Starting phenix.real_space_refine on Thu Apr 11 22:06:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1t_36803/04_2024/8k1t_36803_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1t_36803/04_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_36803/04_2024/8k1t_36803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1t_36803/04_2024/8k1t_36803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1t_36803/04_2024/8k1t_36803_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1t_36803/04_2024/8k1t_36803_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 12.25, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.45 Conformation dependent library (CDL) restraints added in 4.0 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... running ksdssp... Secondary structure from input PDB file: 149 helices and 18 sheets defined 55.6% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.50 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 60 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 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 124 through 137 Processing helix chain 'B' and resid 16 through 28 Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 60 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 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 124 through 137 Processing helix chain 'C' and resid 16 through 28 removed outlier: 3.537A pdb=" N SER C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 47 removed outlier: 4.830A pdb=" N SER C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 65 Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 124 through 137 Processing helix chain 'C' and resid 211 through 216 Processing helix chain 'D' and resid 16 through 28 removed outlier: 3.536A pdb=" N SER D 20 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 47 removed outlier: 4.830A pdb=" N SER D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 65 Processing helix chain 'D' and resid 68 through 70 No H-bonds generated for 'chain 'D' and resid 68 through 70' Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'D' and resid 211 through 219 Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.537A pdb=" N SER E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 47 removed outlier: 4.831A pdb=" N SER E 47 " --> pdb=" O ASN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 Processing helix chain 'E' and resid 68 through 70 No H-bonds generated for 'chain 'E' and resid 68 through 70' Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 124 through 137 Processing helix chain 'E' and resid 172 through 175 No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 211 through 219 Processing helix chain 'F' and resid 16 through 28 removed outlier: 3.537A pdb=" N SER F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 47 removed outlier: 4.830A pdb=" N SER F 47 " --> pdb=" O ASN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 65 Processing helix chain 'F' and resid 68 through 70 No H-bonds generated for 'chain 'F' and resid 68 through 70' Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 107 through 115 Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 211 through 216 Processing helix chain 'G' and resid 16 through 28 Processing helix chain 'G' and resid 39 through 44 Processing helix chain 'G' and resid 60 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 68 through 70 No H-bonds generated for 'chain 'G' and resid 68 through 70' Processing helix chain 'G' and resid 82 through 94 Processing helix chain 'G' and resid 107 through 115 Processing helix chain 'G' and resid 124 through 137 Processing helix chain 'H' and resid 16 through 28 Processing helix chain 'H' and resid 39 through 44 Processing helix chain 'H' and resid 60 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 68 through 70 No H-bonds generated for 'chain 'H' and resid 68 through 70' Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'H' and resid 107 through 115 Processing helix chain 'H' and resid 124 through 137 Processing helix chain 'I' and resid 16 through 35 Processing helix chain 'I' and resid 38 through 40 No H-bonds generated for 'chain 'I' and resid 38 through 40' Processing helix chain 'I' and resid 47 through 58 Processing helix chain 'I' and resid 68 through 71 No H-bonds generated for 'chain 'I' and resid 68 through 71' Processing helix chain 'I' and resid 74 through 89 Processing helix chain 'I' and resid 91 through 101 Processing helix chain 'I' and resid 108 through 117 Processing helix chain 'I' and resid 126 through 156 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 159 through 173 removed outlier: 3.541A pdb=" N PHE I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 207 Processing helix chain 'I' and resid 209 through 217 Processing helix chain 'I' and resid 221 through 223 No H-bonds generated for 'chain 'I' and resid 221 through 223' Processing helix chain 'I' and resid 226 through 249 Processing helix chain 'I' and resid 262 through 274 Processing helix chain 'I' and resid 286 through 288 No H-bonds generated for 'chain 'I' and resid 286 through 288' Processing helix chain 'I' and resid 291 through 302 Processing helix chain 'I' and resid 316 through 330 Processing helix chain 'I' and resid 345 through 372 Processing helix chain 'I' and resid 377 through 388 Processing helix chain 'I' and resid 398 through 400 No H-bonds generated for 'chain 'I' and resid 398 through 400' Processing helix chain 'I' and resid 403 through 418 Processing helix chain 'I' and resid 420 through 427 removed outlier: 3.898A pdb=" N PHE I 427 " --> pdb=" O PHE I 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 35 Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 47 through 58 Processing helix chain 'J' and resid 68 through 71 No H-bonds generated for 'chain 'J' and resid 68 through 71' Processing helix chain 'J' and resid 74 through 89 Processing helix chain 'J' and resid 91 through 101 Processing helix chain 'J' and resid 108 through 117 Processing helix chain 'J' and resid 126 through 156 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 159 through 173 removed outlier: 3.541A pdb=" N PHE J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 192 through 207 Processing helix chain 'J' and resid 209 through 217 Processing helix chain 'J' and resid 221 through 223 No H-bonds generated for 'chain 'J' and resid 221 through 223' Processing helix chain 'J' and resid 226 through 249 Processing helix chain 'J' and resid 262 through 274 Processing helix chain 'J' and resid 286 through 288 No H-bonds generated for 'chain 'J' and resid 286 through 288' Processing helix chain 'J' and resid 291 through 302 Processing helix chain 'J' and resid 316 through 330 Processing helix chain 'J' and resid 345 through 372 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 398 through 400 No H-bonds generated for 'chain 'J' and resid 398 through 400' Processing helix chain 'J' and resid 403 through 418 Processing helix chain 'J' and resid 420 through 427 removed outlier: 3.897A pdb=" N PHE J 427 " --> pdb=" O PHE J 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 35 Processing helix chain 'K' and resid 38 through 40 No H-bonds generated for 'chain 'K' and resid 38 through 40' Processing helix chain 'K' and resid 47 through 58 Processing helix chain 'K' and resid 68 through 71 No H-bonds generated for 'chain 'K' and resid 68 through 71' Processing helix chain 'K' and resid 74 through 89 