Starting phenix.real_space_refine on Sun Sep 29 22:06:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1t_36803/09_2024/8k1t_36803.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1t_36803/09_2024/8k1t_36803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1t_36803/09_2024/8k1t_36803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1t_36803/09_2024/8k1t_36803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1t_36803/09_2024/8k1t_36803.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1t_36803/09_2024/8k1t_36803.cif" } resolution = 2.48 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= 0.088 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 94 5.16 5 Na 4 4.78 5 C 15516 2.51 5 N 3888 2.21 5 O 4336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23866 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "B" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "C" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1498 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 3 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1643 Classifications: {'peptide': 208} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 202} Chain breaks: 2 Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1643 Classifications: {'peptide': 208} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 202} Chain breaks: 2 Chain: "F" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1498 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 3 Chain: "G" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain: "H" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1039 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} 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: 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: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 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: 14.71, per 1000 atoms: 0.62 Number of scatterers: 23866 At special positions: 0 Unit cell: (136.95, 176.79, 111.22, 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 94 16.00 P 24 15.00 Na 4 11.00 O 4336 8.00 N 3888 7.00 C 15516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.16 Conformation dependent library (CDL) restraints added in 3.1 seconds 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5620 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 18 sheets defined 64.7% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 15 through 29 Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 59 through 66 removed outlier: 3.505A pdb=" N LEU A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'B' and resid 15 through 29 Processing helix chain 'B' and resid 38 through 45 Processing helix chain 'B' and resid 59 through 66 removed outlier: 3.505A pdb=" N LEU B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 123 through 138 Processing helix chain 'C' and resid 15 through 29 removed outlier: 3.537A pdb=" N SER C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 59 through 66 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 81 through 95 Processing helix chain 'C' and resid 106 through 116 Processing helix chain 'C' and resid 123 through 138 Processing helix chain 'C' and resid 211 through 217 Processing helix chain 'D' and resid 15 through 29 removed outlier: 3.536A pdb=" N SER D 20 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 46 Processing helix chain 'D' and resid 59 through 66 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 81 through 95 Processing helix chain 'D' and resid 106 through 116 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'D' and resid 211 through 220 Processing helix chain 'E' and resid 15 through 29 removed outlier: 3.537A pdb=" N SER E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 59 through 66 Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 81 through 95 Processing helix chain 'E' and resid 106 through 116 Processing helix chain 'E' and resid 123 through 138 Processing helix chain 'E' and resid 171 through 176 Processing helix chain 'E' and resid 211 through 220 Processing helix chain 'F' and resid 15 through 29 removed outlier: 3.537A pdb=" N SER F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 46 Processing helix chain 'F' and resid 59 through 66 Processing helix chain 'F' and resid 67 through 71 Processing helix chain 'F' and resid 81 through 95 Processing helix chain 'F' and resid 106 through 116 Processing helix chain 'F' and resid 123 through 138 Processing helix chain 'F' and resid 211 through 217 Processing helix chain 'G' and resid 15 through 29 Processing helix chain 'G' and resid 38 through 45 Processing helix chain 'G' and resid 59 through 66 removed outlier: 3.504A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 71 Processing helix chain 'G' and resid 81 through 95 Processing helix chain 'G' and resid 106 through 116 Processing helix chain 'G' and resid 123 through 138 Processing helix chain 'H' and resid 15 through 29 Processing helix chain 'H' and resid 38 through 45 Processing helix chain 'H' and resid 59 through 66 removed outlier: 3.505A pdb=" N LEU H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'H' and resid 81 through 95 Processing helix chain 'H' and resid 106 through 116 Processing helix chain 'H' and resid 123 through 138 Processing helix chain 'I' and resid 16 through 36 Processing helix chain 'I' and resid 37 through 41 removed outlier: 3.542A pdb=" N THR I 41 " --> pdb=" O PRO I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 59 Processing helix chain 'I' and resid 67 through 72 removed outlier: 3.554A pdb=" N PHE I 72 " --> pdb=" O THR I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 90 Processing helix chain 'I' and resid 90 through 102 removed outlier: 3.873A pdb=" N PHE I 94 " --> pdb=" O GLY I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 Processing helix chain 'I' and resid 125 through 157 removed outlier: 4.164A 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 158 through 174 removed outlier: 3.541A pdb=" N PHE I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 208 removed outlier: 4.415A pdb=" N GLY I 208 " --> pdb=" O THR I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 218 Processing helix chain 'I' and resid 220 through 224 Processing helix chain 'I' and resid 225 through 250 Processing helix chain 'I' and resid 261 through 275 Processing helix chain 'I' and resid 285 through 289 Processing helix chain 'I' and resid 290 through 303 Processing helix chain 'I' and resid 315 through 331 Processing helix chain 'I' and resid 344 through 373 Processing helix chain 'I' and resid 376 through 389 Processing helix chain 'I' and resid 397 through 401 Processing helix chain 'I' and resid 402 through 419 Processing helix chain 'I' and resid 419 through 428 removed outlier: 3.898A pdb=" N PHE I 427 " --> pdb=" O PHE I 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 36 Processing helix chain 'J' and resid 37 through 41 removed outlier: 3.541A pdb=" N THR J 41 " --> pdb=" O PRO J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 59 Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.555A pdb=" N PHE J 72 " --> pdb=" O THR J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 90 Processing helix chain 'J' and resid 90 through 102 removed outlier: 3.873A pdb=" N PHE J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 118 Processing helix chain 'J' and