Starting phenix.real_space_refine on Sat Aug 8 01:15:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gam_29900/08_2026/8gam_29900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gam_29900/08_2026/8gam_29900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gam_29900/08_2026/8gam_29900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gam_29900/08_2026/8gam_29900.map" model { file = "/net/cci-nas-00/data/ceres_data/8gam_29900/08_2026/8gam_29900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gam_29900/08_2026/8gam_29900.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 81 5.49 5 S 109 5.16 5 C 15646 2.51 5 N 4528 2.21 5 O 4996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25360 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "B" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "C" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "D" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2261 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "F" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2173 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "G" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2523 Classifications: {'peptide': 325} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 314} Chain breaks: 1 Chain: "H" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1867 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain: "I" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "J" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "K" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 916 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 18, 'rna3p_pur': 12, 'rna3p_pyr': 4} Link IDs: {'rna2p': 26, 'rna3p': 16} Chain: "M" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2110 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 8, 'TRANS': 255} Chain breaks: 1 Chain: "N" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1674 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "L" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 511 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "O" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 5.08, per 1000 atoms: 0.20 Number of scatterers: 25360 At special positions: 0 Unit cell: (143.381, 104.022, 196.798, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 109 16.00 P 81 15.00 O 4996 8.00 N 4528 7.00 C 15646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.1 seconds 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5474 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 29 sheets defined 34.5% alpha, 15.8% beta 14 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 42 through 58 removed outlier: 4.056A pdb=" N LEU A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 90 through 106 removed outlier: 4.306A pdb=" N GLU A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.907A pdb=" N ARG A 110 " --> pdb=" O TYR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 195 through 208 Processing helix chain 'A' and resid 239 through 247 removed outlier: 3.799A pdb=" N LEU A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 58 removed outlier: 4.057A pdb=" N LEU B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 90 through 106 removed outlier: 4.306A pdb=" N GLU B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.909A pdb=" N ARG B 110 " --> pdb=" O TYR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 195 through 208 Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.800A pdb=" N LEU B 243 " --> pdb=" O PRO B 239 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 removed outlier: 4.137A pdb=" N GLY C 27 " --> pdb=" O PRO C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 58 removed outlier: 4.056A pdb=" N LEU C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 90 through 106 removed outlier: 4.306A pdb=" N GLU C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 112 removed outlier: 3.914A pdb=" N ARG C 110 " --> pdb=" O TYR C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 193 Processing helix chain 'C' and resid 195 through 208 Processing helix chain 'C' and resid 239 through 247 removed outlier: 3.804A pdb=" N LEU C 243 " --> pdb=" O PRO C 239 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 58 removed outlier: 4.056A pdb=" N LEU D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 90 through 106 removed outlier: 4.305A pdb=" N GLU D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 112 removed outlier: 3.908A pdb=" N ARG D 110 " --> pdb=" O TYR D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 193 Processing helix chain 'D' and resid 195 through 208 Processing helix chain 'D' and resid 239 through 247 removed