Processing helix chain 'K' and resid 91 through 101 Processing helix chain 'K' and resid 108 through 117 Processing helix chain 'K' and resid 126 through 156 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 159 through 173 removed outlier: 3.542A pdb=" N PHE K 163 " --> pdb=" O SER K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 207 Processing helix chain 'K' and resid 209 through 217 Processing helix chain 'K' and resid 221 through 223 No H-bonds generated for 'chain 'K' and resid 221 through 223' Processing helix chain 'K' and resid 226 through 249 Processing helix chain 'K' and resid 262 through 274 Processing helix chain 'K' and resid 286 through 288 No H-bonds generated for 'chain 'K' and resid 286 through 288' Processing helix chain 'K' and resid 291 through 302 Processing helix chain 'K' and resid 316 through 330 Processing helix chain 'K' and resid 345 through 372 Processing helix chain 'K' and resid 377 through 388 Processing helix chain 'K' and resid 398 through 400 No H-bonds generated for 'chain 'K' and resid 398 through 400' Processing helix chain 'K' and resid 403 through 418 Processing helix chain 'K' and resid 420 through 427 removed outlier: 3.898A pdb=" N PHE K 427 " --> pdb=" O PHE K 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 35 Processing helix chain 'L' and resid 38 through 40 No H-bonds generated for 'chain 'L' and resid 38 through 40' Processing helix chain 'L' and resid 47 through 58 Processing helix chain 'L' and resid 68 through 71 No H-bonds generated for 'chain 'L' and resid 68 through 71' Processing helix chain 'L' and resid 74 through 89 Processing helix chain 'L' and resid 91 through 101 Processing helix chain 'L' and resid 108 through 117 Processing helix chain 'L' and resid 126 through 156 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 159 through 173 removed outlier: 3.542A pdb=" N PHE L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 192 through 207 Processing helix chain 'L' and resid 209 through 217 Processing helix chain 'L' and resid 221 through 223 No H-bonds generated for 'chain 'L' and resid 221 through 223' Processing helix chain 'L' and resid 226 through 249 Processing helix chain 'L' and resid 262 through 274 Processing helix chain 'L' and resid 286 through 288 No H-bonds generated for 'chain 'L' and resid 286 through 288' Processing helix chain 'L' and resid 291 through 302 Processing helix chain 'L' and resid 316 through 330 Processing helix chain 'L' and resid 345 through 372 Processing helix chain 'L' and resid 377 through 388 Processing helix chain 'L' and resid 398 through 400 No H-bonds generated for 'chain 'L' and resid 398 through 400' Processing helix chain 'L' and resid 403 through 418 Processing helix chain 'L' and resid 420 through 427 removed outlier: 3.897A pdb=" N PHE L 427 " --> pdb=" O PHE L 423 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.817A pdb=" N TYR A 73 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLU A 31 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL A 11 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU A 33 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N HIS A 51 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASP A 36 " --> pdb=" O HIS A 51 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL A 53 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.817A pdb=" N TYR B 73 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU B 31 " --> pdb=" O PHE B 9 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL B 11 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU B 33 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS B 51 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ASP B 36 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL B 53 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.747A pdb=" N TYR C 73 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU C 31 " --> pdb=" O PHE C 9 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL C 11 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU C 33 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N HIS C 51 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ASP C 36 " --> pdb=" O HIS C 51 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL C 53 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing sheet with id= D, 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) Processing sheet with id= E, first strand: chain 'C' and resid 182 through 185 removed outlier: 4.005A pdb=" N ILE C 183 " --> pdb=" O CYS C 190 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.748A pdb=" N TYR D 73 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU D 31 " --> pdb=" O PHE D 9 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL D 11 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU D 33 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS D 51 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP D 36 " --> pdb=" O HIS D 51 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL D 53 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing sheet with id= G, 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= H, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.747A pdb=" N TYR E 73 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLU E 31 " --> pdb=" O PHE E 9 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL E 11 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU E 33 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS E 51 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP E 36 " --> pdb=" O HIS E 51 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL E 53 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing sheet with id= I, 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= J, first strand: chain 'F' and resid 120 through 122 removed outlier: 3.747A pdb=" N TYR F 73 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU F 31 " --> pdb=" O PHE F 9 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL F 11 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU F 33 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS F 51 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ASP F 36 " --> pdb=" O HIS F 51 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL F 53 " --> pdb=" O ASP F 36 " (cutoff:3.500A) Processing sheet with id= K, 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) Processing sheet with id= L, first strand: chain 'F' and resid 182 through 185 removed outlier: 4.005A pdb=" N ILE F 183 " --> pdb=" O CYS F 190 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.817A pdb=" N TYR G 73 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU G 31 " --> pdb=" O PHE G 9 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL G 11 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU G 33 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS G 51 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASP G 36 " --> pdb=" O HIS G 51 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL G 53 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 120 through 122 removed outlier: 3.817A pdb=" N TYR H 73 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLU H 31 " --> pdb=" O PHE H 9 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL H 11 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU H 33 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS H 51 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASP H 36 " --> pdb=" O HIS H 51 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL H 53 " --> pdb=" O ASP H 36 " (cutoff:3.500A) Processing sheet with id= O, 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= P, 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= Q, 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= R, 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) 1226 hydrogen bonds defined for protein. 