resid 125 through 157 removed outlier: 4.164A 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 158 through 174 removed outlier: 3.541A pdb=" N PHE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 208 removed outlier: 4.414A pdb=" N GLY J 208 " --> pdb=" O THR J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 218 Processing helix chain 'J' and resid 220 through 224 Processing helix chain 'J' and resid 225 through 250 Processing helix chain 'J' and resid 261 through 275 Processing helix chain 'J' and resid 285 through 289 Processing helix chain 'J' and resid 290 through 303 Processing helix chain 'J' and resid 315 through 331 Processing helix chain 'J' and resid 344 through 373 Processing helix chain 'J' and resid 376 through 389 Processing helix chain 'J' and resid 397 through 401 Processing helix chain 'J' and resid 402 through 419 Processing helix chain 'J' and resid 419 through 428 removed outlier: 3.897A pdb=" N PHE J 427 " --> pdb=" O PHE J 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 36 Processing helix chain 'K' and resid 37 through 41 removed outlier: 3.542A pdb=" N THR K 41 " --> pdb=" O PRO K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 59 Processing helix chain 'K' and resid 67 through 72 removed outlier: 3.554A pdb=" N PHE K 72 " --> pdb=" O THR K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 90 Processing helix chain 'K' and resid 90 through 102 removed outlier: 3.873A pdb=" N PHE K 94 " --> pdb=" O GLY K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 Processing helix chain 'K' and resid 125 through 157 removed outlier: 4.164A 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 158 through 174 removed outlier: 3.542A pdb=" N PHE K 163 " --> pdb=" O SER K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 208 removed outlier: 4.414A pdb=" N GLY K 208 " --> pdb=" O THR K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 218 Processing helix chain 'K' and resid 220 through 224 Processing helix chain 'K' and resid 225 through 250 Processing helix chain 'K' and resid 261 through 275 Processing helix chain 'K' and resid 285 through 289 Processing helix chain 'K' and resid 290 through 303 Processing helix chain 'K' and resid 315 through 331 Processing helix chain 'K' and resid 344 through 373 Processing helix chain 'K' and resid 376 through 389 Processing helix chain 'K' and resid 397 through 401 Processing helix chain 'K' and resid 402 through 419 Processing helix chain 'K' and resid 419 through 428 removed outlier: 3.898A pdb=" N PHE K 427 " --> pdb=" O PHE K 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 36 Processing helix chain 'L' and resid 37 through 41 removed outlier: 3.541A pdb=" N THR L 41 " --> pdb=" O PRO L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 59 Processing helix chain 'L' and resid 67 through 72 removed outlier: 3.554A pdb=" N PHE L 72 " --> pdb=" O THR L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 90 Processing helix chain 'L' and resid 90 through 102 removed outlier: 3.873A pdb=" N PHE L 94 " --> pdb=" O GLY L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 118 Processing helix chain 'L' and resid 125 through 157 removed outlier: 4.164A 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 158 through 174 removed outlier: 3.542A pdb=" N PHE L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 208 removed outlier: 4.414A pdb=" N GLY L 208 " --> pdb=" O THR L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 218 Processing helix chain 'L' and resid 220 through 224 Processing helix chain 'L' and resid 225 through 250 Processing helix chain 'L' and resid 261 through 275 Processing helix chain 'L' and resid 285 through 289 Processing helix chain 'L' and resid 290 through 303 Processing helix chain 'L' and resid 315 through 331 Processing helix chain 'L' and resid 344 through 373 Processing helix chain 'L' and resid 376 through 389 Processing helix chain 'L' and resid 397 through 401 Processing helix chain 'L' and resid 402 through 419 Processing helix chain 'L' and resid 419 through 428 removed outlier: 3.897A pdb=" N PHE L 427 " --> pdb=" O PHE L 423 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.817A pdb=" N TYR A 73 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE A 100 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE A 122 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 102 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.817A pdb=" N TYR B 73 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE B 100 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE B 122 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL B 102 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.747A pdb=" N TYR C 73 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE C 100 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE C 122 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL C 102 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.644A pdb=" N ASN C 143 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET C 208 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE C 180 " --> pdb=" O MET C 208 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N LEU C 181 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER C 192 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE C 183 " --> pdb=" O CYS C 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.748A pdb=" N TYR D 73 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE D 100 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE D 122 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL D 102 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 143 through 145 removed outlier: 3.643A pdb=" N ASN D 143 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N MET D 208 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE D 180 " --> pdb=" O MET D 208 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE D 183 " --> pdb=" O CYS D 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 165 through 166 removed outlier: 3.682A pdb=" N LYS D 165 " --> pdb=" O ILE D 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 51 through 54 removed outlier: 3.747A pdb=" N TYR E 73 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE E 100 " --> pdb=" O ARG E 120 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE E 122 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL E 102 " --> pdb=" O ILE E 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 143 through 145 removed outlier: 3.643A pdb=" N ASN E 143 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET E 208 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE E 180 " --> pdb=" O MET E 208 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE E 183 " --> pdb=" O CYS E 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 165 through 166 removed outlier: 3.877A pdb=" N LYS E 165 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.747A pdb=" N TYR F 73 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE F 100 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE F 122 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL F 102 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 143 through 145 removed outlier: 3.643A pdb=" N ASN F 143 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET F 208 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE F 180 " --> pdb=" O MET F 208 