Starting phenix.real_space_refine on Fri Apr 12 22:34:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1u_36804/04_2024/8k1u_36804_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1u_36804/04_2024/8k1u_36804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1u_36804/04_2024/8k1u_36804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1u_36804/04_2024/8k1u_36804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1u_36804/04_2024/8k1u_36804_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1u_36804/04_2024/8k1u_36804_updated.pdb" } resolution = 2.82 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= 0.000 sd= 0.081 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 24 5.49 5 S 118 5.16 5 Na 4 4.78 5 C 17450 2.51 5 N 4422 2.21 5 O 4942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 26964 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "B" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "D" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "E" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1698 Classifications: {'peptide': 216} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 210} Chain: "F" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "G" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 209} Chain: "H" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1698 Classifications: {'peptide': 216} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 210} Chain: "I" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "J" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "K" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "L" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3293 Classifications: {'peptide': 431} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 414} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' NA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.72, per 1000 atoms: 0.51 Number of scatterers: 26964 At special positions: 0 Unit cell: (173.47, 133.63, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 118 16.00 P 24 15.00 Na 4 11.00 O 4942 8.00 N 4422 7.00 C 17450 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.96 Conformation dependent library (CDL) restraints added in 4.8 seconds 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6364 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 148 helices and 20 sheets defined 49.8% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.99 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 removed outlier: 3.598A pdb=" N SER A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 60 through 66 removed outlier: 3.663A pdb=" N LEU A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 124 through 137 Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.645A pdb=" N LYS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 28 removed outlier: 3.599A pdb=" N SER B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 60 through 66 removed outlier: 3.662A pdb=" N LEU B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 124 through 137 Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.646A pdb=" N LYS B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 28 removed outlier: 3.598A pdb=" N SER C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 60 through 66 removed outlier: 3.663A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 124 through 137 Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.644A pdb=" N LYS C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 28 removed outlier: 3.599A pdb=" N SER D 20 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 60 through 66 removed outlier: 3.663A pdb=" N LEU D 66 " --> pdb=" O GLU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 70 No H-bonds generated for 'chain 'D' and resid 68 through 70' Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'D' and resid 211 through 219 removed outlier: 3.645A pdb=" N LYS D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.598A pdb=" N SER E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 60 through 66 removed outlier: 3.662A pdb=" N LEU E 66 " --> pdb=" O GLU E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 70 No H-bonds generated for 'chain 'E' and resid 68 through 70' Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 124 through 137 Processing helix chain 'E' and resid 211 through 219 removed outlier: 3.645A pdb=" N LYS E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 28 removed outlier: 3.598A pdb=" N SER F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 60 through 66 removed outlier: 3.662A pdb=" N LEU F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 70 No H-bonds generated for 'chain 'F' and resid 68 through 70' Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 107 through 115 Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 211 through 219 removed outlier: 3.645A pdb=" N LYS F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 28 removed outlier: 3.597A pdb=" N SER G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 Processing helix chain 'G' and resid 60 through 66 removed outlier: 3.663A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 70 No H-bonds generated for 'chain 'G' and resid 68 through 70' Processing helix chain 'G' and resid 82 through 94 Processing helix chain 'G' and resid 107 through 115 Processing helix chain 'G' and resid 124 through 137 Processing helix chain 'G' and resid 211 through 219 removed outlier: 3.644A pdb=" N LYS G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 28 removed outlier: 3.598A pdb=" N SER H 20 " --> pdb=" O ARG H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 Processing helix chain 'H' and resid 60 through 66 removed outlier: 3.662A pdb=" N LEU H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 70 No H-bonds generated for 'chain 'H' and resid 68 through 70' Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'H' and resid 107 through 115 Processing helix chain 'H' and resid 124 through 137 Processing helix chain 'H' and resid 211 through 219 removed outlier: 3.646A pdb=" N LYS H 215 " --> pdb=" O LYS H 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 36 removed outlier: 3.750A pdb=" N ILE I 28 " --> pdb=" O PHE I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 58 Processing helix chain 'I' and resid 68 through 71 No H-bonds generated for 'chain 'I' and resid 68 through 71' Processing helix chain 'I' and resid 74 through 89 Processing helix chain 'I' and resid 91 through 102 removed outlier: 3.658A pdb=" N LEU I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 117 removed outlier: 3.562A pdb=" N VAL I 114 " --> pdb=" O GLU I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 156 removed outlier: 3.612A pdb=" N ILE I 150 " --> pdb=" O LEU I 146 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG I 151 " --> pdb=" O ILE I 147 " (cutoff:3.500A) Proline residue: I 154 - end of helix Processing helix chain 'I' and resid 159 through 173 removed outlier: 3.994A pdb=" N PHE I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 206 Processing helix chain 'I' and resid 