3624 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: 8.67 Time building geometry restraints manager: 10.13 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: 100.47 - 108.37: 993 108.37 - 116.27: 15613 116.27 - 124.18: 15989 124.18 - 132.08: 367 132.08 - 139.98: 52 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: 6841 2.82 - 3.40: 26337 3.40 - 3.98: 47246 3.98 - 4.56: 66111 4.56 - 5.14: 96579 Nonbonded interactions: 243114 Sorted by model distance: nonbonded pdb=" O ASN L 195 " pdb=" OG1 THR L 199 " model vdw 2.240 2.440 nonbonded pdb=" O ASN K 195 " pdb=" OG1 THR K 199 " model vdw 2.240 2.440 nonbonded pdb=" O ASN I 195 " pdb=" OG1 THR I 199 " model vdw 2.240 2.440 nonbonded pdb=" O ASN J 195 " pdb=" OG1 THR J 199 " model vdw 2.240 2.440 nonbonded pdb=" OH TYR D 108 " pdb=" OE1 GLU E 60 " model vdw 2.296 2.440 ... (remaining 243109 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 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: 4.100 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: 13.340 Check model and map are aligned: 0.340 Set scattering table: 0.230 Process input model: 64.740 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.490 ------------------------------------------------------------------------------- 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= 0.241 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 : 2.519 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: 1.4040 time to fit residues: 1330.6128 Evaluate side-chains 572 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 569 time to evaluate : 2.807 ------------------------------------------------------------------------------- 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: 2.9990 chunk 78 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 274 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 8 GLN E 38 ASN E 61 ASN E 70 ASN E 134 GLN E 185 HIS F 38 ASN F 43 ASN F 185 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 24318 Z= 0.372 Angle : 0.621 9.608 33014 Z= 0.326 Chirality : 0.045 0.199 3998 Planarity : 0.004 0.045 4016 Dihedral : 10.497 88.081 3474 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.29 % Allowed : 13.09 % Favored : 82.62 % 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: 1.48 (0.15), residues: 3008 helix: 1.76 (0.11), residues: 1820 sheet: 1.38 (0.27), residues: 306 loop : -0.81 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 47 HIS 0.006 0.001 HIS I 168 PHE 0.040 0.002 PHE L 202 TYR 0.016 0.002 TYR E 108 ARG 0.007 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 701 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 591 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7127 (tp30) cc_final: 0.6765 (tp30) REVERT: A 41 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8184 (mptp) REVERT: B 59 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7230 (mt-10) REVERT: C 48 TYR cc_start: 0.8100 (m-80) cc_final: 0.7900 (m-80) REVERT: C 128 MET cc_start: 0.7823 (mmm) cc_final: 0.7511 (mmp) REVERT: D 28 MET cc_start: 0.8572 (mtm) cc_final: 0.8353 (mtm) REVERT: D 60 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: D 126 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7971 (ttmt) REVERT: F 128 MET cc_start: 0.7843 (mmm) cc_final: 0.7531 (mmp) REVERT: F 134 GLN cc_start: 0.8197 (mm110) cc_final: 0.7828 (mm-40) REVERT: G 41 LYS cc_start: 0.8404 (mmtm) cc_final: 0.7834 (mmtt) REVERT: H 41 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8006 (mptp) REVERT: I 110 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6898 (mp0) REVERT: I 123 ILE cc_start: 0.8088 (pt) cc_final: 0.7831 (pt) REVERT: I 140 ILE cc_start: 0.8623 (tt) cc_final: 0.8421 (tt) REVERT: I 251 TYR cc_start: 0.8448 (t80) cc_final: 0.8136 (t80) REVERT: I 298 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8834 (mt) REVERT: I 340 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7469 (mtt-85) REVERT: J 100 MET cc_start: 0.5976 (OUTLIER) cc_final: 0.5643 (mmm) REVERT: J 106 ILE cc_start: 0.7819 (mp) cc_final: 0.7557 (mm) REVERT: J 136 PHE cc_start: 0.7705 (t80) cc_final: 0.7446 (t80) REVERT: J 155 GLN cc_start: 0.7546 (tt0) cc_final: 0.7255 (tt0) REVERT: K 100 MET cc_start: 0.6297 (mtm) cc_final: 0.6051 (mtm) REVERT: K 155 GLN cc_start: 0.7541 (tt0) cc_final: 0.7234 (tt0) REVERT: K 222 LYS cc_start: 0.8336 (mmtt) cc_final: 0.8117 (mmtt) REVERT: K 250 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8553 (mm-30) REVERT: L 110 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6957 (mp0) REVERT: L 123 ILE cc_start: 0.8101 (pt) cc_final: 0.7815 (pt) REVERT: L 140 ILE cc_start: 0.8594 (tt) cc_final: 0.8391 (tt) REVERT: L 251 TYR cc_start: 0.8462 (t80) cc_final: 0.8127 (t80) REVERT: L 298 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8829 (mt) REVERT: L 340 ARG cc_start: 0.7851 (mtt180) cc_final: 0.7490 (mtt-85) outliers start: 110 outliers final: 45 residues processed: 651 average time/residue: 1.4599 time to fit residues: 1079.1563 Evaluate side-chains 613 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 561 time to evaluate : 2.736 ------------------------------------------------------------------------------- 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 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 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 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 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 135 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 150 ILE 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 441 GLU 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 216 MET Chi-restraints excluded: chain J residue 256 THR Chi-restraints excluded: chain J residue 312 SER Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 338 ILE 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 196 LEU Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 312 SER Chi-restraints excluded: chain K residue 314 ILE Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 422 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 139 SER 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 323 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 152 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 186 optimal weight: 0.9990 chunk 75 optimal weight: 0.3980 chunk 274 optimal weight: 5.9990 chunk 296 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 220 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** C 38 ASN C 185 HIS D 185 HIS E 38 ASN E 70 ASN E 185 HIS F 38 ASN F 43 ASN F 185 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN I 119 ASN I 239 ASN J 85 GLN J 115 GLN J 253 ASN 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24318 Z= 0.172 Angle : 0.512 7.413 33014 Z= 0.267 Chirality : 0.042 0.181 3998 Planarity : 0.004 0.045 4016 Dihedral : 9.797 85.240 3474 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.82 % Allowed : 14.69 % Favored : 81.49 % 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: 1.81 (0.15), residues: 3008 helix: 2.19 (0.12), residues: 1796 sheet: 1.24 (0.28), residues: 306 loop : -0.88 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 267 HIS 0.004 0.001 HIS L 168 PHE 0.037 0.001 PHE L 202 TYR 0.017 0.001 TYR I 270 ARG 0.009 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 690 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 592 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7073 (tp30) cc_final: 0.6798 (tp30) REVERT: B 59 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7543 (mt-10) REVERT: C 48 TYR cc_start: 0.8070 (m-80) cc_final: 0.7864 (m-80) REVERT: C 128 MET cc_start: 0.7782 (mmm) cc_final: 0.7480 (mmp) REVERT: E 145 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6739 (tt) REVERT: F 23 LYS cc_start: 0.8180 (mtpm) cc_final: 0.7734 (mtmt) REVERT: F 128 MET cc_start: 0.7811 (mmm) cc_final: 0.7521 (mmp) REVERT: G 41 LYS cc_start: 0.8345 (mmtm) cc_final: 0.7848 (mmtt) REVERT: G 59 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7590 (mt-10) REVERT: I 110 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6906 (mp0) REVERT: I 123 ILE cc_start: 0.8069 (pt) cc_final: 0.7825 (pt) REVERT: I 140 ILE cc_start: 0.8578 (tt) cc_final: 0.8357 (tt) REVERT: I 150 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7619 (mp) REVERT: I 251 TYR cc_start: 0.8461 (t80) cc_final: 0.8200 (t80) REVERT: I 266 LEU cc_start: 0.8581 (mt) cc_final: 0.8303 (mt) REVERT: I 298 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8822 (mt) REVERT: I 373 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.6244 (tt0) REVERT: J 100 MET cc_start: 0.5973 (OUTLIER) cc_final: 0.5666 (mmm) REVERT: J 106 ILE cc_start: 0.7866 (mp) cc_final: 0.7587 (mm) REVERT: J 155 GLN cc_start: 0.7480 (tt0) cc_final: 0.7250 (tt0) REVERT: K 155 GLN cc_start: 0.7480 (tt0) cc_final: 0.7246 (tt0) REVERT: K 237 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7265 (mtp) REVERT: K 250 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8485 (mm-30) REVERT: L 123 ILE cc_start: 0.8075 (pt) cc_final: 0.7815 (pt) REVERT: L 140 ILE cc_start: 0.8600 (tt) cc_final: 0.8359 (tt) REVERT: L 150 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7621 (mp) REVERT: L 251 TYR cc_start: 0.8472 (t80) cc_final: 0.8165 (t80) REVERT: L 266 LEU cc_start: 0.8587 (mt) cc_final: 0.8318 (mt) REVERT: L 298 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8826 (mt) outliers start: 98 outliers final: 40 residues processed: 645 average time/residue: 1.4525 time to fit residues: 1066.9080 Evaluate side-chains 605 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 557 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 SER 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 E residue 95 LEU 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 H residue 47 SER Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 373 GLU Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain I residue 441 GLU 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 196 LEU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain K residue 237 MET 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 96 VAL Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 314 ILE Chi-restraints excluded: chain L residue 439 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 271 optimal weight: 0.9990 chunk 206 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 275 optimal weight: 5.9990 chunk 291 optimal weight: 0.0570 chunk 144 optimal weight: 0.8980 chunk 261 optimal weight: 0.2980 chunk 78 optimal weight: 2.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- 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** C 38 ASN D 38 ASN E 70 ASN F 38 ASN F 134 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN I 18 GLN I 115 GLN I 119 ASN I 239 ASN J 85 GLN J 253 ASN 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24318 Z= 0.172 Angle : 0.503 7.735 33014 Z= 0.263 Chirality : 0.042 0.191 3998 Planarity : 0.003 0.045 4016 Dihedral : 9.643 84.417 3474 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.98 % Allowed : 15.59 % Favored : 80.44 % 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: 1.90 (0.15), residues: 3008 helix: 2.32 (0.12), residues: 1788 sheet: 1.18 (0.28), residues: 306 loop : -0.92 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 47 HIS 0.004 0.001 HIS L 168 PHE 0.035 0.002 PHE L 202 TYR 0.017 0.001 TYR E 107 ARG 0.008 0.001 ARG A 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 674 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 572 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7072 (tp30) cc_final: 0.6798 (tp30) REVERT: A 41 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8010 (mptp) REVERT: C 128 MET cc_start: 0.7760 (mmm) cc_final: 0.7458 (mmp) REVERT: C 145 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6840 (pt) REVERT: E 145 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6721 (tt) REVERT: F 128 MET cc_start: 0.7802 (mmm) cc_final: 0.7502 (mmp) REVERT: G 41 LYS cc_start: 0.8337 (mmtm) cc_final: 0.7826 (mmtt) REVERT: H 41 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7986 (mptp) REVERT: I 123 ILE cc_start: 0.8081 (pt) cc_final: 0.7833 (pt) REVERT: I 140 ILE cc_start: 0.8571 (tt) cc_final: 0.8350 (tt) REVERT: I 150 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7592 (mp) REVERT: I 251 TYR cc_start: 0.8515 (t80) cc_final: 0.8250 (t80) REVERT: I 298 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8844 (mt) REVERT: J 106 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7468 (mm) REVERT: J 155 GLN cc_start: 0.7430 (tt0) cc_final: 0.7219 (tt0) REVERT: J 237 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7197 (mtp) REVERT: K 155 GLN cc_start: 0.7435 (tt0) cc_final: 0.7218 (tt0) REVERT: K 237 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7206 (mtp) REVERT: K 250 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8488 (mm-30) REVERT: L 123 ILE cc_start: 0.8039 (pt) cc_final: 0.7782 (pt) REVERT: L 140 ILE cc_start: 0.8578 (tt) cc_final: 0.8343 (tt) REVERT: L 150 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7592 (mp) REVERT: L 251 TYR cc_start: 0.8473 (t80) cc_final: 0.8172 (t80) REVERT: L 266 LEU cc_start: 0.8580 (mt) cc_final: 0.8302 (mt) REVERT: L 298 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8842 (mt) outliers start: 102 outliers final: 51 residues processed: 630 average time/residue: 1.4630 time to fit residues: 1049.2194 Evaluate side-chains 621 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 559 time to evaluate : 2.684 ------------------------------------------------------------------------------- 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 135 SER Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 145 ILE 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 E residue 95 LEU 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 85 SER Chi-restraints excluded: chain H residue 41 LYS 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 96 VAL Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain I residue 439 ASP Chi-restraints excluded: chain I residue 441 GLU Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 106 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 314 ILE Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain K residue 237 MET 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 139 SER Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 398 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 243 