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N LEU F 181 " --> pdb=" O SER F 192 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER F 192 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE F 183 " --> pdb=" O CYS F 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.817A pdb=" N TYR G 73 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE G 100 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE G 122 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL G 102 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 51 through 54 removed outlier: 3.817A pdb=" N TYR H 73 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE H 100 " --> pdb=" O ARG H 120 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE H 122 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL H 102 " --> pdb=" O ILE H 122 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 336 through 338 removed outlier: 4.633A pdb=" N THR I 336 " --> pdb=" O ILE I 343 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 336 through 338 removed outlier: 4.633A pdb=" N THR J 336 " --> pdb=" O ILE J 343 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 336 through 338 removed outlier: 4.634A pdb=" N THR K 336 " --> pdb=" O ILE K 343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 336 through 338 removed outlier: 4.634A pdb=" N THR L 336 " --> pdb=" O ILE L 343 " (cutoff:3.500A) 1532 hydrogen bonds defined for protein. 4413 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: 8.91 Time building geometry restraints manager: 7.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4015 1.32 - 1.44: 6056 1.44 - 1.57: 14037 1.57 - 1.69: 40 1.69 - 1.81: 170 Bond restraints: 24318 Sorted by residual: bond pdb=" CA LEU J 352 " pdb=" C LEU J 352 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.37e-02 5.33e+03 1.65e+01 bond pdb=" CA LEU L 352 " pdb=" C LEU L 352 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.32e-02 5.74e+03 1.36e+01 bond pdb=" CA LEU I 352 " pdb=" C LEU I 352 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.32e-02 5.74e+03 1.35e+01 bond pdb=" CA LEU K 352 " pdb=" C LEU K 352 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.37e-02 5.33e+03 1.03e+01 bond pdb=" CA SER K 283 " pdb=" CB SER K 283 " ideal model delta sigma weight residual 1.536 1.490 0.046 1.46e-02 4.69e+03 9.79e+00 ... (remaining 24313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 32718 2.04 - 4.07: 243 4.07 - 6.11: 35 6.11 - 8.15: 12 8.15 - 10.19: 6 Bond angle restraints: 33014 Sorted by residual: angle pdb=" N SER L 283 " pdb=" CA SER L 283 " pdb=" C SER L 283 " ideal model delta sigma weight residual 114.56 105.27 9.29 1.27e+00 6.20e-01 5.35e+01 angle pdb=" N SER I 283 " pdb=" CA SER I 283 " pdb=" C SER I 283 " ideal model delta sigma weight residual 114.56 105.35 9.21 1.27e+00 6.20e-01 5.26e+01 angle pdb=" N SER J 283 " pdb=" CA SER J 283 " pdb=" C SER J 283 " ideal model delta sigma weight residual 114.56 106.85 7.71 1.27e+00 6.20e-01 3.69e+01 angle pdb=" N SER K 283 " pdb=" CA SER K 283 " pdb=" C SER K 283 " ideal model delta sigma weight residual 114.56 106.95 7.61 1.27e+00 6.20e-01 3.59e+01 angle pdb=" C THR L 15 " pdb=" N PRO L 16 " pdb=" CA PRO L 16 " ideal model delta sigma weight residual 120.38 114.25 6.13 1.03e+00 9.43e-01 3.55e+01 ... (remaining 33009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13738 17.93 - 35.86: 597 35.86 - 53.79: 65 53.79 - 71.72: 46 71.72 - 89.66: 12 Dihedral angle restraints: 14458 sinusoidal: 5730 harmonic: 8728 Sorted by residual: dihedral pdb=" CA MET J 301 " pdb=" C MET J 301 " pdb=" N PHE J 302 " pdb=" CA PHE J 302 " ideal model delta harmonic sigma weight residual 180.00 164.71 15.29 0 5.00e+00 4.00e-02 9.36e+00 dihedral pdb=" CA MET K 301 " pdb=" C MET K 301 " pdb=" N PHE K 302 " pdb=" CA PHE K 302 " ideal model delta harmonic sigma weight residual 180.00 164.71 15.29 0 5.00e+00 4.00e-02 9.35e+00 dihedral pdb=" CA MET L 301 " pdb=" C MET L 301 " pdb=" N PHE L 302 " pdb=" CA PHE L 302 " ideal model delta harmonic sigma weight residual 180.00 164.71 15.29 0 5.00e+00 4.00e-02 9.35e+00 ... (remaining 14455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2497 0.032 - 0.065: 1101 0.065 - 0.097: 220 0.097 - 0.129: 157 0.129 - 0.162: 23 Chirality restraints: 3998 Sorted by residual: chirality pdb=" CA LEU E 87 " pdb=" N LEU E 87 " pdb=" C LEU E 87 " pdb=" CB LEU E 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.52e-01 chirality pdb=" CA LEU D 87 " pdb=" N LEU D 87 " pdb=" C LEU D 87 " pdb=" CB LEU D 87 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE J 303 " pdb=" N ILE J 303 " pdb=" C ILE J 303 " pdb=" CB ILE J 303 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 ... (remaining 3995 not shown) Planarity restraints: 4016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA L 351 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C ALA L 351 " 0.037 2.00e-02 2.50e+03 pdb=" O ALA L 351 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU L 352 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 351 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.18e+00 pdb=" C ALA J 351 " -0.035 2.00e-02 2.50e+03 pdb=" O ALA J 351 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU J 352 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 86 " 0.009 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C THR G 86 " -0.029 2.00e-02 2.50e+03 pdb=" O THR G 86 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU G 87 " 0.010 2.00e-02 2.50e+03 ... (remaining 4013 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 6808 2.82 - 3.40: 26062 3.40 - 3.98: 46778 3.98 - 4.56: 65663 4.56 - 5.14: 96579 Nonbonded interactions: 241890 Sorted by model distance: nonbonded pdb=" O ASN L 195 " pdb=" OG1 THR L 199 " model vdw 2.240 3.040 nonbonded pdb=" O ASN K 195 " pdb=" OG1 THR K 199 " model vdw 2.240 3.040 nonbonded pdb=" O ASN I 195 " pdb=" OG1 THR I 199 " model vdw 2.240 3.040 nonbonded pdb=" O ASN J 195 " pdb=" OG1 THR J 199 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR D 108 " pdb=" OE1 GLU E 60 " model vdw 2.296 3.040 ... (remaining 241885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 139 or resid 301)) selection = chain 'B' selection = (chain 'G' and (resid 7 through 139 or resid 301)) selection = chain 'H' } ncs_group { reference = (chain 'C' and resid 7 through 217) selection = (chain 'D' and (resid 7 through 172 or resid 179 through 192 or resid 205 throug \ h 217)) selection = (chain 'E' and (resid 7 through 172 or resid 179 through 192 or resid 205 throug \ h 217)) selection = (chain 'F' and resid 7 through 217) } 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 54.940 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.140 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.004 0.056 24318 Z= 0.244 Angle : 0.529 10.186 33014 Z= 0.304 Chirality : 0.042 0.162 3998 Planarity : 0.003 0.031 4016 Dihedral : 10.972 89.655 8838 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.97 % Allowed : 3.66 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 0.84 (0.14), residues: 3008 helix: 1.12 (0.11), residues: 1810 sheet: 1.39 (0.29), residues: 308 loop : -0.82 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 47 HIS 0.002 0.001 HIS L 168 PHE 0.026 0.001 PHE K 202 TYR 0.005 0.001 TYR D 108 ARG 0.002 0.000 ARG L 417 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 813 