Starting phenix.real_space_refine on Fri May 30 02:12:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdn_17615/05_2025/8pdn_17615.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdn_17615/05_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_17615/05_2025/8pdn_17615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdn_17615/05_2025/8pdn_17615.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdn_17615/05_2025/8pdn_17615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdn_17615/05_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 18.67, per 1000 atoms: 0.56 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: 9.34 Conformation dependent library (CDL) restraints added in 4.3 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: 10.90 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: 11.28 Time building geometry restraints manager: 10.76 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: 0.31 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.240 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 77.320 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.230 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: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.370 ------------------------------------------------------------------------------- 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 : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0076 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 : 0.013 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 : 0.332 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: 0.2096 time to fit residues: 12.6040 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 : 0.290 ------------------------------------------------------------------------------- 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 = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.068089 restraints weight = 1485.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.068718 restraints weight = 322.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.068937 restraints weight = 119.673| |-----------------------------------------------------------------------------| 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 = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.067983 restraints weight = 11018.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.070119 restraints weight = 7326.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.071690 restraints weight = 5335.086| |-----------------------------------------------------------------------------| 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 : 11.49 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 G 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 K 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: 0.0073 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 : 0.007 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 : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 TYR cc_start: 0.8537 (m-10) cc_final: 0.7613 (t80) REVERT: F 90 VAL cc_start: 0.8870 (m) cc_final: 0.8505 (t) REVERT: F 134 THR cc_start: 0.8248 (m) cc_final: 0.7968 (p) REVERT: F 170 THR cc_start: 0.9115 (p) cc_final: 0.8794 (t) REVERT: F 303 HIS cc_start: 0.8281 (m-70) cc_final: 0.7759 (m-70) outliers start: 1 outliers final: 1 residues processed: 120 average time/residue: 0.1904 time to fit residues: 26.0855 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 : 0.321 ------------------------------------------------------------------------------- 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: 0.0050 chunk 87 optimal weight: 0.0670 chunk 369 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 chunk 217 optimal weight: 0.0570 chunk 81 optimal weight: 7.9990 chunk 346 optimal weight: 0.4980 chunk 167 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 366 optimal weight: 5.9990 overall best weight: 0.2650 ------------------------------------------------------------------------------- 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 = 0.3274 r_free = 0.3274 target = 0.077555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075591 restraints weight = 1511.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.076410 restraints weight = 561.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.076865 restraints weight = 262.038| |-----------------------------------------------------------------------------| r_work (final): 0.3270 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.081632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.067610 restraints weight = 11506.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.069546 restraints weight = 7664.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.070858 restraints weight = 5639.684| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.493 33890 Z= 1.196 Angle : 0.988 30.058 46104 Z= 0.553 Chirality : 0.046 0.167 5436 Planarity : 0.010 0.104 5580 Dihedral : 12.519 74.436 5760 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 0.01 (0.13), residues: 4020 helix: 0.67 (0.10), residues: 2772 sheet: -1.89 (0.28), residues: 228 loop : -1.16 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 261 HIS 0.003 0.001 HIS E 303 PHE 0.013 0.002 PHE H 244 TYR 0.018 0.002 TYR I 23 ARG 0.018 0.002 ARG I 339 Details of bonding type rmsd hydrogen bonds : bond 0.04565 ( 1969) hydrogen bonds : angle 4.53701 ( 5799) covalent geometry : bond 0.02241 (33888) covalent geometry : angle 0.98836 (46104) Misc. bond : bond 0.31129 ( 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: 0.0067 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 Evaluate side-chains 89 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 