209 through 217 Processing helix chain 'I' and resid 221 through 223 No H-bonds generated for 'chain 'I' and resid 221 through 223' Processing helix chain 'I' and resid 226 through 249 Processing helix chain 'I' and resid 262 through 274 Processing helix chain 'I' and resid 286 through 288 No H-bonds generated for 'chain 'I' and resid 286 through 288' Processing helix chain 'I' and resid 291 through 302 Processing helix chain 'I' and resid 316 through 330 Processing helix chain 'I' and resid 345 through 372 Processing helix chain 'I' and resid 377 through 388 Processing helix chain 'I' and resid 398 through 400 No H-bonds generated for 'chain 'I' and resid 398 through 400' Processing helix chain 'I' and resid 403 through 418 Processing helix chain 'I' and resid 420 through 427 removed outlier: 4.163A pdb=" N PHE I 427 " --> pdb=" O PHE I 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 36 removed outlier: 3.749A pdb=" N ILE J 28 " --> pdb=" O PHE J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 58 Processing helix chain 'J' and resid 68 through 71 No H-bonds generated for 'chain 'J' and resid 68 through 71' Processing helix chain 'J' and resid 74 through 89 Processing helix chain 'J' and resid 91 through 102 removed outlier: 3.659A pdb=" N LEU J 97 " --> pdb=" O THR J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 117 removed outlier: 3.563A pdb=" N VAL J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 156 removed outlier: 3.612A pdb=" N ILE J 150 " --> pdb=" O LEU J 146 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG J 151 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Proline residue: J 154 - end of helix Processing helix chain 'J' and resid 159 through 173 removed outlier: 3.995A pdb=" N PHE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 192 through 206 Processing helix chain 'J' and resid 209 through 217 Processing helix chain 'J' and resid 221 through 223 No H-bonds generated for 'chain 'J' and resid 221 through 223' Processing helix chain 'J' and resid 226 through 249 Processing helix chain 'J' and resid 262 through 274 Processing helix chain 'J' and resid 286 through 288 No H-bonds generated for 'chain 'J' and resid 286 through 288' Processing helix chain 'J' and resid 291 through 302 Processing helix chain 'J' and resid 316 through 330 Processing helix chain 'J' and resid 345 through 372 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 398 through 400 No H-bonds generated for 'chain 'J' and resid 398 through 400' Processing helix chain 'J' and resid 403 through 418 Processing helix chain 'J' and resid 420 through 427 removed outlier: 4.163A pdb=" N PHE J 427 " --> pdb=" O PHE J 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 36 removed outlier: 3.749A pdb=" N ILE K 28 " --> pdb=" O PHE K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 58 Processing helix chain 'K' and resid 68 through 71 No H-bonds generated for 'chain 'K' and resid 68 through 71' Processing helix chain 'K' and resid 74 through 89 Processing helix chain 'K' and resid 91 through 102 removed outlier: 3.658A pdb=" N LEU K 97 " --> pdb=" O THR K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 117 removed outlier: 3.563A pdb=" N VAL K 114 " --> pdb=" O GLU K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 156 removed outlier: 3.612A pdb=" N ILE K 150 " --> pdb=" O LEU K 146 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG K 151 " --> pdb=" O ILE K 147 " (cutoff:3.500A) Proline residue: K 154 - end of helix Processing helix chain 'K' and resid 159 through 173 removed outlier: 3.994A pdb=" N PHE K 163 " --> pdb=" O SER K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 206 Processing helix chain 'K' and resid 209 through 217 Processing helix chain 'K' and resid 221 through 223 No H-bonds generated for 'chain 'K' and resid 221 through 223' Processing helix chain 'K' and resid 226 through 249 Processing helix chain 'K' and resid 262 through 274 Processing helix chain 'K' and resid 286 through 288 No H-bonds generated for 'chain 'K' and resid 286 through 288' Processing helix chain 'K' and resid 291 through 302 Processing helix chain 'K' and resid 316 through 330 Processing helix chain 'K' and resid 345 through 372 Processing helix chain 'K' and resid 377 through 388 Processing helix chain 'K' and resid 398 through 400 No H-bonds generated for 'chain 'K' and resid 398 through 400' Processing helix chain 'K' and resid 403 through 418 Processing helix chain 'K' and resid 420 through 427 removed outlier: 4.163A pdb=" N PHE K 427 " --> pdb=" O PHE K 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 36 removed outlier: 3.749A pdb=" N ILE L 28 " --> pdb=" O PHE L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 58 Processing helix chain 'L' and resid 68 through 71 No H-bonds generated for 'chain 'L' and resid 68 through 71' Processing helix chain 'L' and resid 74 through 89 Processing helix chain 'L' and resid 91 through 102 removed outlier: 3.659A pdb=" N LEU L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 117 removed outlier: 3.562A pdb=" N VAL L 114 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 156 removed outlier: 3.612A pdb=" N ILE L 150 " --> pdb=" O LEU L 146 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG L 151 " --> pdb=" O ILE L 147 " (cutoff:3.500A) Proline residue: L 154 - end of helix Processing helix chain 'L' and resid 159 through 173 removed outlier: 3.994A pdb=" N PHE L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 192 through 206 Processing helix chain 'L' and resid 209 through 217 Processing helix chain 'L' and resid 221 through 223 No H-bonds generated for 'chain 'L' and resid 221 through 223' Processing helix chain 'L' and resid 226 through 249 Processing helix chain 'L' and resid 262 through 274 Processing helix chain 'L' and resid 286 through 288 No H-bonds generated for 'chain 'L' and resid 286 through 288' Processing helix chain 'L' and resid 291 through 302 Processing helix chain 'L' and resid 316 through 330 Processing helix chain 'L' and resid 345 through 372 Processing helix chain 'L' and resid 377 through 388 Processing helix chain 'L' and resid 398 through 400 No H-bonds generated for 'chain 'L' and resid 398 through 400' Processing helix chain 'L' and resid 403 through 418 Processing helix chain 'L' and resid 420 through 427 removed outlier: 4.162A pdb=" N PHE L 427 " --> pdb=" O PHE L 423 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.600A pdb=" N TYR A 73 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU A 31 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL A 11 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU A 33 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS A 51 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASP A 36 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL A 53 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 141 through 146 removed outlier: 6.929A pdb=" N GLU A 155 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR A 144 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP A 146 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TYR A 151 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS A 204 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET A 208 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE A 180 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.599A pdb=" N TYR B 73 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU B 31 " --> pdb=" O PHE B 9 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL B 11 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU B 33 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N HIS B 51 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASP B 36 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL B 53 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 141 through 146 removed outlier: 6.929A pdb=" N GLU B 155 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR B 144 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP B 146 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TYR B 151 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS B 204 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N MET B 208 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE B 180 " --> pdb=" O MET B 208 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.599A pdb=" N TYR C 73 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU C 31 " --> pdb=" O PHE C 9 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL C 11 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU C 33 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N HIS C 51 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ASP C 36 " --> pdb=" O HIS C 51 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL C 53 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 141 through 146 removed outlier: 6.929A pdb=" N GLU C 155 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR C 144 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP C 146 " --> pdb=" O TYR C 151 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR C 151 " --> pdb=" O ASP C 146 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS C 204 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N MET C 208 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE C 180 " --> pdb=" O MET C 208 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.599A pdb=" N TYR D 73 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLU D 31 " --> pdb=" O PHE D 9 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL D 11 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU D 33 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N HIS D 51 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASP D 36 " --> pdb=" O HIS D 51 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL D 53 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 141 through 146 removed outlier: 6.930A pdb=" N GLU D 155 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR D 144 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE D 153 " --> pdb=" O TYR D 144 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP D 146 " --> pdb=" O TYR D 151 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N TYR D 151 " --> pdb=" O ASP D 146 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS D 204 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET D 208 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE D 180 " --> pdb=" O MET D 208 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.600A pdb=" N TYR E 73 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU E 31 " --> pdb=" O PHE E 9 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL E 11 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU E 33 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N HIS E 51 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASP E 36 " --> pdb=" O HIS E 51 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL E 53 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 141 through 146 removed outlier: 6.929A pdb=" N GLU E 155 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR E 144 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE E 153 " --> pdb=" O TYR E 144 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP E 146 " --> pdb=" O TYR E 151 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TYR E 151 " --> pdb=" O ASP E 146 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS E 204 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET E 208 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE E 180 " --> pdb=" O MET E 208 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 120 through 122 removed outlier: 3.599A pdb=" N TYR F 73 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU F 31 " --> pdb=" O PHE F 9 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL F 11 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU F 33 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N HIS F 51 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASP F 36 " --> pdb=" O HIS F 51 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL F 53 " --> pdb=" O ASP F 36 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 141 through 146 removed outlier: 6.929A pdb=" N GLU F 155 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR F 144 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE F 153 " --> pdb=" O TYR F 144 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP F 146 " --> pdb=" O TYR F 151 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N TYR F 151 " --> pdb=" O ASP F 146 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS F 204 " --> pdb=" O LYS F 184 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET F 208 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE F 180 " --> pdb=" O MET F 208 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.599A pdb=" N TYR G 73 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU G 31 " --> pdb=" O PHE G 9 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL G 11 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU G 33 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N HIS G 51 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASP G 36 " --> pdb=" O HIS G 51 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL G 53 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 141 through 146 removed outlier: 6.929A pdb=" N GLU G 155 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR G 144 " --> pdb=" O ILE G 153 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE G 153 " --> pdb=" O TYR G 144 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASP G 146 " --> pdb=" O TYR G 151 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR G 151 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS G 204 " --> pdb=" O LYS G 184 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET G 208 " --> pdb=" O ILE G 180 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE G 180 " --> pdb=" O MET G 208 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 120 through 122 removed outlier: 3.599A pdb=" N TYR H 73 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU H 31 " --> pdb=" O PHE H 9 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL H 11 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU H 33 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N HIS H 51 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ASP H 36 " --> pdb=" O HIS H 51 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL H 53 " --> pdb=" O ASP H 36 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 141 through 146 removed outlier: 6.930A pdb=" N GLU H 155 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR H 144 " --> pdb=" O ILE H 153 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE H 153 " --> pdb=" O TYR H 144 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASP H 146 " --> pdb=" O TYR H 151 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TYR H 151 " --> pdb=" O ASP H 146 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS H 204 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET H 208 " --> pdb=" O ILE H 180 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE H 180 " --> pdb=" O MET H 208 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 336 through 338 removed outlier: 4.659A pdb=" N THR I 336 " --> pdb=" O ILE I 343 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'J' and resid 336 through 338 removed outlier: 4.659A pdb=" N THR J 336 " --> pdb=" O ILE J 343 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 336 through 338 removed outlier: 4.659A pdb=" N THR K 336 " --> pdb=" O ILE K 343 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 336 through 338 removed outlier: 4.659A pdb=" N THR L 336 " --> pdb=" O ILE L 343 " (cutoff:3.500A) 1284 hydrogen bonds defined for protein. 3792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.77 Time building geometry restraints manager: 10.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4874 1.33 - 1.45: 6501 1.45 - 1.57: 15853 1.57 - 1.69: 40 1.69 - 1.81: 200 Bond restraints: 27468 Sorted by residual: bond pdb=" CA VAL I 66 " pdb=" CB VAL I 66 " ideal model delta sigma weight residual 1.545 1.495 0.050 1.51e-02 4.39e+03 1.10e+01 bond pdb=" CA VAL L 66 " pdb=" CB VAL L 66 " ideal model delta sigma weight residual 1.545 1.496 0.049 1.51e-02 4.39e+03 1.07e+01 bond pdb=" CA VAL K 66 " pdb=" CB VAL K 66 " ideal model delta sigma weight residual 1.544 1.499 0.045 1.39e-02 5.18e+03 1.04e+01 bond pdb=" CA VAL K 65 " pdb=" CB VAL K 65 " ideal model delta sigma weight residual 1.540 1.498 0.041 1.37e-02 5.33e+03 8.99e+00 bond pdb=" C HIS H 185 " pdb=" N HIS H 186 " ideal model delta sigma weight residual 1.333 1.292 0.040 1.42e-02 4.96e+03 8.13e+00 ... (remaining 27463 not shown) Histogram of bond angle deviations from ideal: 100.27 - 108.21: 1009 108.21 - 116.15: 17651 116.15 - 124.10: 18111 124.10 - 132.04: 457 132.04 - 139.98: 52 Bond angle restraints: 37280 Sorted by residual: angle pdb=" O VAL J 65 " pdb=" C VAL J 65 " pdb=" N VAL J 66 " ideal model delta sigma weight residual 121.83 127.14 -5.31 1.03e+00 9.43e-01 2.66e+01 angle pdb=" CA VAL J 65 " pdb=" C VAL J 65 " pdb=" N VAL J 66 " ideal model delta sigma weight residual 117.28 111.87 5.41 1.16e+00 7.43e-01 2.17e+01 angle pdb=" N VAL K 65 " pdb=" CA VAL K 65 " pdb=" C VAL K 65 " ideal model delta sigma weight residual 111.00 106.05 4.95 1.09e+00 8.42e-01 2.06e+01 angle pdb=" C VAL K 66 " pdb=" CA VAL K 66 " pdb=" CB VAL K 66 " ideal model delta sigma weight residual 110.95 103.70 7.25 1.61e+00 3.86e-01 2.03e+01 angle pdb=" N HIS G 185 " pdb=" CA HIS G 185 " pdb=" C HIS G 185 " ideal model delta sigma weight residual 108.58 116.01 -7.43 1.82e+00 3.02e-01 1.67e+01 ... (remaining 37275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 15705 17.90 - 35.80: 551 35.80 - 53.70: 104 53.70 - 71.60: 52 71.60 - 89.50: 16 Dihedral angle restraints: 16428 sinusoidal: 6538 harmonic: 9890 Sorted by residual: dihedral pdb=" CA GLU A 201 " pdb=" C GLU A 201 " pdb=" N GLN A 202 " pdb=" CA GLN A 202 " ideal model delta harmonic sigma weight residual 180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLU D 201 " pdb=" C GLU D 201 " pdb=" N GLN D 202 " pdb=" CA GLN D 202 " ideal model delta harmonic sigma weight residual 180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLU F 201 " pdb=" C GLU F 201 " pdb=" N GLN F 202 " pdb=" CA GLN F 202 " ideal model delta harmonic sigma weight residual -180.00 -158.55 -21.45 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 16425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3738 0.055 - 0.110: 650 0.110 - 0.164: 89 0.164 - 0.219: 6 0.219 - 0.274: 3 Chirality restraints: 4486 Sorted by residual: chirality pdb=" CA VAL K 66 " pdb=" N VAL K 66 " pdb=" C VAL K 66 " pdb=" CB VAL K 66 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA VAL J 66 " pdb=" N VAL J 66 " pdb=" C VAL J 66 " pdb=" CB VAL J 66 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA VAL K 65 " pdb=" N VAL K 65 " pdb=" C VAL K 65 " pdb=" CB VAL K 65 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 4483 not shown) Planarity restraints: 4578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA K 64 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C ALA K 64 " 0.028 2.00e-02 2.50e+03 pdb=" O ALA K 64 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL K 65 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR L 15 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO L 16 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO L 16 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 16 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 15 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO J 16 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO J 16 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 16 " -0.023 5.00e-02 4.00e+02 ... (remaining 4575 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 9233 2.86 - 3.43: 28952 3.43 - 4.00: 52085 4.00 - 4.57: 72526 4.57 - 5.14: 106396 Nonbonded interactions: 269192 Sorted by model distance: nonbonded pdb=" OH TYR D 108 " pdb=" OE1 GLU E 60 " model vdw 2.294 2.440 nonbonded pdb=" O ILE J 418 " pdb=" OG1 THR J 422 " model vdw 2.301 2.440 nonbonded pdb=" O ILE I 418 " pdb=" OG1 THR I 422 " model vdw 2.301 2.440 nonbonded pdb=" O ILE K 418 " pdb=" OG1 THR K 422 " model vdw 2.301 2.440 nonbonded pdb=" O ILE L 418 " pdb=" OG1 THR L 422 " model vdw 2.301 2.440 ... (remaining 269187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 221) selection = (chain 'B' and resid 7 through 221) selection = (chain 'C' and resid 7 through 221) selection = (chain 'D' and resid 7 through 221) selection = (chain 'E' and resid 7 through 221) selection = (chain 'F' and resid 7 through 221) selection = (chain 'G' and resid 7 through 221) selection = (chain 'H' and resid 7 through 221) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.240 Check model and map are aligned: 0.440 Set scattering table: 0.230 Process input model: 69.150 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 : 0.002 0.050 27468 Z= 0.138 Angle : 0.503 8.419 37280 Z= 0.276 Chirality : 0.042 0.274 4486 Planarity : 0.003 