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7166 (tp30) cc_final: 0.6932 (tp30) REVERT: C 48 TYR cc_start: 0.7996 (m-80) cc_final: 0.7784 (m-80) REVERT: C 128 MET cc_start: 0.7893 (mmm) cc_final: 0.7547 (mmp) REVERT: D 134 GLN cc_start: 0.7687 (mm-40) cc_final: 0.7201 (mm110) REVERT: E 137 SER cc_start: 0.7971 (t) cc_final: 0.7742 (m) REVERT: F 128 MET cc_start: 0.7972 (mmm) cc_final: 0.7620 (mmp) REVERT: F 181 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7433 (mt) REVERT: I 110 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6819 (mp0) REVERT: I 123 ILE cc_start: 0.8073 (pt) cc_final: 0.7825 (pt) REVERT: I 140 ILE cc_start: 0.8609 (tt) cc_final: 0.8390 (tt) REVERT: I 166 LEU cc_start: 0.8782 (tp) cc_final: 0.8514 (tm) REVERT: I 251 TYR cc_start: 0.8479 (t80) cc_final: 0.8199 (t80) REVERT: I 298 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8875 (mt) REVERT: I 340 ARG cc_start: 0.7816 (mtt180) cc_final: 0.7455 (mtt-85) REVERT: J 97 LEU cc_start: 0.7358 (mt) cc_final: 0.7005 (tp) REVERT: J 136 PHE cc_start: 0.7749 (t80) cc_final: 0.7522 (t80) REVERT: J 156 TYR cc_start: 0.7498 (m-80) cc_final: 0.7260 (m-80) REVERT: J 166 LEU cc_start: 0.8060 (tp) cc_final: 0.7789 (tp) REVERT: K 156 TYR cc_start: 0.7480 (m-80) cc_final: 0.7252 (m-80) REVERT: K 166 LEU cc_start: 0.8071 (tp) cc_final: 0.7808 (tp) REVERT: K 250 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8296 (mm-30) REVERT: K 262 ILE cc_start: 0.7411 (mt) cc_final: 0.7134 (tp) REVERT: L 110 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6798 (mp0) REVERT: L 123 ILE cc_start: 0.8074 (pt) cc_final: 0.7847 (pt) REVERT: L 140 ILE cc_start: 0.8613 (tt) cc_final: 0.8404 (tt) REVERT: L 166 LEU cc_start: 0.8801 (tp) cc_final: 0.8529 (tm) REVERT: L 251 TYR cc_start: 0.8452 (t80) cc_final: 0.8083 (t80) REVERT: L 298 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8867 (mt) REVERT: L 340 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7454 (mtt-85) outliers start: 25 outliers final: 0 residues processed: 831 average time/residue: 1.3613 time to fit residues: 1300.5264 Evaluate side-chains 572 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 569 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain L residue 298 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 154 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 236 optimal weight: 0.0970 chunk 91 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 274 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 81 ASN B 8 GLN B 38 ASN C 38 ASN C 185 HIS D 8 GLN D 70 ASN D 185 HIS E 38 ASN E 61 ASN E 70 ASN E 134 GLN E 185 HIS F 38 ASN F 185 HIS G 8 GLN H 38 ASN H 43 ASN H 70 ASN H 81 ASN I 18 GLN I 119 ASN I 155 GLN I 195 ASN I 239 ASN ** J 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN J 155 GLN J 253 ASN ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN K 155 GLN K 253 ASN K 272 GLN L 18 GLN L 119 ASN L 155 GLN L 195 ASN L 239 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24318 Z= 0.217 Angle : 0.569 9.388 33014 Z= 0.301 Chirality : 0.043 0.179 3998 Planarity : 0.004 0.044 4016 Dihedral : 10.134 84.223 3474 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.70 % Allowed : 13.29 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.94 (0.15), residues: 3008 helix: 2.19 (0.12), residues: 1840 sheet: 1.14 (0.28), residues: 322 loop : -0.70 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 47 HIS 0.003 0.001 HIS I 168 PHE 0.034 0.002 PHE L 202 TYR 0.013 0.001 TYR I 270 ARG 0.008 0.001 ARG E 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 604 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7042 (tp30) cc_final: 0.6787 (tp30) REVERT: B 41 LYS cc_start: 0.8274 (mmtm) cc_final: 0.7749 (mmtt) REVERT: C 48 TYR cc_start: 0.8010 (m-80) cc_final: 0.7766 (m-80) REVERT: C 62 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7166 (mt-10) REVERT: C 128 MET cc_start: 0.7807 (mmm) cc_final: 0.7479 (mmp) REVERT: D 126 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7934 (ttmt) REVERT: E 138 ASP cc_start: 0.7110 (t70) cc_final: 0.6672 (m-30) REVERT: F 62 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7014 (mt-10) REVERT: F 128 MET cc_start: 0.7826 (mmm) cc_final: 0.7521 (mmp) REVERT: G 41 LYS cc_start: 0.8271 (mmtm) cc_final: 0.7793 (mmtt) REVERT: I 110 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6830 (mp0) REVERT: I 123 ILE cc_start: 0.8055 (pt) cc_final: 0.7815 (pt) REVERT: I 251 TYR cc_start: 0.8480 (t80) cc_final: 0.8165 (t80) REVERT: I 298 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8763 (mt) REVERT: I 340 ARG cc_start: 0.7838 (mtt180) cc_final: 0.7483 (mtt-85) REVERT: J 97 LEU cc_start: 0.7336 (mt) cc_final: 0.7133 (tp) REVERT: J 100 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.5719 (mmm) REVERT: J 106 ILE cc_start: 0.7740 (mp) cc_final: 0.7480 (mm) REVERT: J 136 PHE cc_start: 0.7610 (t80) cc_final: 0.7408 (t80) REVERT: J 155 GLN cc_start: 0.7598 (tt0) cc_final: 0.7242 (tt0) REVERT: J 216 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6224 (mtp) REVERT: K 97 LEU cc_start: 0.7330 (mt) cc_final: 0.7086 (tp) REVERT: K 155 GLN cc_start: 0.7588 (tt0) cc_final: 0.7241 (tt0) REVERT: K 216 MET cc_start: 0.7327 (mmp) cc_final: 0.6219 (mtp) REVERT: K 250 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8461 (mm-30) REVERT: L 110 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6829 (mp0) REVERT: L 123 ILE cc_start: 0.8036 (pt) cc_final: 0.7789 (pt) REVERT: L 251 TYR cc_start: 0.8442 (t80) cc_final: 0.8117 (t80) REVERT: L 298 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8726 (mt) REVERT: L 340 ARG cc_start: 0.7867 (mtt180) cc_final: 0.7577 (mtt-85) outliers start: 95 outliers final: 33 residues processed: 659 average time/residue: 1.3891 time to fit residues: 1041.8896 Evaluate side-chains 594 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 556 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 323 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 152 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 228 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 274 optimal weight: 6.9990 chunk 296 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 70 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS D 8 GLN D 70 ASN D 134 GLN D 185 HIS E 134 GLN E 185 HIS F 185 HIS G 8 GLN H 70 ASN I 18 GLN I 119 ASN I 239 ASN J 85 GLN J 115 GLN J 253 ASN J 374 GLN K 85 GLN K 115 GLN K 253 ASN K 272 GLN L 18 GLN L 119 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24318 Z= 0.360 Angle : 0.627 8.980 33014 Z= 0.330 Chirality : 0.046 0.210 3998 Planarity : 0.004 0.048 4016 Dihedral : 10.180 81.361 3474 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.83 % Allowed : 13.48 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.72 (0.15), residues: 3008 helix: 2.06 (0.12), residues: 1840 sheet: 0.77 (0.28), residues: 318 loop : -0.76 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 158 HIS 0.006 0.001 HIS I 168 PHE 0.038 0.002 PHE I 202 TYR 0.018 0.002 TYR L 270 ARG 0.008 0.001 ARG H 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 572 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7150 (tp30) cc_final: 0.6858 (tp30) REVERT: A 41 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8089 (mptp) REVERT: B 41 LYS cc_start: 0.8385 (mmtm) cc_final: 0.7808 (mmtt) REVERT: B 127 ASP cc_start: 0.7317 (m-30) cc_final: 0.7109 (m-30) REVERT: C 23 LYS cc_start: 0.8265 (mtpm) cc_final: 0.7814 (mtmt) REVERT: C 48 TYR cc_start: 0.8153 (m-80) cc_final: 0.7948 (m-80) REVERT: C 62 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7376 (mt-10) REVERT: C 128 MET cc_start: 0.7813 (mmm) cc_final: 0.7514 (mmp) REVERT: D 60 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: D 126 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8002 (ttmt) REVERT: D 139 GLU cc_start: 0.7039 (pm20) cc_final: 0.6836 (pm20) REVERT: E 208 MET cc_start: 0.6162 (ptt) cc_final: 0.5886 (ptt) REVERT: F 23 LYS cc_start: 0.8234 (mtpm) cc_final: 0.7798 (mtmt) REVERT: F 128 MET cc_start: 0.7800 (mmm) cc_final: 0.7504 (mmp) REVERT: F 208 MET cc_start: 0.6436 (ttp) cc_final: 0.6167 (ttp) REVERT: G 41 LYS cc_start: 0.8387 (mmtm) cc_final: 0.7839 (mmtt) REVERT: H 41 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8051 (mptp) REVERT: I 150 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7867 (mp) REVERT: I 251 TYR cc_start: 0.8458 (t80) cc_final: 0.8142 (t80) REVERT: I 298 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8800 (mt) REVERT: J 100 MET cc_start: 0.5923 (OUTLIER) cc_final: 0.5560 (mmm) REVERT: J 136 PHE cc_start: 0.7743 (t80) cc_final: 0.7496 (t80) REVERT: J 155 GLN cc_start: 0.7718 (tt0) cc_final: 0.7419 (tt0) REVERT: J 216 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.6282 (mtp) REVERT: J 220 ARG cc_start: 0.6597 (tpt170) cc_final: 0.6372 (tpt170) REVERT: J 237 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7285 (mtp) REVERT: K 155 GLN cc_start: 0.7716 (tt0) cc_final: 0.7442 (tt0) REVERT: K 216 MET cc_start: 0.7482 (mmp) cc_final: 0.6276 (mtp) REVERT: K 237 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7256 (mtp) REVERT: K 373 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7235 (mt-10) REVERT: L 150 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7880 (mp) REVERT: L 251 TYR cc_start: 0.8427 (t80) cc_final: 0.8067 (t80) REVERT: L 298 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8786 (mt) outliers start: 124 outliers final: 49 residues processed: 644 average time/residue: 1.3596 time to fit residues: 1001.1937 Evaluate side-chains 610 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 548 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 312 SER Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 422 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 237 MET Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 312 SER Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 323 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 271 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 184 optimal weight: 9.9990 chunk 275 optimal weight: 2.9990 chunk 291 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN D 134 GLN F 134 GLN F 185 HIS G 8 GLN G 134 GLN I 18 GLN I 119 ASN I 239 ASN J 85 GLN J 115 GLN J 253 ASN J 374 GLN K 85 GLN K 115 GLN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24318 Z= 0.300 Angle : 0.584 8.536 33014 Z= 0.309 Chirality : 0.044 0.207 3998 Planarity : 0.004 0.048 4016 Dihedral : 10.112 82.068 3474 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.64 % Allowed : 14.26 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.69 (0.15), residues: 3008 helix: 2.08 (0.12), residues: 1840 sheet: 0.70 (0.28), residues: 302 loop : -0.82 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 47 HIS 0.005 0.001 HIS I 168 PHE 0.039 0.002 PHE I 202 TYR 0.017 0.002 TYR L 270 ARG 0.010 0.001 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 571 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7125 (tp30) cc_final: 0.6842 (tp30) REVERT: A 41 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8056 (mptp) REVERT: B 41 LYS cc_start: 0.8373 (mmtm) cc_final: 0.7848 (mmtt) REVERT: C 23 LYS cc_start: 0.8238 (mtpm) cc_final: 0.8014 (mttt) REVERT: C 62 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7391 (mt-10) REVERT: C 128 MET cc_start: 0.7765 (mmm) cc_final: 0.7485 (mmp) REVERT: C 208 MET cc_start: 0.6451 (ttp) cc_final: 0.6140 (ttm) REVERT: D 60 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: D 115 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7725 (mptp) REVERT: E 120 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8015 (ttt180) REVERT: E 145 ILE cc_start: 0.7231 (OUTLIER) cc_final: 0.6890 (tt) REVERT: E 208 MET cc_start: 0.6212 (ptt) cc_final: 0.5931 (ptt) REVERT: F 43 ASN cc_start: 0.8591 (m110) cc_final: 0.8310 (m110) REVERT: F 48 TYR cc_start: 0.8099 (m-80) cc_final: 0.7798 (m-80) REVERT: F 128 MET cc_start: 0.7798 (mmm) cc_final: 0.7523 (mmp) REVERT: F 208 MET cc_start: 0.6414 (ttp) cc_final: 0.6149 (ttm) REVERT: G 41 LYS cc_start: 0.8363 (mmtm) cc_final: 0.7861 (mmtt) REVERT: H 41 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8056 (mptp) REVERT: I 89 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8393 (mp) REVERT: I 110 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6548 (mt-10) REVERT: I 150 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7638 (pt) REVERT: I 219 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.6413 (mmt-90) REVERT: I 251 TYR cc_start: 0.8458 (t80) cc_final: 0.8152 (t80) REVERT: I 298 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8783 (mt) REVERT: J 100 MET cc_start: 0.5784 (OUTLIER) cc_final: 0.5468 (mmm) REVERT: J 136 PHE cc_start: 0.7738 (t80) cc_final: 0.7484 (t80) REVERT: J 155 GLN cc_start: 0.7659 (tt0) cc_final: 0.7425 (tt0) REVERT: J 216 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.6228 (mtp) REVERT: J 220 ARG cc_start: 0.6558 (tpt170) cc_final: 0.6242 (tpt170) REVERT: J 333 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7834 (mmtt) REVERT: K 155 GLN cc_start: 0.7674 (tt0) cc_final: 0.7386 (tt0) REVERT: K 156 TYR cc_start: 0.7609 (m-80) cc_final: 0.7393 (m-80) REVERT: K 216 MET cc_start: 0.7520 (mmp) cc_final: 0.6306 (mtp) REVERT: K 333 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7839 (mmtt) REVERT: K 373 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7190 (mt-10) REVERT: L 110 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6531 (mt-10) REVERT: L 150 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7644 (pt) REVERT: L 251 TYR cc_start: 0.8479 (t80) cc_final: 0.8188 (t80) REVERT: L 298 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8771 (mt) outliers start: 119 outliers final: 46 residues processed: 642 average time/residue: 1.3670 time to fit residues: 999.1677 Evaluate side-chains 613 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 548 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 120 ARG Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 219 ARG Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 333 LYS Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 333 LYS Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 314 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 243 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 chunk 120 optimal weight: 0.0170 chunk 249 optimal weight: 0.9990 chunk 201 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 262 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 134 GLN D 8 GLN D 38 ASN D 134 GLN E 8 GLN G 134 GLN I 18 GLN I 119 ASN I 239 ASN J 85 GLN J 115 GLN J 253 ASN J 374 GLN K 85 GLN K 115 GLN K 253 ASN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24318 Z= 0.174 Angle : 0.525 9.332 33014 Z= 0.277 Chirality : 0.042 