13 TYR cc_start: 0.8590 (m-10) cc_final: 0.7626 (t80) REVERT: F 14 LYS cc_start: 0.8759 (mttt) cc_final: 0.8241 (mmtt) REVERT: F 145 ASN cc_start: 0.8253 (m110) cc_final: 0.8007 (m110) REVERT: F 149 ASN cc_start: 0.8159 (p0) cc_final: 0.7564 (m110) REVERT: F 162 LEU cc_start: 0.9611 (mt) cc_final: 0.9329 (mt) REVERT: F 239 LYS cc_start: 0.8273 (mttm) cc_final: 0.7903 (tptt) REVERT: F 272 MET cc_start: 0.7741 (mpp) cc_final: 0.7354 (mpp) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.1605 time to fit residues: 16.4866 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 : 0.286 ------------------------------------------------------------------------------- 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: 8.9990 chunk 120 optimal weight: 0.0870 chunk 211 optimal weight: 1.9990 chunk 258 optimal weight: 7.9990 chunk 135 optimal weight: 0.0870 chunk 268 optimal weight: 0.0370 chunk 368 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 0.4014 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 HIS F 275 HIS F 303 HIS F 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.080122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.077931 restraints weight = 1354.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.078863 restraints weight = 560.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.079473 restraints weight = 274.063| |-----------------------------------------------------------------------------| r_work (final): 0.3281 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.082054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.067849 restraints weight = 12137.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.069757 restraints weight = 8225.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.071120 restraints weight = 6129.190| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.505 33890 Z= 1.189 Angle : 0.929 28.954 46104 Z= 0.524 Chirality : 0.044 0.164 5436 Planarity : 0.007 0.110 5580 Dihedral : 12.150 73.919 5760 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.70 % Allowed : 2.79 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.15 (0.13), residues: 4020 helix: 0.40 (0.10), residues: 2844 sheet: -2.23 (0.25), residues: 228 loop : -0.69 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 261 HIS 0.007 0.002 HIS J 303 PHE 0.010 0.001 PHE C 244 TYR 0.020 0.002 TYR I 23 ARG 0.023 0.001 ARG D 339 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 1969) hydrogen bonds : angle 4.27235 ( 5799) covalent geometry : bond 0.02217 (33888) covalent geometry : angle 0.92894 (46104) Misc. bond : bond 0.31688 ( 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: 0.0071 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 77 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 TYR cc_start: 0.8631 (m-10) cc_final: 0.7556 (t80) REVERT: F 14 LYS cc_start: 0.8678 (mttt) cc_final: 0.8368 (mmtt) REVERT: F 70 ILE cc_start: 0.8937 (mm) cc_final: 0.8735 (mm) REVERT: F 149 ASN cc_start: 0.8033 (p0) cc_final: 0.7773 (p0) REVERT: F 162 LEU cc_start: 0.9639 (mt) cc_final: 0.9330 (mt) REVERT: F 171 LYS cc_start: 0.8854 (mmpt) cc_final: 0.8448 (mmmt) REVERT: F 239 LYS cc_start: 0.8229 (mttm) cc_final: 0.7783 (tptt) outliers start: 2 outliers final: 1 residues processed: 76 average time/residue: 0.1391 time to fit residues: 12.7346 Evaluate side-chains 53 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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: 0.5980 chunk 375 optimal weight: 8.9990 chunk 333 optimal weight: 4.9990 chunk 383 optimal weight: 0.8980 chunk 187 optimal weight: 5.9990 chunk 162 optimal weight: 0.6980 chunk 299 optimal weight: 9.9990 chunk 86 optimal weight: 0.0970 chunk 164 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 39 optimal weight: 0.0270 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.076333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.074371 restraints weight = 1375.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.075031 restraints weight = 509.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.075582 restraints weight = 270.408| |-----------------------------------------------------------------------------| r_work (final): 0.3250 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.081899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.069398 restraints weight = 12103.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.071441 restraints weight = 8032.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.072906 restraints weight = 5780.387| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.6968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.513 33890 Z= 1.185 Angle : 0.910 29.044 46104 Z= 0.519 Chirality : 0.043 0.168 5436 Planarity : 0.006 0.090 5580 Dihedral : 11.919 73.684 5760 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.50 (0.10), residues: 2844 sheet: -2.16 (0.27), residues: 228 loop : -0.71 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 261 HIS 0.007 0.002 HIS G 15 PHE 0.010 0.001 PHE A 244 TYR 0.022 0.002 TYR H 23 ARG 0.028 0.002 ARG E 339 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 1969) hydrogen bonds : angle 4.34402 ( 5799) covalent geometry : bond 0.02224 (33888) covalent geometry : angle 0.91019 (46104) Misc. bond : bond 0.27695 ( 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: 0.0062 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 71 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 TYR cc_start: 0.8590 (m-10) cc_final: 0.7434 (t80) REVERT: F 14 LYS cc_start: 0.8766 (mttt) cc_final: 0.8178 (mmtm) REVERT: F 149 ASN cc_start: 0.7929 (p0) cc_final: 0.7609 (p0) REVERT: F 162 LEU cc_start: 0.9637 (mt) cc_final: 0.9350 (mt) REVERT: F 171 