0.040 4578 Dihedral : 10.679 89.502 10064 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.51 % Allowed : 3.12 % Favored : 95.37 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: -1.57 (0.12), residues: 3422 helix: -1.28 (0.09), residues: 1836 sheet: 0.83 (0.27), residues: 400 loop : -1.03 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 101 HIS 0.004 0.001 HIS E 185 PHE 0.021 0.001 PHE L 202 TYR 0.005 0.001 TYR C 107 ARG 0.003 0.000 ARG J 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 843 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.7279 (mmm) cc_final: 0.7002 (mmp) REVERT: C 41 LYS cc_start: 0.8254 (mmtp) cc_final: 0.7985 (mmtt) REVERT: I 390 THR cc_start: 0.8141 (p) cc_final: 0.7890 (p) REVERT: L 390 THR cc_start: 0.8107 (p) cc_final: 0.7834 (p) outliers start: 44 outliers final: 6 residues processed: 869 average time/residue: 1.2942 time to fit residues: 1316.4089 Evaluate side-chains 501 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 495 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain L residue 352 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 0.7980 chunk 257 optimal weight: 0.7980 chunk 142 optimal weight: 0.0570 chunk 88 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 198 optimal weight: 0.4980 chunk 308 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN C 81 ASN C 134 GLN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 HIS ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN ** G 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN I 120 GLN I 253 ASN J 119 ASN J 195 ASN J 253 ASN J 434 ASN K 18 GLN K 119 ASN K 120 GLN K 253 ASN K 434 ASN L 85 GLN L 120 GLN L 253 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 27468 Z= 0.159 Angle : 0.503 7.954 37280 Z= 0.265 Chirality : 0.042 0.179 4486 Planarity : 0.004 0.032 4578 Dihedral : 9.381 86.489 3915 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.81 % Allowed : 13.21 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.31 (0.13), residues: 3422 helix: 0.90 (0.11), residues: 1848 sheet: 0.75 (0.27), residues: 400 loop : -1.03 (0.16), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 101 HIS 0.013 0.001 HIS G 185 PHE 0.037 0.001 PHE J 202 TYR 0.017 0.001 TYR I 270 ARG 0.007 0.000 ARG L 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 531 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.7098 (mmm) cc_final: 0.6758 (mmp) REVERT: B 183 ILE cc_start: 0.8129 (mt) cc_final: 0.7708 (mp) REVERT: D 27 ARG cc_start: 0.7337 (mtm110) cc_final: 0.6952 (ttm-80) REVERT: E 86 THR cc_start: 0.8631 (t) cc_final: 0.8313 (m) REVERT: G 134 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7666 (mp10) REVERT: H 81 ASN cc_start: 0.7019 (t0) cc_final: 0.6783 (t0) REVERT: H 86 THR cc_start: 0.8569 (t) cc_final: 0.8230 (m) REVERT: I 106 ILE cc_start: 0.6898 (mm) cc_final: 0.6674 (tp) REVERT: I 222 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7693 (ptmm) REVERT: J 91 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7207 (t80) REVERT: K 220 ARG cc_start: 0.6704 (mmt180) cc_final: 0.6494 (mmp80) REVERT: K 348 ILE cc_start: 0.8732 (mm) cc_final: 0.8500 (mm) outliers start: 82 outliers final: 23 residues processed: 584 average time/residue: 1.2592 time to fit residues: 865.3489 Evaluate side-chains 487 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 462 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 140 ILE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 140 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 256 optimal weight: 0.0980 chunk 210 optimal weight: 0.0980 chunk 85 optimal weight: 0.6980 chunk 309 optimal weight: 0.7980 chunk 334 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 chunk 306 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS B 105 GLN B 134 GLN C 134 GLN D 210 HIS G 83 GLN I 85 GLN I 239 ASN I 253 ASN J 119 ASN J 434 ASN ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 ASN K 434 ASN L 85 GLN L 253 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 27468 Z= 0.160 Angle : 0.486 7.619 37280 Z= 0.253 Chirality : 0.042 0.185 4486 Planarity : 0.003 0.034 4578 Dihedral : 8.666 85.840 3908 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.05 % Allowed : 14.48 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.91 (0.14), residues: 3422 helix: 1.57 (0.11), residues: 1880 sheet: 0.58 (0.27), residues: 374 loop : -0.97 (0.16), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP I 47 HIS 0.007 0.001 HIS F 185 PHE 0.034 0.001 PHE J 202 TYR 0.015 0.001 TYR F 107 ARG 0.007 0.000 ARG I 436 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 509 time to evaluate : 3.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.7210 (mmm) cc_final: 0.6870 (mmp) REVERT: B 134 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7569 (mp10) REVERT: B 183 ILE cc_start: 0.8199 (mt) cc_final: 0.7805 (mp) REVERT: B 189 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6432 (tp) REVERT: C 66 LEU cc_start: 0.8646 (mt) cc_final: 0.8371 (mt) REVERT: C 134 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7575 (mp10) REVERT: C 183 ILE cc_start: 0.8350 (mt) cc_final: 0.7975 (mp) REVERT: D 27 ARG cc_start: 0.7340 (mtm110) cc_final: 0.7006 (ttm-80) REVERT: D 181 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6197 (mp) REVERT: E 86 THR cc_start: 0.8709 (t) cc_final: 0.8437 (m) REVERT: H 81 ASN cc_start: 0.7049 (t0) cc_final: 0.6818 (t0) REVERT: H 86 THR cc_start: 0.8643 (t) cc_final: 0.8347 (m) REVERT: I 222 LYS cc_start: 0.8076 (mmmt) cc_final: 0.7756 (ptmm) REVERT: J 91 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7176 (t80) REVERT: J 373 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6338 (mt-10) REVERT: K 324 THR cc_start: 0.8602 (m) cc_final: 0.8393 (m) REVERT: L 36 MET cc_start: 0.7304 (mmm) cc_final: 0.7087 (mmt) REVERT: L 222 LYS cc_start: 0.8124 (mmmt) cc_final: 0.7731 (ptmm) REVERT: L 291 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6714 (tt0) REVERT: L 439 ASP cc_start: 0.7511 (m-30) cc_final: 0.7289 (m-30) outliers start: 89 outliers final: 33 residues processed: 562 average time/residue: 1.3344 time to fit residues: 877.7616 Evaluate side-chains 520 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 480 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 134 GLN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 400 GLU Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain K residue 151 ARG Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 400 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 0.9990 chunk 232 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 207 optimal weight: 0.5980 chunk 310 optimal weight: 0.9980 chunk 328 optimal weight: 0.0770 chunk 162 optimal weight: 7.9990 chunk 294 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 143 ASN C 134 GLN C 143 ASN D 210 HIS F 134 GLN G 8 GLN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN H 30 HIS I 85 GLN I 253 ASN J 119 ASN J 434 ASN K 119 ASN K 434 ASN L 85 GLN L 253 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 27468 Z= 0.157 