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 262 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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** B 134 GLN C 38 ASN E 38 ASN E 70 ASN F 38 ASN F 134 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN I 18 GLN I 119 ASN I 218 ASN I 239 ASN ** J 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN J 253 ASN ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24318 Z= 0.233 Angle : 0.537 9.768 33014 Z= 0.281 Chirality : 0.043 0.202 3998 Planarity : 0.004 0.046 4016 Dihedral : 9.802 84.941 3474 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.40 % Allowed : 16.68 % 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: 1.80 (0.15), residues: 3008 helix: 2.21 (0.12), residues: 1788 sheet: 1.12 (0.28), residues: 306 loop : -0.90 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 47 HIS 0.004 0.001 HIS I 168 PHE 0.036 0.002 PHE I 202 TYR 0.016 0.001 TYR I 270 ARG 0.007 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 673 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 560 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7047 (tp30) cc_final: 0.6778 (tp30) REVERT: A 41 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8017 (mptp) REVERT: B 64 LEU cc_start: 0.8627 (mt) cc_final: 0.8406 (mm) REVERT: C 128 MET cc_start: 0.7807 (mmm) cc_final: 0.7494 (mmp) REVERT: C 145 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6853 (pt) REVERT: C 208 MET cc_start: 0.6336 (ttp) cc_final: 0.6116 (ttm) REVERT: D 138 ASP cc_start: 0.7387 (t70) cc_final: 0.6545 (p0) REVERT: E 145 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6796 (tt) REVERT: F 128 MET cc_start: 0.7827 (mmm) cc_final: 0.7512 (mmp) REVERT: F 145 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.6896 (pt) REVERT: G 64 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8388 (mm) REVERT: H 41 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8186 (mptp) REVERT: I 110 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6510 (mt-10) REVERT: I 123 ILE cc_start: 0.8070 (pt) cc_final: 0.7818 (pt) REVERT: I 140 ILE cc_start: 0.8598 (tt) cc_final: 0.8378 (tt) REVERT: I 150 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7673 (pt) REVERT: I 251 TYR cc_start: 0.8455 (t80) cc_final: 0.8214 (t80) REVERT: I 266 LEU cc_start: 0.8597 (mt) cc_final: 0.8319 (mt) REVERT: I 298 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8851 (mt) REVERT: J 106 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7370 (mm) REVERT: J 155 GLN cc_start: 0.7454 (tt0) cc_final: 0.7243 (tt0) REVERT: J 237 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7207 (mtp) REVERT: J 333 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7728 (mmtm) REVERT: K 155 GLN cc_start: 0.7454 (tt0) cc_final: 0.7236 (tt0) REVERT: K 237 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7242 (mtp) REVERT: K 333 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7745 (mmtm) REVERT: L 110 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6506 (mt-10) REVERT: L 123 ILE cc_start: 0.8034 (pt) cc_final: 0.7779 (pt) REVERT: L 150 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7671 (pt) REVERT: L 251 TYR cc_start: 0.8438 (t80) cc_final: 0.8165 (t80) REVERT: L 266 LEU cc_start: 0.8608 (mt) cc_final: 0.8331 (mt) REVERT: L 298 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8850 (mt) outliers start: 113 outliers final: 52 residues processed: 624 average time/residue: 1.4543 time to fit residues: 1033.7384 Evaluate side-chains 619 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 550 time to evaluate : 2.779 ------------------------------------------------------------------------------- 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 135 SER Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 145 ILE 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 E residue 95 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F 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 7 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 85 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 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 139 SER Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain I residue 263 VAL 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 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 106 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 333 LYS Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 216 MET Chi-restraints excluded: chain K residue 237 MET 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 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 139 SER Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU 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: 9.9990 chunk 262 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 292 optimal weight: 2.9990 chunk 242 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 96 optimal weight: 0.3980 chunk 153 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN C 38 ASN E 38 ASN E 171 ASN F 38 ASN F 134 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN H 81 ASN I 18 GLN I 119 ASN I 239 ASN J 85 GLN J 253 ASN 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: 0.8248 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24318 Z= 0.281 Angle : 0.562 8.271 33014 Z= 0.295 Chirality : 0.044 0.211 3998 Planarity : 0.004 0.047 4016 Dihedral : 9.960 86.380 3474 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.21 % Allowed : 17.69 % Favored : 78.10 % 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: 1.67 (0.15), residues: 3008 helix: 2.12 (0.12), residues: 1782 sheet: 1.07 (0.27), residues: 298 loop : -0.93 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 158 HIS 0.006 0.001 HIS L 168 PHE 0.037 0.002 PHE I 202 TYR 0.013 0.001 TYR J 345 ARG 0.009 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 668 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 560 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7065 (tp30) cc_final: 0.6805 (tp30) REVERT: A 41 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8176 (mptp) REVERT: B 62 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7281 (mt-10) REVERT: B 64 LEU cc_start: 0.8598 (mt) cc_final: 0.8373 (mm) REVERT: C 128 MET cc_start: 0.7838 (mmm) cc_final: 0.7525 (mmp) REVERT: C 131 LYS cc_start: 0.8409 (mmtm) cc_final: 0.8189 (mmtm) REVERT: C 134 GLN cc_start: 0.8201 (mm110) cc_final: 0.7801 (mm-40) REVERT: C 145 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6879 (pt) REVERT: D 134 GLN cc_start: 0.7833 (tp40) cc_final: 0.7589 (mm-40) REVERT: D 138 ASP cc_start: 0.7436 (t70) cc_final: 0.6631 (p0) REVERT: E 60 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: E 145 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6815 (tt) REVERT: F 128 MET cc_start: 0.7853 (mmm) cc_final: 0.7540 (mmp) REVERT: F 131 LYS cc_start: 0.8396 (mmtm) cc_final: 0.8188 (mmtm) REVERT: F 145 ILE cc_start: 0.7253 (OUTLIER) cc_final: 0.6901 (pt) REVERT: H 41 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8184 (mptp) REVERT: I 110 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6526 (mt-10) REVERT: I 123 ILE cc_start: 0.8066 (pt) cc_final: 0.7792 (pt) REVERT: I 150 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7747 (pt) REVERT: I 251 TYR cc_start: 0.8456 (t80) cc_final: 0.8194 (t80) REVERT: I 266 LEU cc_start: 0.8612 (mt) cc_final: 0.8339 (mt) REVERT: I 298 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8853 (mt) REVERT: J 106 