LYS cc_start: 0.8731 (mmpt) cc_final: 0.8297 (mmmt) REVERT: F 216 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8744 (tm-30) REVERT: F 239 LYS cc_start: 0.8231 (mttm) cc_final: 0.7985 (tptt) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1290 time to fit residues: 11.1216 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 : 0.279 ------------------------------------------------------------------------------- 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: 0.1980 chunk 324 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 259 optimal weight: 2.9990 chunk 124 optimal weight: 0.0020 chunk 36 optimal weight: 10.0000 chunk 366 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 138 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 overall best weight: 0.7928 ------------------------------------------------------------------------------- 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 269 ASN ** 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 = 0.3250 r_free = 0.3250 target = 0.074345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.072738 restraints weight = 1416.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.073421 restraints weight = 487.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.073761 restraints weight = 239.203| |-----------------------------------------------------------------------------| r_work (final): 0.3246 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.082633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.069495 restraints weight = 12346.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.071531 restraints weight = 8262.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.072941 restraints weight = 6038.114| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.7321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.512 33890 Z= 1.182 Angle : 0.864 29.368 46104 Z= 0.506 Chirality : 0.042 0.166 5436 Planarity : 0.005 0.047 5580 Dihedral : 11.895 73.425 5760 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.35 % Allowed : 4.53 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.10 (0.13), residues: 4020 helix: 0.59 (0.10), residues: 2844 sheet: -2.27 (0.28), residues: 228 loop : -0.58 (0.22), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 123 HIS 0.003 0.001 HIS F 303 PHE 0.013 0.001 PHE E 244 TYR 0.019 0.002 TYR G 252 ARG 0.017 0.001 ARG K 339 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 1969) hydrogen bonds : angle 4.41962 ( 5799) covalent geometry : bond 0.02218 (33888) covalent geometry : angle 0.86436 (46104) Misc. bond : bond 0.27425 ( 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: 0.0067 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 : 0.010 Evaluate side-chains 64 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.329 Fit side-chains REVERT: F 14 LYS cc_start: 0.8741 (mttt) cc_final: 0.8385 (mmtp) REVERT: F 70 ILE cc_start: 0.9004 (mm) cc_final: 0.8794 (mm) REVERT: F 162 LEU cc_start: 0.9633 (mt) cc_final: 0.9386 (mt) REVERT: F 171 LYS cc_start: 0.8641 (mmpt) cc_final: 0.8204 (mmmt) REVERT: F 216 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8732 (tm-30) REVERT: F 239 LYS cc_start: 0.8477 (mttm) cc_final: 0.7870 (tptt) outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.1399 time to fit residues: 10.9868 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 : 0.289 ------------------------------------------------------------------------------- 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: 0.9990 chunk 341 optimal weight: 6.9990 chunk 274 optimal weight: 2.9990 chunk 243 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 215 optimal weight: 0.0170 chunk 325 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 268 optimal weight: 0.0670 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 ** 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 = 0.3249 r_free = 0.3249 target = 0.073323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.071679 restraints weight = 1664.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.072286 restraints weight = 459.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072623 restraints weight = 216.926| |-----------------------------------------------------------------------------| r_work (final): 0.3242 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.081881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.068903 restraints weight = 11971.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.070999 restraints weight = 7726.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.072491 restraints weight = 5513.269| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.7626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.511 33890 Z= 1.184 Angle : 0.885 29.457 46104 Z= 0.507 Chirality : 0.042 0.125 5436 Planarity : 0.008 0.141 5580 Dihedral : 11.878 73.436 5760 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 0.29 (0.13), residues: 4020 helix: 0.71 (0.10), residues: 2808 sheet: -2.38 (0.29), residues: 228 loop : -0.33 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 261 HIS 0.013 0.002 HIS K 15 PHE 0.010 0.001 PHE A 244 TYR 0.018 0.002 TYR G 252 ARG 0.036 0.002 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 1969) hydrogen bonds : angle 4.49830 ( 5799) covalent geometry : bond 0.02222 (33888) covalent geometry : angle 0.88491 (46104) Misc. bond : bond 0.27491 ( 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 : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0070 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 67 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.283 Fit side-chains REVERT: F 14 LYS cc_start: 0.8615 (mttt) cc_final: 0.8186 (mmtm) REVERT: F 162 LEU