0.188 3998 Planarity : 0.004 0.045 4016 Dihedral : 9.699 79.351 3474 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.66 % Allowed : 16.33 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.94 (0.15), residues: 3008 helix: 2.33 (0.12), residues: 1838 sheet: 0.56 (0.28), residues: 300 loop : -0.77 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 267 HIS 0.003 0.001 HIS C 110 PHE 0.036 0.001 PHE I 202 TYR 0.018 0.001 TYR L 270 ARG 0.008 0.001 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 583 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7051 (tp30) cc_final: 0.6842 (tp30) REVERT: C 23 LYS cc_start: 0.8182 (mtpm) cc_final: 0.7937 (mttt) REVERT: C 62 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7387 (mt-10) REVERT: C 105 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: C 128 MET cc_start: 0.7702 (mmm) cc_final: 0.7409 (mmp) REVERT: C 208 MET cc_start: 0.6422 (ttp) cc_final: 0.6032 (ttm) REVERT: D 60 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: D 115 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7753 (mptp) REVERT: D 139 GLU cc_start: 0.6950 (pm20) cc_final: 0.6696 (pm20) REVERT: E 145 ILE cc_start: 0.7190 (OUTLIER) cc_final: 0.6864 (tt) REVERT: E 208 MET cc_start: 0.6172 (ptt) cc_final: 0.5940 (ptt) REVERT: F 48 TYR cc_start: 0.8007 (m-80) cc_final: 0.7761 (m-80) REVERT: F 105 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: F 128 MET cc_start: 0.7703 (mmm) cc_final: 0.7417 (mmp) REVERT: F 181 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7349 (mp) REVERT: F 208 MET cc_start: 0.6366 (ttp) cc_final: 0.6049 (ttm) REVERT: G 41 LYS cc_start: 0.8350 (mmtm) cc_final: 0.7870 (mmtt) REVERT: I 110 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6570 (mt-10) REVERT: I 150 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7654 (pt) REVERT: I 251 TYR cc_start: 0.8501 (t80) cc_final: 0.8259 (t80) REVERT: I 298 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8735 (mt) REVERT: J 24 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.7144 (t80) REVERT: J 155 GLN cc_start: 0.7655 (tt0) cc_final: 0.7412 (tt0) REVERT: J 156 TYR cc_start: 0.7478 (m-80) cc_final: 0.7274 (m-80) REVERT: J 216 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.6207 (mtp) REVERT: J 220 ARG cc_start: 0.6513 (tpt170) cc_final: 0.6160 (tpt170) REVERT: K 106 ILE cc_start: 0.7824 (mp) cc_final: 0.7621 (mm) REVERT: K 155 GLN cc_start: 0.7667 (tt0) cc_final: 0.7346 (tt0) REVERT: K 156 TYR cc_start: 0.7565 (m-80) cc_final: 0.7272 (m-80) REVERT: K 216 MET cc_start: 0.7517 (mmp) cc_final: 0.6284 (mtp) REVERT: L 110 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6579 (mt-10) REVERT: L 150 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7612 (pt) REVERT: L 251 TYR cc_start: 0.8489 (t80) cc_final: 0.8200 (t80) REVERT: L 298 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8727 (mt) outliers start: 94 outliers final: 40 residues processed: 634 average time/residue: 1.4252 time to fit residues: 1034.7478 Evaluate side-chains 608 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 554 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 170 ILE Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 98 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 292 optimal weight: 0.6980 chunk 242 optimal weight: 0.2980 chunk 135 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 96 optimal weight: 0.0070 chunk 153 optimal weight: 5.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN D 134 GLN E 8 GLN G 134 GLN I 18 GLN I 119 ASN I 239 ASN ** J 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 GLN J 85 GLN J 115 GLN J 253 ASN J 374 GLN K 77 GLN K 85 GLN K 115 GLN K 253 ASN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24318 Z= 0.160 Angle : 0.521 8.163 33014 Z= 0.274 Chirality : 0.042 0.185 3998 Planarity : 0.004 0.047 4016 Dihedral : 9.455 77.774 3474 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.47 % Allowed : 17.61 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.97 (0.15), residues: 3008 helix: 2.37 (0.12), residues: 1838 sheet: 0.45 (0.29), residues: 302 loop : -0.77 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 267 HIS 0.003 0.001 HIS C 110 PHE 0.034 0.001 PHE I 202 TYR 0.018 0.001 TYR I 270 ARG 0.010 0.001 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 573 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7057 (tp30) cc_final: 0.6838 (tp30) REVERT: A 41 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7953 (mptp) REVERT: B 41 LYS cc_start: 0.8250 (mmtm) cc_final: 0.7776 (mmtt) REVERT: B 59 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7508 (mt-10) REVERT: B 62 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7217 (mt-10) REVERT: C 23 LYS cc_start: 0.8167 (mtpm) cc_final: 0.7929 (mttt) REVERT: C 128 MET cc_start: 0.7685 (mmm) cc_final: 0.7417 (mmp) REVERT: C 131 LYS cc_start: 0.8396 (mmtm) cc_final: 0.8158 (mmtm) REVERT: C 208 MET cc_start: 0.6365 (ttp) cc_final: 0.6141 (ttm) REVERT: D 115 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7762 (mptp) REVERT: D 138 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.5953 (p0) REVERT: E 145 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6855 (tt) REVERT: E 208 MET cc_start: 0.6146 (ptt) cc_final: 0.5944 (ptt) REVERT: F 128 MET cc_start: 0.7658 (mmm) cc_final: 0.7389 (mmp) REVERT: F 208 MET cc_start: 0.6365 (ttp) cc_final: 0.6045 (ttm) REVERT: G 41 LYS cc_start: 0.8342 (mmtm) cc_final: 0.7859 (mmtt) REVERT: H 41 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7957 (mptp) REVERT: H 63 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8195 (mp) REVERT: I 58 THR cc_start: 0.8723 (t) cc_final: 0.8517 (m) REVERT: I 110 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6536 (mt-10) REVERT: I 150 ILE cc_start: 0.8070 (pp) cc_final: 0.7605 (pt) REVERT: I 251 TYR cc_start: 0.8509 (t80) cc_final: 0.8292 (t80) REVERT: I 298 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8728 (mt) REVERT: J 155 GLN cc_start: 0.7590 (tt0) cc_final: 0.7352 (tt0) REVERT: J 216 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.6244 (mtp) REVERT: J 220 ARG cc_start: 0.6486 (tpt170) cc_final: 0.6086 (tpt170) REVERT: K 155 GLN cc_start: 0.7615 (tt0) cc_final: 0.7357 (tt0) REVERT: K 216 MET cc_start: 0.7506 (mmp) cc_final: 0.6281 (mtp) REVERT: L 110 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6547 (mt-10) REVERT: L 150 ILE cc_start: 0.8075 (pp) cc_final: 0.7627 (pt) REVERT: L 251 TYR cc_start: 0.8505 (t80) cc_final: 0.8248 (t80) REVERT: L 298 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8715 (mt) outliers start: 89 outliers final: 47 residues processed: 625 average time/residue: 1.3359 time to fit residues: 952.1043 Evaluate side-chains 607 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 549 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 123 ILE Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 257 LEU Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 281 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 166 optimal weight: 0.5980 chunk 213 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 245 optimal weight: 9.9990 chunk 163 optimal weight: 0.9980 chunk 291 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN B 134 GLN D 38 ASN D 134 GLN G 134 GLN I 18 GLN I 119 ASN I 239 ASN ** J 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN J 115 GLN J 253 ASN ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN K 253 ASN K 272 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24318 Z= 0.270 Angle : 0.583 9.154 33014 Z= 0.307 Chirality : 0.044 0.208 3998 Planarity : 0.004 0.046 4016 Dihedral : 9.825 80.799 3472 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.90 % Allowed : 18.20 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.83 (0.15), residues: 3008 helix: 2.22 (0.12), residues: 1838 sheet: 0.48 (0.28), residues: 302 loop : -0.73 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 181 HIS 0.005 0.001 HIS L 168 PHE 0.035 0.002 PHE I 202 TYR 0.018 0.002 TYR L 270 ARG 0.010 0.001 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 553 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8037 (mptp) REVERT: A 63 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8225 (mp) REVERT: B 41 LYS cc_start: 0.8316 (mmtm) cc_final: 0.7851 (mmtt) REVERT: C 23 LYS cc_start: 0.8165 (mtpm) cc_final: 0.7921 (mttt) REVERT: C 128 MET cc_start: 0.7743 (mmm) cc_final: 0.7472 (mmp) REVERT: C 208 MET cc_start: 0.6375 (ttp) cc_final: 0.6139 (ttm) REVERT: D 115 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7754 (mptp) REVERT: E 120 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7963 (ttt180) REVERT: E 145 ILE cc_start: 0.7212 (OUTLIER) cc_final: 0.6888 (tt) REVERT: F 128 MET cc_start: 0.7742 (mmm) cc_final: 0.7479 (mmp) REVERT: F 208 MET cc_start: 0.6466 (ttp) cc_final: 0.6166 (ttp) REVERT: G 41 LYS cc_start: 0.8412 (mmtm) cc_final: 0.7901 (mmtt) REVERT: H 41 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8022 (mptp) REVERT: H 63 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8244 (mp) REVERT: I 110 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6559 (mt-10) REVERT: I 150 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7658 (pt) REVERT: I 251 TYR cc_start: 0.8506 (t80) cc_final: 0.8262 (t80) REVERT: I 298 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8768 (mt) REVERT: J 155 GLN cc_start: 0.7603 (tt0) cc_final: 0.7342 (tt0) REVERT: J 216 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6233 (mtp) REVERT: K 100 MET cc_start: 0.6274 (mtm) cc_final: 0.5664 (mmm) REVERT: K 155 GLN cc_start: 0.7654 (tt0) cc_final: 0.7431 (tt0) REVERT: K 216 MET cc_start: 0.7537 (mmp) cc_final: 0.6252 (mtp) REVERT: K 373 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: L 110 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6567 (mt-10) REVERT: L 150 ILE cc_start: 0.8169 (pp) cc_final: 0.7733 (pt) REVERT: L 251 TYR cc_start: 0.8504 (t80) cc_final: 0.8219 (t80) REVERT: L 298 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8763 (mt) outliers start: 100 outliers final: 46 residues processed: 609 average time/residue: 1.4377 time to fit residues: 1009.4988 Evaluate side-chains 604 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 544 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 120 ARG Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 180 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 185 optimal weight: 0.9980 chunk 198 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 228 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN B 38 ASN B 134 GLN D 134 GLN G 134 GLN H 81 ASN I 18 GLN I 119 ASN I 239 ASN J 115 GLN J 253 ASN K 85 GLN K 253 ASN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24318 Z= 0.192 Angle : 0.545 10.610 33014 Z= 0.287 Chirality : 0.043 0.195 3998 Planarity : 0.004 0.045 4016 Dihedral : 9.618 80.303 3472 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.20 % Allowed : 19.37 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.91 (0.15), residues: 3008 helix: 2.30 (0.12), residues: 1838 sheet: 0.44 (0.29), residues: 302 loop : -0.74 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 267 HIS 0.003 0.001 HIS I 168 PHE 0.036 0.001 PHE I 202 TYR 0.017 0.001 TYR I 270 ARG 0.010 0.001 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 552 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7971 (mptp) REVERT: A 63 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8207 (mp) REVERT: B 41 LYS cc_start: 0.8272 (mmtm) cc_final: 0.7798 (mmtt) REVERT: C 23 LYS cc_start: 0.8164 (mtpm) cc_final: 0.7921 (mttt) REVERT: C 128 MET cc_start: 0.7715 (mmm) cc_final: 0.7466 (mmp) REVERT: C 208 MET cc_start: 0.6315 (ttp) cc_final: 0.6112 (ttm) REVERT: D 115 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7753 (mptp) REVERT: D 138 ASP cc_start: 0.6897 (OUTLIER) cc_final: 0.6113 (p0) REVERT: D 139 GLU cc_start: 0.6957 (pm20) cc_final: 0.6585 (pm20) REVERT: D 208 MET cc_start: 0.6343 (ptt) cc_final: 0.6106 (ptp) REVERT: E 145 ILE cc_start: 0.7135 (OUTLIER) cc_final: 0.6854 (tt) REVERT: F 62 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7187 (pt0) REVERT: F 128 MET cc_start: 0.7720 (mmm) cc_final: 0.7448 (mmp) REVERT: F 208 MET cc_start: 0.6376 (ttp) cc_final: 0.6063 (ttm) REVERT: G 41 LYS cc_start: 0.8391 (mmtm) cc_final: 0.7906 (mmtt) REVERT: G 64 LEU cc_start: 0.8630 (mm) cc_final: 0.8369 (mt) REVERT: H 41 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7982 (mptp) REVERT: H 63 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8218 (mp) REVERT: I 110 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6540 (mt-10) REVERT: I 150 ILE cc_start: 0.8102 (pp) cc_final: 0.7678 (pt) REVERT: I 216 MET cc_start: 0.7409 (tpp) cc_final: 0.7061 (mtp) REVERT: I 251 TYR cc_start: 0.8514 (t80) cc_final: 0.8310 (t80) REVERT: I 298 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8746 (mt) REVERT: J 155 GLN cc_start: 0.7609 (tt0) cc_final: 0.7345 (tt0) REVERT: J 216 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.6241 (mtp) REVERT: K 100 MET cc_start: 0.6230 (mtm) cc_final: 0.5859 (mtp) REVERT: K 155 GLN cc_start: 0.7650 (tt0) cc_final: 0.7407 (tt0) REVERT: K 216 MET cc_start: 0.7527 (mmp) cc_final: 0.6246 (mtp) REVERT: K 220 ARG cc_start: 0.6617 (tpt170) cc_final: 0.6174 (tpt170) REVERT: K 222 LYS cc_start: 0.8339 (mmtt) cc_final: 0.8022 (mmtt) REVERT: L 110 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6560 (mt-10) REVERT: L 150 ILE cc_start: 0.8104 (pp) cc_final: 0.7687 (pt) REVERT: L 298 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8740 (mt) outliers start: 82 outliers final: 42 residues processed: 595 average time/residue: 1.4014 time to fit residues: 946.7079 Evaluate side-chains 588 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 534 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 264 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 254 optimal weight: 5.9990 chunk 271 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 245 optimal weight: 0.6980 chunk 256 optimal weight: 2.9990 chunk 270 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN B 134 GLN C 43 ASN D 38 ASN D 134 GLN G 134 GLN H 81 ASN I 18 GLN I 119 ASN I 239 ASN ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN K 253 ASN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24318 Z= 0.189 Angle : 0.553 12.883 33014 Z= 0.291 Chirality : 0.043 0.194 3998 Planarity : 0.004 0.045 4016 Dihedral : 9.533 80.396 3472 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.20 % Allowed : 19.76 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.87 (0.15), residues: 3008 helix: 2.26 (0.12), residues: 1842 sheet: 0.40 (0.29), residues: 302 loop : -0.71 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 267 HIS 0.003 0.001 HIS L 168 PHE 