outlier: 3.804A pdb=" N LEU D 243 " --> pdb=" O PRO D 239 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 27 removed outlier: 3.546A pdb=" N ALA E 26 " --> pdb=" O ASP E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 58 removed outlier: 4.056A pdb=" N LEU E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 81 Processing helix chain 'E' and resid 90 through 106 removed outlier: 4.305A pdb=" N GLU E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 112 removed outlier: 3.914A pdb=" N ARG E 110 " --> pdb=" O TYR E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 193 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 239 through 247 removed outlier: 3.805A pdb=" N LEU E 243 " --> pdb=" O PRO E 239 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 58 removed outlier: 4.056A pdb=" N LEU F 46 " --> pdb=" O THR F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 81 Processing helix chain 'F' and resid 90 through 106 removed outlier: 4.306A pdb=" N GLU F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 112 removed outlier: 3.904A pdb=" N ARG F 110 " --> pdb=" O TYR F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 193 Processing helix chain 'F' and resid 195 through 208 Processing helix chain 'F' and resid 239 through 247 removed outlier: 3.806A pdb=" N LEU F 243 " --> pdb=" O PRO F 239 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 15 removed outlier: 4.082A pdb=" N GLU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 77 Processing helix chain 'G' and resid 98 through 118 removed outlier: 3.807A pdb=" N GLN G 103 " --> pdb=" O GLN G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 131 removed outlier: 3.571A pdb=" N VAL G 127 " --> pdb=" O GLY G 123 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU G 131 " --> pdb=" O VAL G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 142 removed outlier: 3.918A pdb=" N MET G 141 " --> pdb=" O LYS G 137 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN G 142 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 150 removed outlier: 4.041A pdb=" N CYS G 149 " --> pdb=" O ASN G 145 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA G 150 " --> pdb=" O TRP G 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 145 through 150' Processing helix chain 'G' and resid 174 through 183 removed outlier: 3.666A pdb=" N TYR G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 189 removed outlier: 3.748A pdb=" N ASP G 188 " --> pdb=" O THR G 185 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN G 189 " --> pdb=" O GLN G 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 185 through 189' Processing helix chain 'G' and resid 243 through 258 removed outlier: 4.606A pdb=" N GLU G 249 " --> pdb=" O GLN G 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 359 Processing helix chain 'H' and resid 376 through 382 Processing helix chain 'H' and resid 383 through 385 No H-bonds generated for 'chain 'H' and resid 383 through 385' Processing helix chain 'H' and resid 400 through 406 Processing helix chain 'H' and resid 412 through 427 removed outlier: 3.999A pdb=" N LEU H 416 " --> pdb=" O PRO H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 448 removed outlier: 3.851A pdb=" N LYS H 438 " --> pdb=" O ALA H 434 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ALA H 439 " --> pdb=" O SER H 435 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR H 440 " --> pdb=" O LEU H 436 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE H 441 " --> pdb=" O LEU H 437 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 486 Processing helix chain 'H' and resid 493 through 498 Processing helix chain 'H' and resid 504 through 510 removed outlier: 3.973A pdb=" N VAL H 508 " --> pdb=" O THR H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 522 Processing helix chain 'H' and resid 525 through 541 removed outlier: 3.613A pdb=" N ALA H 529 " --> pdb=" O PHE H 525 " (cutoff:3.500A) Processing helix chain 'H' and resid 551 through 570 removed outlier: 4.157A pdb=" N GLY H 556 " --> pdb=" O LEU H 552 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU H 557 " --> pdb=" O GLU H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 574 through 580 Processing helix chain 'I' and resid 9 through 29 removed outlier: 4.104A pdb=" N ASN I 29 " --> pdb=" O GLN I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 45 removed outlier: 3.618A pdb=" N PHE I 41 " --> pdb=" O ALA I 37 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY I 42 " --> pdb=" O ASP I 38 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER I 43 " --> pdb=" O ARG I 39 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 65 removed outlier: 