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7386 (mm) REVERT: J 155 GLN cc_start: 0.7505 (tt0) cc_final: 0.7284 (tt0) REVERT: J 220 ARG cc_start: 0.6481 (tpm170) cc_final: 0.5663 (tpt170) REVERT: J 237 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7227 (mtp) REVERT: J 333 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7766 (mmtm) REVERT: K 155 GLN cc_start: 0.7509 (tt0) cc_final: 0.7272 (tt0) REVERT: K 237 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7226 (mtp) REVERT: K 333 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7786 (mmtm) REVERT: L 110 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6536 (mt-10) REVERT: L 123 ILE cc_start: 0.8038 (pt) cc_final: 0.7769 (pt) REVERT: L 150 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7737 (pt) REVERT: L 251 TYR cc_start: 0.8442 (t80) cc_final: 0.8139 (t80) REVERT: L 266 LEU cc_start: 0.8621 (mt) cc_final: 0.8349 (mt) REVERT: L 298 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8851 (mt) outliers start: 108 outliers final: 51 residues processed: 624 average time/residue: 1.4339 time to fit residues: 1019.8680 Evaluate side-chains 615 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 547 time to evaluate : 2.767 ------------------------------------------------------------------------------- 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 B residue 7 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 145 ILE 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 E residue 60 GLU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain F 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 7 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 85 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 109 LYS Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 15 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 106 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 333 LYS Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 216 MET 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 314 ILE Chi-restraints excluded: chain K residue 333 LYS 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 139 SER Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 323 LEU 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: 4.9990 chunk 32 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 213 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 245 optimal weight: 9.9990 chunk 163 optimal weight: 0.8980 chunk 291 optimal weight: 0.2980 chunk 182 optimal weight: 0.0050 chunk 177 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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** B 134 GLN C 38 ASN F 38 ASN F 134 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN I 18 GLN I 119 ASN I 239 ASN J 85 GLN J 115 GLN J 253 ASN K 85 GLN K 115 GLN K 272 GLN L 18 GLN L 119 ASN L 218 ASN L 239 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24318 Z= 0.153 Angle : 0.505 7.424 33014 Z= 0.263 Chirality : 0.042 0.189 3998 Planarity : 0.003 0.043 4016 Dihedral : 9.608 84.633 3474 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.35 % Allowed : 19.10 % Favored : 77.55 % 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: 1.82 (0.15), residues: 3008 helix: 2.26 (0.12), residues: 1790 sheet: 0.99 (0.28), residues: 306 loop : -0.89 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 267 HIS 0.004 0.001 HIS I 168 PHE 0.035 0.001 PHE I 202 TYR 0.014 0.001 TYR I 270 ARG 0.008 0.001 ARG A 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 662 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 576 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7037 (tp30) cc_final: 0.6721 (tp30) REVERT: A 41 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8153 (mptp) REVERT: B 64 LEU cc_start: 0.8554 (mt) cc_final: 0.8335 (mm) REVERT: C 128 MET cc_start: 0.7746 (mmm) cc_final: 0.7459 (mmp) REVERT: C 131 LYS cc_start: 0.8375 (mmtm) cc_final: 0.8146 (mmtm) REVERT: C 145 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6916 (pt) REVERT: D 134 GLN cc_start: 0.7804 (tp40) cc_final: 0.7586 (mm-40) REVERT: D 138 ASP cc_start: 0.7438 (t70) cc_final: 0.6591 (p0) REVERT: D 139 GLU cc_start: 0.6882 (pm20) cc_final: 0.6682 (pm20) REVERT: E 120 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7772 (ttt180) REVERT: E 145 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6781 (tt) REVERT: F 128 MET cc_start: 0.7743 (mmm) cc_final: 0.7451 (mmp) REVERT: F 131 LYS cc_start: 0.8384 (mmtm) cc_final: 0.8162 (mmtm) REVERT: F 138 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.6484 (t70) REVERT: F 145 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6897 (pt) REVERT: H 41 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7955 (mptp) REVERT: I 110 GLU cc_start: 0.7201 (mp0) cc_final: 0.6512 (mt-10) REVERT: I 123 ILE cc_start: 0.8035 (pt) cc_final: 0.7763 (pt) REVERT: I 150 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7661 (pt) REVERT: I 251 TYR cc_start: 0.8480 (t80) cc_final: 0.8250 (t80) REVERT: I 298 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8832 (mt) REVERT: J 106 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7375 (mm) REVERT: J 155 GLN cc_start: 0.7489 (tt0) cc_final: 0.7268 (tt0) REVERT: J 220 ARG cc_start: 0.6415 (tpm170) cc_final: 0.5595 (tpt170) REVERT: K 155 GLN cc_start: 0.7493 (tt0) cc_final: 0.7228 (tt0) REVERT: K 333 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7766 (mmtm) REVERT: L 110 GLU cc_start: 0.7198 (mp0) cc_final: 0.6502 (mt-10) REVERT: L 123 ILE cc_start: 0.8019 (pt) cc_final: 0.7760 (pt) REVERT: L 150 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7660 (pt) REVERT: L 251 TYR cc_start: 0.8481 (t80) cc_final: 0.8205 (t80) REVERT: L 298 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8829 (mt) outliers start: 86 outliers final: 40 residues processed: 629 average time/residue: 1.4865 time to fit residues: 1064.7245 Evaluate side-chains 603 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 550 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain C residue 145 ILE 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 E residue 120 ARG Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F 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 7 LYS Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 106 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 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 165 SER Chi-restraints excluded: chain K residue 216 MET 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 421 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 421 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 180 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 228 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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** B 51 HIS B 134 GLN C 38 ASN D 8 GLN F 38 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN I 18 GLN I 115 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 253 ASN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24318 Z= 0.165 Angle : 0.509 7.480 33014 Z= 0.266 Chirality : 0.042 0.191 3998 Planarity : 0.003 0.045 4016 Dihedral : 9.515 84.162 3474 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.08 % Allowed : 20.69 % Favored : 76.23 % 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: 1.82 (0.15), residues: 3008 helix: 2.29 (0.12), residues: 1792 sheet: 0.94 (0.28), residues: 312 loop : -0.97 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 