Angle : 0.480 7.589 37280 Z= 0.250 Chirality : 0.042 0.188 4486 Planarity : 0.003 0.040 4578 Dihedral : 8.403 86.356 3908 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.26 % Allowed : 15.24 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 1.15 (0.14), residues: 3422 helix: 1.88 (0.12), residues: 1864 sheet: 0.50 (0.27), residues: 364 loop : -0.96 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 181 HIS 0.006 0.001 HIS F 185 PHE 0.032 0.001 PHE J 202 TYR 0.017 0.001 TYR F 107 ARG 0.008 0.000 ARG L 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 496 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.7239 (mmm) cc_final: 0.6826 (mmp) REVERT: A 189 ILE cc_start: 0.6788 (OUTLIER) cc_final: 0.6392 (tp) REVERT: B 59 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: B 66 LEU cc_start: 0.8703 (mt) cc_final: 0.8498 (mt) REVERT: B 183 ILE cc_start: 0.8261 (mt) cc_final: 0.7881 (mp) REVERT: B 213 ASP cc_start: 0.6308 (m-30) cc_final: 0.6091 (m-30) REVERT: C 66 LEU cc_start: 0.8682 (mt) cc_final: 0.8478 (mt) REVERT: C 183 ILE cc_start: 0.8333 (mt) cc_final: 0.7960 (mp) REVERT: D 27 ARG cc_start: 0.7293 (mtm110) cc_final: 0.7033 (ttp-110) REVERT: E 86 THR cc_start: 0.8832 (t) cc_final: 0.8479 (m) REVERT: G 134 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7658 (mp10) REVERT: H 81 ASN cc_start: 0.7064 (t0) cc_final: 0.6816 (t0) REVERT: H 86 THR cc_start: 0.8771 (t) cc_final: 0.8407 (m) REVERT: I 222 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7828 (ptmm) REVERT: J 109 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.8023 (mmmm) REVERT: J 373 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6221 (mt-10) REVERT: L 222 LYS cc_start: 0.8115 (mmmt) cc_final: 0.7791 (ptmm) REVERT: L 291 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6634 (tt0) outliers start: 95 outliers final: 51 residues processed: 557 average time/residue: 1.2999 time to fit residues: 851.0354 Evaluate side-chains 531 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 475 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 213 ASP Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 244 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 280 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 294 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN B 134 GLN C 105 GLN C 134 GLN D 210 HIS F 134 GLN G 8 GLN G 30 HIS G 134 GLN H 38 ASN I 85 GLN I 253 ASN I 282 ASN J 119 ASN J 434 ASN K 119 ASN K 434 ASN L 85 GLN L 253 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 27468 Z= 0.252 Angle : 0.534 7.986 37280 Z= 0.278 Chirality : 0.043 0.223 4486 Planarity : 0.003 0.046 4578 Dihedral : 8.583 79.486 3908 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.05 % Allowed : 15.55 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.92 (0.14), residues: 3422 helix: 1.69 (0.12), residues: 1852 sheet: 0.34 (0.27), residues: 364 loop : -1.02 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 181 HIS 0.005 0.001 HIS L 168 PHE 0.035 0.002 PHE J 202 TYR 0.017 0.001 TYR F 107 ARG 0.009 0.001 ARG L 436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 464 time to evaluate : 2.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8237 (mt) REVERT: A 128 MET cc_start: 0.7280 (mmm) cc_final: 0.6857 (mmp) REVERT: A 189 ILE cc_start: 0.7005 (OUTLIER) cc_final: 0.6575 (tp) REVERT: B 66 LEU cc_start: 0.8789 (mt) cc_final: 0.8498 (mt) REVERT: B 183 ILE cc_start: 0.8356 (mt) cc_final: 0.7997 (mp) REVERT: C 66 LEU cc_start: 0.8795 (mt) cc_final: 0.8509 (mt) REVERT: C 183 ILE cc_start: 0.8473 (mt) cc_final: 0.8107 (mp) REVERT: C 189 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6428 (tp) REVERT: J 91 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7233 (t80) REVERT: J 109 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8069 (mmmm) REVERT: J 373 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6276 (mt-10) outliers start: 118 outliers final: 63 residues processed: 546 average time/residue: 1.2815 time to fit residues: 823.4432 Evaluate side-chains 526 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 457 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 249 LEU Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 151 ARG Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 0.9980 chunk 295 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 192 optimal weight: 7.9990 chunk 81 optimal weight: 0.1980 chunk 328 optimal weight: 0.9990 chunk 273 optimal weight: 6.9990 chunk 152 optimal weight: 0.0670 chunk 27 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN B 134 GLN C 105 GLN C 134 GLN D 210 HIS E 83 GLN F 134 GLN G 134 GLN H 83 GLN J 119 ASN J 434 ASN K 77 GLN K 119 ASN K 434 ASN L 85 GLN L 253 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 27468 Z= 0.143 Angle : 0.474 7.441 37280 Z= 0.247 Chirality : 0.042 0.183 4486 Planarity : 0.003 0.046 4578 Dihedral : 8.277 77.934 3908 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.05 % Allowed : 17.09 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 1.16 (0.14), residues: 3422 helix: 1.90 (0.12), residues: 1870 sheet: 0.35 (0.27), residues: 364 loop : -0.95 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 181 HIS 0.007 0.001 HIS F 185 PHE 0.031 0.001 PHE J 202 TYR 0.012 0.001 TYR F 107 ARG 0.010 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 476 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8234 (mt) REVERT: A 128 MET cc_start: 0.7250 (mmm) cc_final: 0.6821 (mmp) REVERT: A 189 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6522 (tp) REVERT: B 183 ILE cc_start: 0.8364 (mt) cc_final: 0.8008 (mp) REVERT: B 189 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6365 (tp) REVERT: C 59 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: C 183 ILE cc_start: 0.8407 (mt) cc_final: 0.8044 (mp) REVERT: C 189 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6411 (tp) REVERT: E 86 THR cc_start: 0.8825 (t) cc_final: 0.8426 (m) REVERT: H 81 ASN cc_start: 0.7134 (t0) cc_final: 0.6778 (t0) REVERT: H 86 THR cc_start: 0.8761 (t) cc_final: 0.8383 (m) REVERT: J 41 THR cc_start: 0.7562 (OUTLIER) cc_final: 0.7360 (p) REVERT: J 109 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7966 (mmmm) REVERT: J 245 THR cc_start: 0.8338 (m) cc_final: 0.8087 (m) REVERT: J 352 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7922 (tt) REVERT: J 373 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6203 (mt-10) REVERT: K 373 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.6251 (mt-10) REVERT: L 291 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6607 (tt0) outliers start: 89 outliers final: 44 residues processed: 530 average time/residue: 1.2870 time to fit residues: 803.6940 Evaluate side-chains 509 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 454 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 400 GLU Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 chunk 186 optimal weight: 0.8980 chunk 276 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 327 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN C 134 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN G 134 GLN I 253 ASN J 119 ASN J 434 ASN K 77 GLN K 119 ASN K 434 ASN L 85 GLN L 253 ASN L 282 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 27468 Z= 0.330 Angle : 0.583 8.310 37280 Z= 0.302 Chirality : 0.045 0.250 4486 Planarity : 0.004 0.047 4578 Dihedral : 8.736 79.323 3908 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.08 % Allowed : 16.88 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.74 (0.14), residues: 3422 helix: 1.46 (0.12), residues: 1882 sheet: 0.21 (0.26), residues: 376 loop : -0.99 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 181 HIS 0.007 0.001 HIS I 168 PHE 0.036 0.002 PHE J 202 TYR 0.012 0.002 TYR F 107 ARG 0.007 0.001 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 455 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8215 (mt) REVERT: A 128 MET cc_start: 0.7298 (mmm) cc_final: 0.6867 (mmp) REVERT: A 189 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6658 (tp) REVERT: B 183 ILE cc_start: 0.8507 (mt) cc_final: 0.8166 (mp) REVERT: B 189 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.6550 (tp) REVERT: C 183 ILE cc_start: 0.8516 (mt) cc_final: 0.8161 (mp) REVERT: C 189 ILE cc_start: 0.6683 (OUTLIER) cc_final: 0.6381 (tp) REVERT: D 66 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8224 (mt) REVERT: E 222 MET cc_start: 0.7218 (ttp) cc_final: 0.6958 (ttm) REVERT: G 93 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8059 (tmtt) REVERT: G 134 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: I 92 MET cc_start: 0.6076 (mmt) cc_final: 0.5772 (tpp) REVERT: I 158 TRP cc_start: 0.7857 (m100) cc_final: 0.7475 (m-90) REVERT: I 439 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7103 (m-30) REVERT: J 41 THR cc_start: 0.7681 (OUTLIER) cc_final: 0.7478 (p) REVERT: J 91 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7306 (t80) REVERT: J 109 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8103 (mmmm) REVERT: J 165 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.8179 (p) REVERT: K 373 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6304 (mt-10) REVERT: L 158 TRP cc_start: 0.7840 (m100) cc_final: 0.7448 (m-90) outliers start: 119 outliers final: 70 residues processed: 537 average time/residue: 1.2863 time to fit residues: 810.7537 Evaluate side-chains 527 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 444 time to evaluate : 3.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 400 GLU Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 91 PHE Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 116 GLU Chi-restraints excluded: chain K residue 151 ARG Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 400 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 208 optimal weight: 0.4980 chunk 223 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 257 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN B 134 GLN C 105 GLN C 134 GLN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN F 134 GLN H 30 HIS J 119 ASN J 434 ASN K 77 GLN K 119 ASN K 434 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 27468 Z= 0.162 Angle : 0.499 7.515 37280 Z= 0.259 Chirality : 0.042 0.188 4486 Planarity : 0.003 0.041 4578 Dihedral : 8.411 79.766 3908 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.57 % Allowed : 17.95 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 1.03 (0.14), residues: 3422 helix: 1.77 (0.12), residues: 1866 sheet: 0.22 (0.26), residues: 376 loop : -0.92 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 181 HIS 0.005 0.001 HIS L 168 PHE 0.030 0.001 PHE J 202 TYR 0.015 0.001 TYR F 107 ARG 0.009 0.000 ARG F 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 460 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8239 (mt) REVERT: A 128 MET cc_start: 0.7250 (mmm) cc_final: 0.6816 (mmp) REVERT: A 189 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6610 (tp) REVERT: B 183 ILE cc_start: 0.8480 (mt) cc_final: 0.8144 (mp) REVERT: B 189 ILE cc_start: 0.6870 (OUTLIER) cc_final: 0.6547 (tp) REVERT: C 183 ILE cc_start: 0.8452 (mt) cc_final: 0.8107 (mp) REVERT: C 189 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6438 (tp) REVERT: D 66 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8253 (mt) REVERT: E 40 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6879 (mm-30) REVERT: E 81 ASN cc_start: 0.7354 (t0) cc_final: 0.7080 (t0) REVERT: E 86 THR cc_start: 0.8860 (t) cc_final: 0.8408 (m) REVERT: F 135 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8193 (m) REVERT: G 93 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.7958 (tmtt) REVERT: H 81 ASN cc_start: 0.7178 (t0) cc_final: 0.6858 (t0) REVERT: H 86 THR cc_start: 0.8790 (t) cc_final: 0.8372 (m) REVERT: I 92 MET cc_start: 0.5999 (mmt) cc_final: 0.5774 (tpp) REVERT: I 158 TRP cc_start: 0.7733 (m100) cc_final: 0.7423 (m-90) REVERT: I 222 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7934 (ptpt) REVERT: J 109 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7947 (mmmm) REVERT: J 165 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.8158 (p) REVERT: K 373 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.6256 (mt-10) REVERT: L 222 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7978 (ptpt) outliers start: 104 outliers final: 60 residues processed: 527 average time/residue: 1.2978 time to fit residues: 805.2535 Evaluate side-chains 519 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 446 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 123 ILE Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 400 GLU Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 116 GLU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 400 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 0.9980 chunk 313 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 chunk 305 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 239 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 chunk 288 optimal weight: 0.5980 chunk 304 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN C 134 GLN D 210 HIS E 140 ASN F 134 GLN G 134 GLN I 155 GLN J 119 ASN J 434 ASN K 77 GLN K 119 ASN K 434 ASN L 155 GLN L 253 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 27468 Z= 0.171 Angle : 0.504 7.635 37280 Z= 0.262 Chirality : 0.042 0.187 4486 Planarity : 0.003 0.041 4578 Dihedral : 8.354 78.848 3908 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.26 % Allowed : 18.57 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 1.08 (0.14), residues: 3422 helix: 1.83 (0.12), residues: 1868 sheet: 0.22 (0.27), residues: 364 loop : -0.91 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 181 HIS 0.005 0.001 HIS I 168 PHE 0.030 0.001 PHE J 202 TYR 0.017 0.001 TYR F 107 ARG 0.009 0.000 ARG F 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 456 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8291 (mt) REVERT: A 128 MET cc_start: 0.7254 (mmm) cc_final: 0.6819 (mmp) REVERT: A 189 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6690 (tp) REVERT: B 183 ILE cc_start: 0.8481 (mt) cc_final: 