4.066A pdb=" N GLY I 53 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N THR I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Proline residue: I 60 - end of helix Processing helix chain 'I' and resid 68 through 84 Processing helix chain 'I' and resid 94 through 113 removed outlier: 3.510A pdb=" N ALA I 102 " --> pdb=" O GLN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 123 Processing helix chain 'J' and resid 9 through 29 removed outlier: 4.104A pdb=" N ASN J 29 " --> pdb=" O GLN J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 45 removed outlier: 3.618A pdb=" N PHE J 41 " --> pdb=" O ALA J 37 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY J 42 " --> pdb=" O ASP J 38 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER J 45 " --> pdb=" O PHE J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 65 removed outlier: 4.066A pdb=" N GLY J 53 " --> pdb=" O ILE J 49 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N THR J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) Proline residue: J 60 - end of helix Processing helix chain 'J' and resid 68 through 84 Processing helix chain 'J' and resid 94 through 113 removed outlier: 3.510A pdb=" N ALA J 102 " --> pdb=" O GLN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 123 Processing helix chain 'M' and resid 23 through 27 removed outlier: 4.203A pdb=" N GLY M 27 " --> pdb=" O PRO M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.965A pdb=" N LEU M 46 " --> pdb=" O THR M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 105 Processing helix chain 'M' and resid 106 through 112 removed outlier: 4.043A pdb=" N ARG M 110 " --> pdb=" O TYR M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 193 Processing helix chain 'M' and resid 195 through 207 Processing helix chain 'M' and resid 239 through 247 removed outlier: 3.747A pdb=" N ILE M 247 " --> pdb=" O LEU M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 262 No H-bonds generated for 'chain 'M' and resid 260 through 262' Processing helix chain 'N' and resid 30 through 42 Processing helix chain 'N' and resid 117 through 131 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 3.889A pdb=" N ASP A 17 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 250 Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 41 removed outlier: 6.926A pdb=" N GLN B 220 " --> pdb=" O GLN B 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AA6, first strand: chain 'B' and resid 248 through 250 Processing sheet with id=AA7, first strand: chain 'C' and resid 40 through 41 removed outlier: 6.920A pdb=" N GLN C 220 " --> pdb=" O GLN C 16 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 250 Processing sheet with id=AB1, first strand: chain 'D' and resid 40 through 41 removed outlier: 3.919A pdb=" N ASP D 17 " --> pdb=" O GLN D 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 130 through 131 Processing sheet with id=AB3, first strand: chain 'D' and resid 248 through 250 Processing sheet with id=AB4, first strand: chain 'E' and resid 40 through 41 removed outlier: 3.872A pdb=" N ASP E 17 " --> pdb=" O GLN E 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AB6, first strand: chain 'E' and resid 248 through 250 Processing sheet with id=AB7, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.888A pdb=" N ASP F 17 " --> pdb=" O GLN F 220 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 130 through 131 Processing sheet with id=AB9, first strand: chain 'F' and resid 248 through 250 Processing sheet with id=AC1, first strand: chain 'G' and resid 25 through 30 removed outlier: 3.709A pdb=" N ARG G 59 " --> pdb=" O ILE G 30 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 42 through 47 removed outlier: 3.955A pdb=" N SER G 158 " --> pdb=" O PHE G 32 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 210 through 211 Processing sheet with id=AC4, first strand: chain 'G' and resid 270 through 273 Processing sheet with id=AC5, first strand: chain 'M' and resid 38 through 41 removed outlier: 4.694A pdb=" N GLY M 39 " --> pdb=" O SER M 136 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG M 135 " --> pdb=" O ARG M 179 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG M 179 " --> pdb=" O ARG M 135 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU M 177 " --> pdb=" O ILE M 137 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TYR M 7 " --> pdb=" O GLU M 230 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU M 230 " --> pdb=" O TYR M 7 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE M 9 " --> pdb=" O VAL M 228 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL M 228 " --> pdb=" O PHE M 9 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE M 11 " --> pdb=" O LEU M 226 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU M 226 " --> pdb=" O PHE M 11 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE M 13 " --> pdb=" O ARG M 224 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ARG M 224 " --> pdb=" O PHE M 13 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N VAL M 15 " --> pdb=" O ASN M 222 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASN M 222 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP M 17 " --> pdb=" O GLN M 220 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 143 through 145 Processing sheet with id=AC7, first strand: chain 'M' and resid 148 through 149 Processing sheet with id=AC8, first strand: chain 'M' and resid 248 through 251 Processing sheet with id=AC9, first strand: chain 'N' and resid 47 through 56 removed outlier: 5.581A pdb=" N TRP N 49 " --> pdb=" O ASP N 107 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP N 107 " --> pdb=" O TRP N 49 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N VAL N 51 " --> pdb=" O ASP N 105 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP N 105 " --> pdb=" O VAL N 51 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 23 through 24 removed outlier: 3.511A pdb=" N MET N 93 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 171 through 172 930 hydrogen bonds defined for protein. 2568 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 4.89 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7501 1.33 - 1.45: 4380 1.45 - 1.57: 13796 1.57 - 1.69: 159 1.69 - 1.81: 184 Bond restraints: 26020 Sorted by residual: bond pdb=" N9 DA O 16 " pdb=" C4 DA O 16 " ideal model delta sigma weight residual 1.374 1.390 -0.016 6.00e-03 2.78e+04 7.24e+00 bond pdb=" C1' DC L 56 " pdb=" N1 DC L 56 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.67e+00 bond pdb=" C1' DC L 39 " pdb=" N1 DC L 39 " ideal model delta sigma weight residual 1.468 1.501 -0.033 1.40e-02 5.10e+03 5.48e+00 bond pdb=" C5' DT L 55 " pdb=" C4' DT L 55 " ideal model delta sigma weight residual 1.512 1.528 -0.016 7.00e-03 2.04e+04 5.25e+00 bond pdb=" C1' DT L 51 " pdb=" N1 DT L 51 " ideal model delta sigma weight residual 1.468 1.500 -0.032 1.40e-02 5.10e+03 5.24e+00 ... (remaining 26015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 34347 1.28 - 2.56: 894 2.56 - 3.84: 169 3.84 - 5.12: 21 5.12 - 6.40: 14 Bond angle restraints: 35445 Sorted by residual: angle pdb=" C MET B 167 " pdb=" CA MET B 167 " pdb=" CB MET B 167 " ideal model delta sigma weight residual 115.79 109.56 6.23 1.19e+00 7.06e-01 2.74e+01 angle pdb=" O4' DC L 53 " pdb=" C4' DC L 53 " pdb=" C3' DC L 53 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.63e+01 angle pdb=" C3' G K 4 " pdb=" O3' G K 4 " pdb=" P A K 5 " ideal model delta sigma weight residual 119.70 125.76 -6.06 1.20e+00 6.94e-01 2.55e+01 angle pdb=" O4' U K 13 " pdb=" C1' U K 13 " pdb=" N1 U K 13 " ideal model delta sigma weight residual 108.20 111.90 -3.70 8.00e-01 1.56e+00 2.14e+01 angle pdb=" C ALA A 26 " pdb=" CA ALA A 26 " pdb=" CB ALA A 26 " ideal model delta sigma weight residual 117.07 110.67 6.40 1.44e+00 4.82e-01 1.98e+01 ... (remaining 35440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 15216 35.82 - 71.63: 376 71.63 - 107.45: 34 107.45 - 143.27: 2 143.27 - 179.09: 3 Dihedral angle restraints: 15631 sinusoidal: 7117 harmonic: 8514 Sorted by residual: dihedral pdb=" C4' C K 34 " pdb=" C3' C K 34 " pdb=" C2' C K 34 " pdb=" C1' C K 34 " ideal model delta sinusoidal sigma weight residual -35.00 33.45 -68.45 1 8.00e+00 1.56e-02 9.49e+01 dihedral pdb=" C5' C K 34 " pdb=" C4' C K 34 " pdb=" C3' C K 34 " pdb=" O3' C K 34 " ideal model delta sinusoidal sigma weight residual 147.00 82.52 64.48 1 8.00e+00 1.56e-02 8.54e+01 dihedral pdb=" O4' C K 34 " pdb=" C2' C K 34 " pdb=" C1' C K 34 " pdb=" C3' C K 34 " ideal model delta sinusoidal sigma weight residual -35.00 22.42 -57.42 1 8.00e+00 1.56e-02 6.92e+01 ... (remaining 15628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3371 0.059 - 0.117: 446 0.117 - 0.176: 33 0.176 - 0.235: 2 0.235 - 0.293: 1 Chirality restraints: 3853 Sorted by residual: chirality pdb=" C3' C K 34 " pdb=" C4' C K 34 " pdb=" O3' C K 34 " pdb=" C2' C K 34 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C3' G K 4 " pdb=" C4' G K 4 " pdb=" O3' G K 4 " pdb=" C2' G K 4 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C3' A K 9 " pdb=" C4' A K 9 " pdb=" O3' A K 9 " pdb=" C2' A K 9 " both_signs ideal model delta sigma weight residual False -2.74 -2.53 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 3850 not shown) Planarity restraints: 4393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U