cc_start: 0.9628 (mt) cc_final: 0.9372 (mt) REVERT: F 171 LYS cc_start: 0.8565 (mmpt) cc_final: 0.8114 (mmmt) REVERT: F 203 ILE cc_start: 0.9261 (mm) cc_final: 0.9047 (pt) REVERT: F 216 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8807 (tm-30) REVERT: F 239 LYS cc_start: 0.8483 (mttm) cc_final: 0.7918 (tptt) REVERT: F 272 MET cc_start: 0.7617 (mpp) cc_final: 0.6283 (mmm) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1648 time to fit residues: 13.0055 Evaluate side-chains 45 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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: 0.9990 chunk 7 optimal weight: 8.9990 chunk 135 optimal weight: 0.0980 chunk 286 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 385 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 171 optimal weight: 0.0980 chunk 389 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 161 optimal weight: 0.0170 overall best weight: 0.2818 ------------------------------------------------------------------------------- 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 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 = 0.3239 r_free = 0.3239 target = 0.072662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.070977 restraints weight = 1606.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.071500 restraints weight = 490.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.071935 restraints weight = 254.581| |-----------------------------------------------------------------------------| r_work (final): 0.3229 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.083501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.069890 restraints weight = 12200.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.072067 restraints weight = 7939.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.073659 restraints weight = 5665.212| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.7915 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= 1.184 Angle : 0.906 29.615 46104 Z= 0.515 Chirality : 0.042 0.129 5436 Planarity : 0.006 0.060 5580 Dihedral : 11.707 73.416 5760 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 0.32 (0.14), residues: 4020 helix: 0.72 (0.10), residues: 2832 sheet: -2.32 (0.30), residues: 228 loop : -0.30 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 261 HIS 0.005 0.001 HIS H 15 PHE 0.015 0.001 PHE D 244 TYR 0.018 0.002 TYR G 252 ARG 0.023 0.002 ARG K 339 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 1969) hydrogen bonds : angle 4.54460 ( 5799) covalent geometry : bond 0.02223 (33888) covalent geometry : angle 0.90562 (46104) Misc. bond : bond 0.27483 ( 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: 0.0062 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: 0 poor density : 68 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: F 14 LYS cc_start: 0.8660 (mttt) cc_final: 0.8228 (mmtp) REVERT: F 48 CYS cc_start: 0.9448 (m) cc_final: 0.9173 (m) REVERT: F 162 LEU cc_start: 0.9646 (mt) cc_final: 0.9389 (mt) REVERT: F 171 LYS cc_start: 0.8390 (mmpt) cc_final: 0.7977 (mmmt) REVERT: F 216 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8875 (tm-30) REVERT: F 239 LYS cc_start: 0.8463 (mttm) cc_final: 0.7869 (tptt) REVERT: F 272 MET cc_start: 0.7729 (mpp) cc_final: 0.7433 (mmm) REVERT: F 278 VAL cc_start: 0.9213 (t) cc_final: 0.8917 (p) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1642 time to fit residues: 13.0744 Evaluate side-chains 45 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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: 0.0570 chunk 45 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 356 optimal weight: 1.9990 chunk 349 optimal weight: 5.9990 chunk 186 optimal weight: 0.6980 chunk 64 optimal weight: 0.0670 chunk 195 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 173 optimal weight: 6.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- 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 ** 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 = 0.3202 r_free = 0.3202 target = 0.072736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.071849 restraints weight = 1451.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072140 restraints weight = 375.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.072374 restraints weight = 164.485| |-----------------------------------------------------------------------------| r_work (final): 0.3264 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.082119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.069012 restraints weight = 11634.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070878 restraints weight = 7730.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.072253 restraints weight = 5648.024| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.8285 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= 1.184 Angle : 0.931 29.523 46104 Z= 0.515 Chirality : 0.043 0.137 5436 Planarity : 0.005 0.060 5580 Dihedral : 11.774 73.410 5760 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: 0.47 (0.14), residues: 4020 helix: 0.81 (0.10), residues: 2844 sheet: -2.26 (0.30), residues: 228 loop : -0.20 (0.23), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 261 HIS 0.004 0.001 HIS G 15 PHE 0.013 0.001 PHE G 244 TYR 0.019 0.002 TYR J 61 ARG 0.023 0.001 ARG K 339 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 1969) hydrogen bonds : angle 4.43803 ( 5799) covalent geometry : bond 0.02224 (33888) covalent geometry : angle 0.93104 (46104) Misc. bond : bond 0.27680 ( 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: 0.0062 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 62 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: F 14 LYS