267 HIS 0.004 0.001 HIS L 168 PHE 0.034 0.002 PHE L 202 TYR 0.019 0.001 TYR E 107 ARG 0.009 0.001 ARG H 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 642 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 563 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7060 (tp30) cc_final: 0.6777 (tp30) REVERT: A 41 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8153 (mptp) REVERT: A 63 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8393 (mp) REVERT: B 64 LEU cc_start: 0.8554 (mt) cc_final: 0.8342 (mm) REVERT: C 24 GLU cc_start: 0.7745 (tp30) cc_final: 0.7517 (tp30) REVERT: C 128 MET cc_start: 0.7748 (mmm) cc_final: 0.7462 (mmp) REVERT: C 145 ILE cc_start: 0.7242 (OUTLIER) cc_final: 0.6933 (pt) REVERT: D 134 GLN cc_start: 0.7791 (tp40) cc_final: 0.7551 (mm-40) REVERT: D 138 ASP cc_start: 0.7424 (t70) cc_final: 0.6592 (p0) REVERT: E 120 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7785 (ttt180) REVERT: E 145 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6775 (tt) REVERT: F 128 MET cc_start: 0.7747 (mmm) cc_final: 0.7457 (mmp) REVERT: F 131 LYS cc_start: 0.8411 (mmtm) cc_final: 0.8180 (mmtm) REVERT: F 138 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.6356 (t70) REVERT: F 145 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6908 (pt) REVERT: G 41 LYS cc_start: 0.8309 (mttt) cc_final: 0.7544 (mmtt) REVERT: H 41 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8158 (mptp) REVERT: I 110 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6487 (mt-10) REVERT: I 123 ILE cc_start: 0.8060 (pt) cc_final: 0.7783 (pt) REVERT: I 150 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7678 (pt) REVERT: I 251 TYR cc_start: 0.8483 (t80) cc_final: 0.8252 (t80) REVERT: I 298 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8832 (mt) REVERT: J 106 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7266 (mm) REVERT: J 155 GLN cc_start: 0.7516 (tt0) cc_final: 0.7300 (tt0) REVERT: K 100 MET cc_start: 0.6169 (mtm) cc_final: 0.5560 (mmm) REVERT: K 106 ILE cc_start: 0.8302 (mm) cc_final: 0.8007 (mp) REVERT: K 155 GLN cc_start: 0.7526 (tt0) cc_final: 0.7300 (tt0) REVERT: K 222 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7503 (mmtm) REVERT: K 250 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8497 (mm-30) REVERT: L 97 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.7004 (mp) REVERT: L 110 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6517 (mt-10) REVERT: L 123 ILE cc_start: 0.8013 (pt) cc_final: 0.7762 (pt) REVERT: L 150 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7655 (pt) REVERT: L 251 TYR cc_start: 0.8485 (t80) cc_final: 0.8217 (t80) REVERT: L 298 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8832 (mt) outliers start: 79 outliers final: 40 residues processed: 613 average time/residue: 1.4686 time to fit residues: 1023.8520 Evaluate side-chains 600 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 544 time to evaluate : 2.526 ------------------------------------------------------------------------------- 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 85 SER Chi-restraints excluded: chain C residue 145 ILE 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 E residue 120 ARG Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F 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 7 LYS Chi-restraints excluded: chain G residue 47 SER 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 109 LYS Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 106 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 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 216 MET 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 97 LEU Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 421 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 264 optimal weight: 1.9990 chunk 278 optimal weight: 8.9990 chunk 254 optimal weight: 0.4980 chunk 271 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 83 optimal weight: 0.2980 chunk 245 optimal weight: 10.0000 chunk 256 optimal weight: 4.9990 chunk 270 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN F 38 ASN F 134 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN I 18 GLN I 119 ASN I 239 ASN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 253 ASN K 85 GLN K 272 GLN L 18 GLN L 119 ASN L 239 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24318 Z= 0.165 Angle : 0.519 8.613 33014 Z= 0.270 Chirality : 0.042 0.188 3998 Planarity : 0.003 0.045 4016 Dihedral : 9.485 83.764 3474 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.84 % Allowed : 21.20 % Favored : 75.95 % 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: 1.84 (0.15), residues: 3008 helix: 2.26 (0.12), residues: 1794 sheet: 1.06 (0.28), residues: 308 loop : -0.91 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 267 HIS 0.004 0.001 HIS L 168 PHE 0.034 0.001 PHE I 202 TYR 0.016 0.001 TYR K 345 ARG 0.009 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 626 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 553 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7045 (tp30) cc_final: 0.6739 (tp30) REVERT: A 41 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8148 (mptp) REVERT: A 63 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8389 (mp) REVERT: B 64 LEU cc_start: 0.8575 (mt) cc_final: 0.8367 (mm) REVERT: C 24 GLU cc_start: 0.7697 (tp30) cc_final: 0.7369 (tp30) REVERT: C 128 MET cc_start: 0.7717 (mmm) cc_final: 0.7429 (mmp) REVERT: C 131 LYS cc_start: 0.8390 (mmtm) cc_final: 0.8139 (mmtm) REVERT: C 145 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6878 (pt) REVERT: D 134 GLN cc_start: 0.7799 (tp40) cc_final: 0.7469 (mp10) REVERT: D 138 ASP cc_start: 0.7388 (t70) cc_final: 0.6550 (p0) REVERT: E 120 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7760 (ttt180) REVERT: E 145 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6746 (tt) REVERT: F 128 MET cc_start: 0.7750 (mmm) cc_final: 0.7459 (mmp) REVERT: F 131 LYS cc_start: 0.8386 (mmtm) cc_final: 0.8156 (mmtm) REVERT: F 145 ILE cc_start: 0.7256 (OUTLIER) cc_final: 0.6901 (pt) REVERT: G 41 LYS cc_start: 0.8318 (mttt) cc_final: 0.7666 (mmtt) REVERT: H 41 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8160 (mptp) REVERT: I 110 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6515 (mt-10) REVERT: I 123 ILE cc_start: 0.8044 (pt) cc_final: 0.7777 (pt) REVERT: I 150 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7650 (pt) REVERT: I 251 TYR cc_start: 0.8483 (t80) cc_final: 0.8260 (t80) REVERT: I 298 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8823 (mt) REVERT: J 106 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7284 (mm) REVERT: J 155 GLN cc_start: 0.7516 (tt0) cc_final: 0.7301 (tt0) REVERT: J 220 ARG cc_start: 0.6347 (tpm170) cc_final: 0.5495 (tpt170) REVERT: K 100 MET cc_start: 0.6137 (mtm) cc_final: 0.5494 (mmm) REVERT: K 106 ILE cc_start: 0.8293 (mm) cc_final: 0.8000 (mp) REVERT: K 155 GLN cc_start: 0.7540 (tt0) cc_final: 0.7295 (tt0) REVERT: K 222 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7537 (mmtm) REVERT: L 110 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6523 (mt-10) REVERT: L 123 ILE cc_start: 0.8009 (pt) cc_final: 0.7755 (pt) REVERT: L 150 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7635 (pt) REVERT: L 251 TYR cc_start: 0.8481 (t80) cc_final: 0.8220 (t80) REVERT: L 298 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8822 (mt) outliers start: 73 