K 13 " 0.026 2.00e-02 2.50e+03 1.40e-02 4.41e+00 pdb=" N1 U K 13 " -0.031 2.00e-02 2.50e+03 pdb=" C2 U K 13 " 0.003 2.00e-02 2.50e+03 pdb=" O2 U K 13 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U K 13 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U K 13 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U K 13 " 0.008 2.00e-02 2.50e+03 pdb=" C5 U K 13 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U K 13 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U K 19 " 0.017 2.00e-02 2.50e+03 9.51e-03 2.03e+00 pdb=" N1 U K 19 " -0.022 2.00e-02 2.50e+03 pdb=" C2 U K 19 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U K 19 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U K 19 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U K 19 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U K 19 " 0.004 2.00e-02 2.50e+03 pdb=" C5 U K 19 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U K 19 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G K 12 " 0.017 2.00e-02 2.50e+03 7.81e-03 1.83e+00 pdb=" N9 G K 12 " -0.021 2.00e-02 2.50e+03 pdb=" C8 G K 12 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G K 12 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G K 12 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G K 12 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G K 12 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G K 12 " 0.000 2.00e-02 2.50e+03 pdb=" C2 G K 12 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G K 12 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G K 12 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G K 12 " -0.001 2.00e-02 2.50e+03 ... (remaining 4390 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 919 2.71 - 3.26: 25436 3.26 - 3.80: 42445 3.80 - 4.35: 55472 4.35 - 4.90: 90370 Nonbonded interactions: 214642 Sorted by model distance: nonbonded pdb=" NH2 ARG E 68 " pdb=" O2' G K 41 " model vdw 2.159 3.120 nonbonded pdb=" O THR B 148 " pdb=" O2' U K 19 " model vdw 2.164 3.040 nonbonded pdb=" OE2 GLU C 144 " pdb=" OG SER J 43 " model vdw 2.179 3.040 nonbonded pdb=" N2 G K 16 " pdb=" O2 DC L 39 " model vdw 2.180 3.120 nonbonded pdb=" N2 G K 11 " pdb=" O2 DC L 44 " model vdw 2.195 2.496 ... (remaining 214637 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'B' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'C' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'D' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'E' and (resid 2 through 74 or resid 94 through 152 or resid 165 through \ 284)) selection = (chain 'F' and (resid 2 through 74 or resid 94 through 284)) selection = (chain 'M' and (resid 2 through 152 or resid 165 through 284)) } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 23.920 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4605 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26020 Z= 0.162 Angle : 0.503 6.402 35445 Z= 0.341 Chirality : 0.040 0.293 3853 Planarity : 0.003 0.033 4393 Dihedral : 14.145 179.085 10157 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 2.22 % Allowed : 15.25 % Favored : 82.53 % Rotamer: Outliers : 2.25 % Allowed : 5.48 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.13), residues: 2931 helix: -0.61 (0.16), residues: 926 sheet: -1.34 (0.21), residues: 538 loop : -3.71 (0.12), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 16 TYR 0.010 0.001 TYR G 250 PHE 0.011 0.001 PHE M 9 TRP 0.005 0.001 TRP G 342 HIS 0.002 0.000 HIS G 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.16 (26020) covalent geometry : angle 0.50281 / 0.34 (35445) hydrogen bonds : bond 0.12688 / 8.73 ( 901) hydrogen bonds : angle 5.71679 / 4.06 ( 2614) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 804 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 THR cc_start: 0.4155 (m) cc_final: 0.3922 (p) REVERT: B 226 LEU cc_start: 0.4517 (tp) cc_final: 0.3964 (tt) REVERT: C 54 ILE cc_start: 0.5029 (mt) cc_final: 0.4819 (mt) REVERT: E 49 LYS cc_start: 0.6911 (mttm) cc_final: 0.6681 (tttm) REVERT: E 150 MET cc_start: 0.4004 (ptp) cc_final: 0.2837 (mpp) REVERT: E 172 THR cc_start: 0.6033 (t) cc_final: 0.5792 (t) REVERT: E 247 ILE cc_start: 0.1228 (mm) cc_final: 0.0993 (mm) REVERT: F 4 GLU cc_start: 0.7297 (pp20) cc_final: 0.7096 (pm20) REVERT: F 134 SER cc_start: 0.5896 (m) cc_final: 0.5291 (t) REVERT: G 81 LEU cc_start: 0.8041 (mm) cc_final: 0.7827 (mm) REVERT: G 87 TYR cc_start: 0.4009 (m-80) cc_final: 0.2940 (m-80) REVERT: H 536 ILE cc_start: 0.5485 (tt) cc_final: 0.5024 (tt) REVERT: I 24 ILE cc_start: 0.8262 (mm) cc_final: 0.7890 (mm) REVERT: I 41 PHE cc_start: 0.6905 (t80) cc_final: 0.6603 (t80) REVERT: I 97 GLN cc_start: 