cc_start: 0.8775 (mttt) cc_final: 0.8403 (mmtt) REVERT: F 70 ILE cc_start: 0.9028 (mm) cc_final: 0.8826 (mm) REVERT: F 162 LEU cc_start: 0.9627 (mt) cc_final: 0.9363 (mt) REVERT: F 171 LYS cc_start: 0.8471 (mmpt) cc_final: 0.8074 (mmmt) REVERT: F 216 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8820 (tm-30) REVERT: F 239 LYS cc_start: 0.8437 (mttm) cc_final: 0.7819 (tptt) REVERT: F 272 MET cc_start: 0.7770 (mpp) cc_final: 0.7214 (mmm) REVERT: F 278 VAL cc_start: 0.9285 (t) cc_final: 0.8994 (p) REVERT: F 301 LEU cc_start: 0.8232 (tt) cc_final: 0.7924 (tt) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1419 time to fit residues: 10.6194 Evaluate side-chains 45 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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: 5.9990 chunk 336 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 278 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 347 optimal weight: 6.9990 chunk 131 optimal weight: 0.0770 chunk 345 optimal weight: 0.0470 chunk 279 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 ** 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 = 0.3239 r_free = 0.3239 target = 0.072637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.070841 restraints weight = 1466.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.071489 restraints weight = 472.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.071865 restraints weight = 210.772| |-----------------------------------------------------------------------------| r_work (final): 0.3221 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.082988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.069676 restraints weight = 12013.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.071681 restraints weight = 8018.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.073025 restraints weight = 5819.005| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.8610 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= 1.184 Angle : 0.930 29.506 46104 Z= 0.521 Chirality : 0.041 0.131 5436 Planarity : 0.005 0.051 5580 Dihedral : 11.737 73.440 5760 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.64 (0.14), residues: 4020 helix: 0.88 (0.10), residues: 2820 sheet: -2.27 (0.31), residues: 228 loop : 0.12 (0.23), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 261 HIS 0.003 0.001 HIS G 15 PHE 0.013 0.001 PHE F 244 TYR 0.018 0.002 TYR J 252 ARG 0.022 0.001 ARG K 339 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 1969) hydrogen bonds : angle 4.44638 ( 5799) covalent geometry : bond 0.02222 (33888) covalent geometry : angle 0.92960 (46104) Misc. bond : bond 0.27731 ( 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 : 0.008 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 : 0.006 Evaluate side-chains 60 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: F 14 LYS cc_start: 0.8829 (mttt) cc_final: 0.8443 (mmtp) REVERT: F 80 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8592 (tm-30) REVERT: F 161 LEU cc_start: 0.9448 (pp) cc_final: 0.8932 (pp) REVERT: F 162 LEU cc_start: 0.9624 (mt) cc_final: 0.9390 (mt) REVERT: F 239 LYS cc_start: 0.8374 (mttm) cc_final: 0.7739 (tptt) REVERT: F 272 MET cc_start: 0.7797 (mpp) cc_final: 0.7427 (mtt) REVERT: F 278 VAL cc_start: 0.9294 (t) cc_final: 0.9007 (p) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1201 time to fit residues: 8.9740 Evaluate side-chains 40 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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: 0.9990 chunk 276 optimal weight: 9.9990 chunk 389 optimal weight: 0.0870 chunk 109 optimal weight: 3.9990 chunk 348 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 270 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 216 optimal weight: 0.8980 chunk 326 optimal weight: 2.9990 chunk 261 optimal weight: 0.4980 overall best weight: 0.6962 ------------------------------------------------------------------------------- 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 ** 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 = 0.3245 r_free = 0.3245 target = 0.072391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.070504 restraints weight = 1412.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.071277 restraints weight = 476.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.071827 restraints weight = 236.838| |-----------------------------------------------------------------------------| r_work (final): 0.3229 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.084024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.070339 restraints weight = 11685.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.072331 restraints weight = 7863.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.073847 restraints weight = 5740.168| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.8802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.515 33890 Z= 1.183 Angle : 0.912 29.486 46104 Z= 0.511 Chirality : 0.043 0.192 5436 Planarity : 0.005 0.046 5580 Dihedral : 11.691 73.431 5760 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.78 (0.14), residues: 4020 helix: 0.96 (0.10), residues: 2820 sheet: -2.25 (0.31), residues: 228 loop : 0.27 (0.23), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 261 HIS 0.004 0.001 HIS L 220 PHE 0.019 0.002 PHE F 248 TYR 0.016 0.002 TYR J 252 ARG 0.019 0.001 ARG D 339 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 1969) hydrogen bonds : angle 4.45677 ( 5799) covalent geometry : bond 0.02220 (33888) covalent geometry : angle 0.91226 (46104) Misc. bond : bond 0.27609 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5231.63 seconds wall clock time: 95 minutes 38.31 seconds (5738.31 seconds total)