.8594 (mmtt) REVERT: F 80 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8382 (tm-30) REVERT: F 216 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8729 (tm-30) REVERT: F 239 LYS cc_start: 0.8361 (mttm) cc_final: 0.7737 (tptt) REVERT: F 272 MET cc_start: 0.7929 (mpp) cc_final: 0.7414 (mmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1209 time to fit residues: 8.7000 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 : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 163 optimal weight: 0.0070 chunk 276 optimal weight: 8.9990 chunk 389 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 348 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 270 optimal weight: 0.0070 chunk 175 optimal weight: 7.9990 chunk 216 optimal weight: 0.5980 chunk 326 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 overall best weight: 0.8818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.070990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.069300 restraints weight = 1469.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.070047 restraints weight = 501.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.070491 restraints weight = 241.005| |-----------------------------------------------------------------------------| r_work (final): 0.3220 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.081693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.068259 restraints weight = 11852.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.070250 restraints weight = 7974.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.071674 restraints weight = 5852.937| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.8971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.515 33890 Z= 1.183 Angle : 0.900 29.479 46104 Z= 0.507 Chirality : 0.041 0.143 5436 Planarity : 0.005 0.049 5580 Dihedral : 11.646 73.408 5760 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.13), residues: 4020 helix: 0.67 (0.10), residues: 2760 sheet: -1.26 (0.38), residues: 180 loop : 0.03 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 261 HIS 0.004 0.001 HIS H 303 PHE 0.019 0.002 PHE F 248 TYR 0.014 0.002 TYR J 252 ARG 0.021 0.001 ARG D 339 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 1969) hydrogen bonds : angle 4.56208 ( 5799) covalent geometry : bond 0.02218 (33888) covalent geometry : angle 0.90019 (46104) Misc. bond : bond 0.27874 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5577.68 seconds wall clock time: 100 minutes 39.16 seconds (6039.16 seconds total)