0.7850 (mm110) cc_final: 0.7628 (mm-40) REVERT: M 265 LEU cc_start: 0.6470 (tt) cc_final: 0.6266 (mt) REVERT: N 93 MET cc_start: 0.6076 (mtm) cc_final: 0.5775 (mtm) outliers start: 57 outliers final: 18 residues processed: 843 average time/residue: 0.1760 time to fit residues: 223.9083 Evaluate side-chains 453 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 435 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 252 LYS Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain G residue 9 TYR Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 250 TYR Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain N residue 47 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN A 191 GLN ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN B 81 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 145 HIS B 222 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 HIS C 83 GLN C 214 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN D 63 HIS D 214 HIS ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN E 248 GLN E 272 ASN F 55 GLN F 58 GLN F 83 GLN F 181 HIS F 212 HIS F 231 HIS G 79 ASN ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 383 ASN ** H 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 427 GLN H 442 ASN ** H 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 486 ASN H 521 ASN H 531 GLN H 538 GLN H 549 HIS I 8 GLN I 81 GLN I 97 GLN J 8 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN M 121 ASN M 124 GLN ** M 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.180818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.164104 restraints weight = 72243.836| |-----------------------------------------------------------------------------| r_work (start): 0.4673 rms_B_bonded: 3.55 r_work: 0.4558 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 26020 Z= 0.312 Angle : 0.909 10.518 35445 Z= 0.481 Chirality : 0.053 0.458 3853 Planarity : 0.007 0.067 4393 Dihedral : 17.286 175.045 4375 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.96 % Favored : 89.66 % Rotamer: Outliers : 4.65 % Allowed : 14.08 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.14), residues: 2931 helix: -0.40 (0.16), residues: 950 sheet: -1.19 (0.21), residues: 580 loop : -3.26 (0.14), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG J 80 TYR 0.039 0.004 TYR H 374 PHE 0.036 0.004 PHE C 244 TRP 0.042 0.005 TRP H 534 HIS 0.018 0.003 HIS G 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.31 (26020) covalent geometry : angle 0.90949 / 0.48 (35445) hydrogen bonds : bond 0.05937 / 3.83 ( 901) hydrogen bonds : angle 5.14207 / 3.63 ( 2614) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 488 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7869 (ttm170) REVERT: B 220 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.6740 (tp-100) REVERT: C 220 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6509 (pt0) REVERT: D 8 ASP cc_start: 0.7342 (t0) cc_final: 0.6870 (m-30) REVERT: D 9 PHE cc_start: 0.3781 (p90) cc_final: 0.3448 (p90) REVERT: D 105 ARG cc_start: 0.5060 (ttt90) cc_final: 0.4639 (ptm160) REVERT: D 245 LYS cc_start: 0.7533 (mmmt) cc_final: 0.7173 (tppt) REVERT: E 5 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8515 (ptpt) REVERT: E 7 TYR cc_start: 0.5720 (m-80) cc_final: 0.5376 (m-80) REVERT: E 221 MET cc_start: 0.4968 (OUTLIER) cc_final: 0.3699 (ttm) REVERT: E 271 LYS cc_start: 0.7706 (mttt) cc_final: 0.7405 (mmtt) REVERT: F 69 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7476 (mm-30) REVERT: F 93 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7728 (tm-30) REVERT: F 141 MET cc_start: -0.0303 (mpp) cc_final: -0.1215 (tmm) REVERT: F 221 MET cc_start: 0.1270 (ptp) cc_final: 0.1054 (ttp) REVERT: G 80 LEU cc_start: 0.7083 (mt) cc_final: 0.6573 (mm) REVERT: G 82 TRP cc_start: 0.6758 (p-90) cc_final: 0.6541 (p-90) REVERT: G 141 MET cc_start: 0.7354 (mpp) cc_final: 0.7068 (mpp) REVERT: G 142 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7677 (mp10) REVERT: G 247 MET cc_start: 0.8484 (tmm) cc_final: 0.8066 (tmm) REVERT: G 254 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7820 (tp) REVERT: G 324 LYS cc_start: 0.8007 (ptmm) cc_final: 0.7755 (mmtt) REVERT: H 460 LEU cc_start: 0.5802 (tp) cc_final: 0.5438 (tp) REVERT: H 536 ILE cc_start: 0.7239 (OUTLIER) cc_final: 0.6889 (tt) REVERT: I 24 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7890 (mm) REVERT: I 71 ARG cc_start: 0.5453 (ttm170) cc_final: 0.5219 (ttm170) REVERT: M 56 MET cc_start: 0.3265 (mmp) cc_final: 0.2860 (mmm) REVERT: M 265 LEU cc_start: 0.7467 (tt) cc_final: 0.7203 (mt) REVERT: N 21 VAL cc_start: 0.7675 (m) cc_final: 0.7437 (m) outliers start: 118 outliers final: 60 