0.035 0.002 PHE I 202 TYR 0.019 0.001 TYR E 107 ARG 0.008 0.001 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 549 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7973 (mptp) REVERT: A 63 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8237 (mp) REVERT: B 41 LYS cc_start: 0.8266 (mmtm) cc_final: 0.7806 (mmtt) REVERT: C 23 LYS cc_start: 0.8160 (mtpm) cc_final: 0.7926 (mttt) REVERT: C 128 MET cc_start: 0.7708 (mmm) cc_final: 0.7468 (mmp) REVERT: D 115 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7762 (mptp) REVERT: D 138 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6087 (p0) REVERT: E 145 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6853 (tt) REVERT: F 128 MET cc_start: 0.7719 (mmm) cc_final: 0.7446 (mmp) REVERT: F 208 MET cc_start: 0.6394 (ttp) cc_final: 0.6090 (ttm) REVERT: G 41 LYS cc_start: 0.8391 (mmtm) cc_final: 0.7897 (mmtt) REVERT: G 64 LEU cc_start: 0.8479 (mm) cc_final: 0.8263 (mt) REVERT: H 41 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7980 (mptp) REVERT: H 63 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8222 (mp) REVERT: I 110 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6538 (mt-10) REVERT: I 150 ILE cc_start: 0.8119 (pp) cc_final: 0.7699 (pt) REVERT: I 216 MET cc_start: 0.7431 (tpp) cc_final: 0.7100 (mtp) REVERT: I 251 TYR cc_start: 0.8512 (t80) cc_final: 0.8310 (t80) REVERT: I 298 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8746 (mt) REVERT: J 155 GLN cc_start: 0.7613 (tt0) cc_final: 0.7331 (tt0) REVERT: J 216 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6233 (mtp) REVERT: K 155 GLN cc_start: 0.7661 (tt0) cc_final: 0.7372 (tt0) REVERT: K 216 MET cc_start: 0.7524 (mmp) cc_final: 0.6247 (mtp) REVERT: L 110 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6548 (mt-10) REVERT: L 150 ILE cc_start: 0.8125 (pp) cc_final: 0.7681 (pt) REVERT: L 298 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8746 (mt) outliers start: 82 outliers final: 43 residues processed: 592 average time/residue: 1.4242 time to fit residues: 964.3823 Evaluate side-chains 597 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 542 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 178 optimal weight: 4.9990 chunk 286 optimal weight: 0.9980 chunk 175 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 300 optimal weight: 0.0970 chunk 276 optimal weight: 7.9990 chunk 239 optimal weight: 3.9990 chunk 24 optimal weight: 0.0980 chunk 185 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN B 134 GLN D 134 GLN E 8 GLN F 134 GLN G 134 GLN H 81 ASN I 18 GLN I 119 ASN I 239 ASN J 253 ASN ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN K 253 ASN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24318 Z= 0.166 Angle : 0.550 11.652 33014 Z= 0.288 Chirality : 0.042 0.186 3998 Planarity : 0.004 0.044 4016 Dihedral : 9.320 79.648 3472 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.57 % Allowed : 20.97 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.88 (0.15), residues: 3008 helix: 2.29 (0.12), residues: 1842 sheet: 0.34 (0.29), residues: 298 loop : -0.74 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 267 HIS 0.003 0.001 HIS I 168 PHE 0.034 0.001 PHE L 202 TYR 0.022 0.001 TYR I 270 ARG 0.012 0.001 ARG E 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6016 Ramachandran restraints generated. 3008 Oldfield, 0 Emsley, 3008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 553 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7966 (mptp) REVERT: A 63 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8191 (mp) REVERT: B 41 LYS cc_start: 0.8271 (mmtm) cc_final: 0.7818 (mmtt) REVERT: B 59 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7487 (pt0) REVERT: B 62 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6843 (mt-10) REVERT: C 23 LYS cc_start: 0.8141 (mtpm) cc_final: 0.7907 (mttt) REVERT: C 128 MET cc_start: 0.7689 (mmm) cc_final: 0.7421 (mmp) REVERT: D 115 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7761 (mptp) REVERT: D 138 ASP cc_start: 0.6842 (OUTLIER) cc_final: 0.6085 (p0) REVERT: D 139 GLU cc_start: 0.7047 (pm20) cc_final: 0.6760 (pm20) REVERT: D 208 MET cc_start: 0.6304 (ptt) cc_final: 0.6091 (ptp) REVERT: E 139 GLU cc_start: 0.7058 (pm20) cc_final: 0.6834 (pm20) REVERT: E 145 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6900 (tt) REVERT: F 128 MET cc_start: 0.7648 (mmm) cc_final: 0.7385 (mmp) REVERT: F 208 MET cc_start: 0.6383 (ttp) cc_final: 0.6093 (ttm) REVERT: G 41 LYS cc_start: 0.8387 (mmtm) cc_final: 0.7903 (mmtt) REVERT: G 59 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7432 (mt-10) REVERT: H 41 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7998 (mptp) REVERT: H 63 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8187 (mp) REVERT: I 110 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6511 (mt-10) REVERT: I 150 ILE cc_start: 0.8104 (pp) cc_final: 0.7689 (pt) REVERT: I 216 MET cc_start: 0.7437 (tpp) cc_final: 0.7129 (mtp) REVERT: I 298 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8735 (mt) REVERT: J 155 GLN cc_start: 0.7631 (tt0) cc_final: 0.7351 (tt0) REVERT: J 216 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.6196 (mtp) REVERT: J 222 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7454 (mmtm) REVERT: K 155 GLN cc_start: 0.7683 (tt0) cc_final: 0.7378 (tt0) REVERT: K 216 MET cc_start: 0.7513 (mmp) cc_final: 0.6240 (mtp) REVERT: L 110 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6508 (mt-10) REVERT: L 150 ILE cc_start: 0.8081 (pp) cc_final: 0.7654 (pt) REVERT: L 298 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8733 (mt) outliers start: 66 outliers final: 36 residues processed: 590 average time/residue: 1.4346 time to fit residues: 961.7072 Evaluate side-chains 582 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 534 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain G residue 7 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 190 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 220 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 239 optimal weight: 4.9990 chunk 100 optimal weight: 0.0980 chunk 246 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN B 38 ASN B 134 GLN C 38 ASN D 134 GLN F 134 GLN G 134 GLN H 30 HIS H 70 ASN H 81 ASN I 18 GLN I 119 ASN I 239 ASN J 85 GLN J 115 GLN J 253 ASN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 253 ASN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.168931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129001 restraints weight = 25942.542| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.83 r_work: 0.3314 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24318 Z= 0.175 Angle : 0.555 10.932 33014 Z= 0.290 Chirality : 0.043 0.189 3998 Planarity : 0.004 0.045 4016 Dihedral : 9.318 79.701 3472 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.57 % Allowed : 20.93 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % 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: 1.90 (0.15), residues: 3008 helix: 2.30 (0.12), residues: 1834 sheet: 0.34 (0.29), residues: 302 loop : -0.68 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 267 HIS 0.004 0.001 HIS C 110 PHE 0.034 0.002 PHE L 202 TYR 0.021 0.001 TYR K 345 ARG 0.011 0.001 ARG E 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14132.89 seconds wall clock time: 246 minutes 16.65 seconds (14776.65 seconds total)