0.8147 (mp) REVERT: B 189 ILE cc_start: 0.6850 (OUTLIER) cc_final: 0.6521 (tp) REVERT: C 183 ILE cc_start: 0.8459 (mt) cc_final: 0.8115 (mp) REVERT: C 189 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6414 (tp) REVERT: D 59 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7166 (mt-10) REVERT: D 62 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7382 (mt-10) REVERT: D 66 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8307 (mt) REVERT: E 81 ASN cc_start: 0.7316 (t0) cc_final: 0.7023 (t0) REVERT: E 86 THR cc_start: 0.8850 (t) cc_final: 0.8393 (m) REVERT: G 93 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.7964 (tmtt) REVERT: H 81 ASN cc_start: 0.7112 (t0) cc_final: 0.6765 (t0) REVERT: H 86 THR cc_start: 0.8805 (t) cc_final: 0.8361 (m) REVERT: I 158 TRP cc_start: 0.7729 (m100) cc_final: 0.7470 (m-90) REVERT: I 222 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7939 (ptpt) REVERT: I 439 ASP cc_start: 0.7189 (m-30) cc_final: 0.6827 (m-30) REVERT: J 109 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7940 (mmmm) REVERT: J 165 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.8117 (p) REVERT: J 373 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6208 (mt-10) REVERT: K 373 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6262 (mt-10) REVERT: L 158 TRP cc_start: 0.7833 (m100) cc_final: 0.7501 (m-90) REVERT: L 222 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8000 (ptpt) REVERT: L 291 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6612 (tt0) outliers start: 95 outliers final: 60 residues processed: 520 average time/residue: 1.3267 time to fit residues: 810.4678 Evaluate side-chains 519 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 446 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 400 GLU Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 116 GLU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 400 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 2.9990 chunk 322 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 338 optimal weight: 5.9990 chunk 311 optimal weight: 7.9990 chunk 269 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 165 optimal weight: 0.1980 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN D 210 HIS G 134 GLN I 155 GLN J 119 ASN J 434 ASN K 77 GLN K 119 ASN K 434 ASN L 155 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 27468 Z= 0.318 Angle : 0.581 8.181 37280 Z= 0.301 Chirality : 0.045 0.240 4486 Planarity : 0.003 0.043 4578 Dihedral : 8.675 79.818 3906 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.16 % Allowed : 19.15 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.75 (0.14), residues: 3422 helix: 1.48 (0.12), residues: 1878 sheet: 0.17 (0.26), residues: 376 loop : -0.96 (0.16), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 181 HIS 0.005 0.001 HIS L 168 PHE 0.036 0.002 PHE I 134 TYR 0.018 0.001 TYR F 107 ARG 0.008 0.001 ARG G 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 446 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8268 (mt) REVERT: A 128 MET cc_start: 0.7318 (mmm) cc_final: 0.6879 (mmp) REVERT: A 189 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.6705 (tp) REVERT: B 183 ILE cc_start: 0.8532 (mt) cc_final: 0.8206 (mp) REVERT: B 189 ILE cc_start: 0.6850 (OUTLIER) cc_final: 0.6562 (tp) REVERT: C 183 ILE cc_start: 0.8538 (mt) cc_final: 0.8195 (mp) REVERT: C 189 ILE cc_start: 0.6819 (OUTLIER) cc_final: 0.6534 (tp) REVERT: D 66 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8267 (mt) REVERT: F 134 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7656 (mp10) REVERT: G 93 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.7989 (tmtt) REVERT: I 97 LEU cc_start: 0.8269 (mt) cc_final: 0.8066 (mt) REVERT: I 135 LEU cc_start: 0.7539 (pp) cc_final: 0.6884 (mm) REVERT: I 158 TRP cc_start: 0.7774 (m100) cc_final: 0.7409 (m-90) REVERT: I 222 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7942 (ptpt) REVERT: J 109 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8055 (mmmm) REVERT: J 165 SER cc_start: 0.8430 (OUTLIER) cc_final: 0.8200 (p) REVERT: K 373 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6288 (mt-10) REVERT: L 71 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7577 (tp40) REVERT: L 92 MET cc_start: 0.5980 (mmt) cc_final: 0.5698 (tpp) REVERT: L 158 TRP cc_start: 0.7782 (m100) cc_final: 0.7415 (m-90) REVERT: L 222 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7993 (ptpt) outliers start: 92 outliers final: 60 residues processed: 510 average time/residue: 1.2507 time to fit residues: 752.0296 Evaluate side-chains 505 residues out of total 2914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 433 time to evaluate : 3.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 137 SER Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 187 SER Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain I residue 357 THR Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 400 GLU Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 109 LYS Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 321 VAL Chi-restraints excluded: chain J residue 373 GLU Chi-restraints excluded: chain J residue 442 VAL Chi-restraints excluded: chain K residue 24 PHE Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain K residue 116 GLU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 334 LYS Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 442 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain L residue 222 LYS Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 291 GLU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 357 THR Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 400 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 0.9980 chunk 287 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 270 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 277 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN B 134 GLN C 105 GLN C 134 GLN D 210 HIS F 134 GLN I 155 GLN J 119 ASN J 434 ASN K 77 GLN K 119 ASN K 434 ASN L 85 GLN L 115 GLN L 155 GLN L 253 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.176442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.134578 restraints weight = 29407.683| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.33 r_work: 0.3277 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27468 Z= 0.180 Angle : 0.514 7.645 37280 Z= 0.268 Chirality : 0.043 0.195 4486 Planarity : 0.003 0.039 4578 Dihedral : 8.434 80.060 3906 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.85 % Allowed : 19.49 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % 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: 0.97 (0.14), residues: 3422 helix: 1.70 (0.12), residues: 1874 sheet: 0.17 (0.26), residues: 376 loop : -0.92 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 181 HIS 0.004 0.001 HIS I 168 PHE 0.031 0.001 PHE J 202 TYR 0.020 0.001 TYR F 107 ARG 0.008 0.000 ARG F 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12590.46 seconds wall clock time: 225 minutes 5.96 seconds (13505.96 seconds total)