residues processed: 570 average time/residue: 0.1712 time to fit residues: 151.0944 Evaluate side-chains 449 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 382 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 183 PHE Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain G residue 9 TYR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 325 PHE Chi-restraints excluded: chain G residue 343 HIS Chi-restraints excluded: chain H residue 416 LEU Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 536 ILE Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 77 TRP Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 186 THR Chi-restraints excluded: chain M residue 255 VAL Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 177 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 286 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 221 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS B 83 GLN B 145 HIS ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 ASN ** F 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 HIS ** F 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 HIS G 183 ASN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 HIS I 97 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 ASN N 61 GLN ** N 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN N 133 GLN N 166 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.181043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.164006 restraints weight = 72180.743| |-----------------------------------------------------------------------------| r_work (start): 0.4667 rms_B_bonded: 3.58 r_work: 0.4551 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.4551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26020 Z= 0.176 Angle : 0.700 11.367 35445 Z= 0.367 Chirality : 0.046 0.431 3853 Planarity : 0.005 0.118 4393 Dihedral : 17.033 179.268 4366 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.46 % Favored : 88.20 % Rotamer: Outliers : 4.22 % Allowed : 16.76 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.15), residues: 2931 helix: -0.07 (0.16), residues: 952 sheet: -0.92 (0.22), residues: 562 loop : -3.13 (0.14), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 7 TYR 0.025 0.002 TYR H 440 PHE 0.035 0.002 PHE D 53 TRP 0.028 0.003 TRP F 203 HIS 0.012 0.001 HIS G 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (26020) covalent geometry : angle 0.69995 / 0.37 (35445) hydrogen bonds : bond 0.05411 / 3.27 ( 901) hydrogen bonds : angle 4.90441 / 3.50 ( 2614) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 430 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.7150 (mm-40) cc_final: 0.6905 (mm110) REVERT: A 194 PHE cc_start: 0.2900 (t80) cc_final: 0.2571 (m-80) REVERT: A 245 LYS cc_start: 0.6341 (mttt) cc_final: 0.5764 (ttpt) REVERT: B 220 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7232 (tp-100) REVERT: C 96 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7449 (tp30) REVERT: C 220 GLN cc_start: 0.6927 (OUTLIER) cc_final: 0.6441 (pt0) REVERT: D 16 GLN cc_start: 0.6832 (mp10) cc_final: 0.6380 (mm-40) REVERT: D 171 PHE cc_start: 0.7889 (m-80) cc_final: 0.7663 (m-80) REVERT: D 245 LYS cc_start: 0.7275 (mmmt) cc_final: 0.7038 (tppt) REVERT: E 204 GLN cc_start: 0.7907 (tp40) cc_final: 0.7387 (tp-100) REVERT: E 221 MET cc_start: 0.5383 (mtp) cc_final: 0.3997 (mtm) REVERT: E 271 LYS cc_start: 0.7729 (mttt) cc_final: 0.7379 (mmtt) REVERT: F 221 MET cc_start: 0.1471 (ptp) cc_final: 0.0871 (ptp) REVERT: F 231 HIS cc_start: 0.5187 (OUTLIER) cc_final: 0.4660 (t70) REVERT: G 141 MET cc_start: 0.7359 (mpp) cc_final: 0.6968 (mpp) REVERT: G 142 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7644 (mp10) REVERT: G 204 ILE cc_start: 0.6101 (OUTLIER) cc_final: 0.5813 (tt) REVERT: G 324 LYS cc_start: 0.8031 (ptmm) cc_final: 0.7754 (mmtm) REVERT: H 431 TYR cc_start: 0.5728 (OUTLIER) cc_final: 0.4552 (t80) REVERT: H 474 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8500 (tp) REVERT: I 24 ILE cc_start: 0.8216 (mm) cc_final: 0.7925 (mm) REVERT: I 97 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8163 (mm-40) REVERT: J 56 MET cc_start: 0.6559 (mmt) cc_final: 0.6145 (mmp) REVERT: M 209 MET cc_start: 0.5812 (ppp) cc_final: 0.5409 (ttp) REVERT: M 265 LEU cc_start: 0.7247 (tt) cc_final: 0.7023 (mt) REVERT: M 280 ARG cc_start: 0.6513 (mpp80) cc_final: 0.6111 (mtm-85) REVERT: N 21 VAL cc_start: 0.7627 (m) cc_final: 0.7424 (m) outliers start: 107 outliers final: 56 residues processed: 505 average time/residue: 0.1550 time to fit residues: 122.7865 Evaluate side-chains 423 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 360 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 