outliers final: 42 residues processed: 597 average time/residue: 1.4690 time to fit residues: 1001.8945 Evaluate side-chains 600 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 544 time to evaluate : 2.850 ------------------------------------------------------------------------------- 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 85 SER Chi-restraints excluded: chain C residue 145 ILE 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 E residue 120 ARG Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F 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 7 LYS Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 65 SER 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 109 LYS Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 106 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 338 ILE Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 216 MET 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 97 LEU Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 298 LEU Chi-restraints excluded: chain L residue 323 LEU Chi-restraints excluded: chain L residue 398 THR Chi-restraints excluded: chain L residue 421 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 178 optimal weight: 7.9990 chunk 286 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 199 optimal weight: 0.9990 chunk 300 optimal weight: 3.9990 chunk 276 optimal weight: 0.0670 chunk 239 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN C 38 ASN F 38 ASN F 134 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 HIS G 134 GLN I 18 GLN I 119 ASN I 239 ASN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 253 ASN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 272 GLN L 18 GLN L 239 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24318 Z= 0.246 Angle : 0.563 10.307 33014 Z= 0.293 Chirality : 0.043 0.204 3998 Planarity : 0.004 0.045 4016 Dihedral : 9.771 85.095 3474 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.84 % Allowed : 21.36 % Favored : 75.80 % 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: 1.67 (0.15), residues: 3008 helix: 2.12 (0.12), residues: 1794 sheet: 1.00 (0.27), residues: 308 loop : -0.94 (0.18), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 181 HIS 0.005 0.001 HIS I 168 PHE 0.035 0.002 PHE I 202 TYR 0.016 0.001 TYR I 270 ARG 0.009 0.001 ARG C 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 620 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 547 time to evaluate : 2.685 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: 0.6785 (tp30) REVERT: A 41 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7992 (mptp) REVERT: A 63 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8416 (mp) REVERT: C 128 MET cc_start: 0.7801 (mmm) cc_final: 0.7504 (mmp) REVERT: C 131 LYS cc_start: 0.8420 (mmtm) cc_final: 0.8174 (mmtm) REVERT: C 145 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6871 (pt) REVERT: D 138 ASP cc_start: 0.7433 (t70) cc_final: 0.6613 (p0) REVERT: D 139 GLU cc_start: 0.6878 (pm20) cc_final: 0.6663 (pm20) REVERT: E 120 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7834 (ttt180) REVERT: E 145 ILE cc_start: 0.7051 (OUTLIER) cc_final: 0.6782 (tt) REVERT: F 128 MET cc_start: 0.7810 (mmm) cc_final: 0.7551 (mmp) REVERT: F 131 LYS cc_start: 0.8396 (mmtm) cc_final: 0.8165 (mmtm) REVERT: F 145 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6882 (pt) REVERT: G 41 LYS cc_start: 0.8403 (mttt) cc_final: 0.7709 (mmtt) REVERT: G 62 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6867 (mt-10) REVERT: H 41 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8167 (mptp) REVERT: I 91 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7963 (t80) REVERT: I 110 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6513 (mt-10) REVERT: I 123 ILE cc_start: 0.8047 (pt) cc_final: 0.7776 (pt) REVERT: I 150 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7760 (pt) REVERT: I 251 TYR cc_start: 0.8485 (t80) cc_final: 0.8245 (t80) REVERT: I 298 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8846 (mt) REVERT: J 106 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7200 (mm) REVERT: J 220 ARG cc_start: 0.6395 (tpm170) cc_final: 0.5590 (tpt170) REVERT: K 100 MET cc_start: 0.6179 (mtm) cc_final: 0.5506 (mmm) REVERT: K 106 ILE cc_start: 0.8312 (mm) cc_final: 0.8013 (mp) REVERT: K 222 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7532 (mmtm) REVERT: K 383 GLU cc_start: 0.8051 (tp30) cc_final: 0.7829 (tp30) REVERT: L 110 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6505 (mt-10) REVERT: L 123 ILE cc_start: 0.8019 (pt) cc_final: 0.7757 (pt) REVERT: L 150 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7761 (pt) REVERT: L 251 TYR cc_start: 0.8482 (t80) cc_final: 0.8253 (t80) REVERT: L 298 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8850 (mt) outliers start: 73 outliers final: 39 residues processed: 594 average time/residue: 1.4139 time to fit residues: 955.4179 Evaluate side-chains 590 residues out of total 2566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 536 time to evaluate : 1.885 ------------------------------------------------------------------------------- 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 85 SER Chi-restraints excluded: chain C residue 145 ILE 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 E residue 120 ARG Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F 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 7 LYS Chi-restraints excluded: chain G residue 47 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 I residue 15 THR Chi-restraints excluded: chain I residue 91 PHE Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 298 LEU Chi-restraints excluded: chain I residue 398 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 106 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 15 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 216 MET 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 97 LEU Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 298 LEU 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 190 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 chunk 100 optimal weight: 0.0470 chunk 246 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN C 38 ASN F 134 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN H 105 GLN I 18 GLN I 119 ASN I 239 ASN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 GLN J 253 ASN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 GLN K 272 GLN L 18 GLN L 239 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.166954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.127348 restraints weight = 26081.651| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.94 r_work: 0.3285 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24318 Z= 0.199 Angle : 0.548 12.879 33014 Z= 0.284 Chirality : 0.043 0.197 3998 Planarity : 0.004 0.045 4016 Dihedral : 9.717 85.199 3474 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.92 % Allowed : 21.43 % Favored : 75.64 % 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: 1.70 (0.15), residues: 3008 helix: 2.15 (0.12), residues: 1784 sheet: 1.01 (0.28), residues: 308 loop : -0.91 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 47 HIS 0.005 0.001 HIS I 168 PHE 0.035 0.002 PHE I 202 TYR 0.014 0.001 TYR I 345 ARG 0.009 0.001 ARG C 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14035.30 seconds wall clock time: 251 minutes 16.95 seconds (15076.95 seconds total)