231 HIS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 325 PHE Chi-restraints excluded: chain G residue 343 HIS Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 431 TYR Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain H residue 474 LEU Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 77 TRP Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 228 VAL Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 35 ARG Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 214 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 chunk 237 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 chunk 60 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 199 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS B 145 HIS B 187 HIS ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 HIS ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 GLN ** G 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 549 HIS ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 GLN M 121 ASN ** N 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.172756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.153222 restraints weight = 69860.252| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 3.68 r_work: 0.4354 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 26020 Z= 0.245 Angle : 0.783 9.729 35445 Z= 0.410 Chirality : 0.049 0.445 3853 Planarity : 0.006 0.115 4393 Dihedral : 17.107 177.668 4364 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 24.15 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.68 % Favored : 89.01 % Rotamer: Outliers : 5.48 % Allowed : 17.03 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.14), residues: 2931 helix: -0.22 (0.16), residues: 962 sheet: -0.86 (0.24), residues: 479 loop : -3.08 (0.13), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 59 TYR 0.028 0.003 TYR J 106 PHE 0.033 0.003 PHE C 11 TRP 0.023 0.003 TRP J 77 HIS 0.013 0.002 HIS G 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.24 (26020) covalent geometry : angle 0.78253 / 0.41 (35445) hydrogen bonds : bond 0.05682 / 3.48 ( 901) hydrogen bonds : angle 5.14131 / 3.65 ( 2614) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 416 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.7760 (t0) cc_final: 0.7509 (t0) REVERT: A 100 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7126 (mm110) REVERT: A 150 MET cc_start: 0.4273 (OUTLIER) cc_final: 0.4010 (mtt) REVERT: A 171 PHE cc_start: 0.8474 (m-80) cc_final: 0.8182 (m-80) REVERT: B 144 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6308 (mp0) REVERT: B 160 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5166 (mt-10) REVERT: C 82 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6536 (pp20) REVERT: C 96 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7519 (tp30) REVERT: D 8 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6854 (m-30) REVERT: D 16 GLN cc_start: 0.7267 (mp10) cc_final: 0.6626 (mm-40) REVERT: D 171 PHE cc_start: 0.8075 (m-80) cc_final: 0.7663 (m-80) REVERT: E 132 THR cc_start: 0.6923 (p) cc_final: 0.6467 (t) REVERT: E 221 MET cc_start: 0.4757 (OUTLIER) cc_final: 0.4067 (mtm) REVERT: E 264 TYR cc_start: 0.4659 (t80) cc_final: 0.4395 (t80) REVERT: F 112 PHE cc_start: 0.7062 (m-10) cc_final: 0.6848 (m-10) REVERT: F 177 LEU cc_start: 0.2821 (mt) cc_final: 0.2494 (mt) REVERT: F 221 MET cc_start: 0.2054 (ptp) cc_final: 0.1193 (ptp) REVERT: F 224 ARG cc_start: 0.7675 (mtt-85) cc_final: 0.7200 (mtt-85) REVERT: G 1 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.7090 (ppp) REVERT: G 28 LYS cc_start: 0.8284 (tptt) cc_final: 0.7824 (tptt) REVERT: G 80 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6393 (mm) REVERT: G 236 GLN cc_start: 0.6224 (OUTLIER) cc_final: 0.5900 (tm-30) REVERT: G 254 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7909 (tp) REVERT: G 324 LYS cc_start: 0.8250 (ptmm) cc_final: 0.7592 (mmtt) REVERT: H 431 TYR cc_start: 0.6601 (OUTLIER) cc_final: 0.4985 (t80) REVERT: H 460 LEU cc_start: 0.5170 (OUTLIER) cc_final: 0.4873 (tp) REVERT: I 88 ARG cc_start: 0.5835 (mmp-170) cc_final: 0.5376 (mmp-170) REVERT: I 97 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7956 (mm-40) REVERT: J 110 GLN cc_start: 0.7814 (tp40) cc_final: 0.7587 (tp-100) REVERT: M 33 ASP cc_start: 0.6447 (OUTLIER) cc_final: 0.5896 (t0) REVERT: M 70 LYS cc_start: 0.6778 (tptt) cc_final: 0.6432 (tppt) REVERT: M 265 LEU cc_start: 0.7569 (tt) cc_final: 0.7238 (mt) REVERT: M 280 ARG cc_start: 0.6555 (mpp80) cc_final: 0.6265 (ttp-170) REVERT: N 21 VAL cc_start: 0.8189 (m) cc_final: 0.7985 (m) REVERT: N 72 THR cc_start: 0.6558 (p) cc_final: 0.6308 (p) REVERT: N 74 MET cc_start: 0.5618 (mtp) cc_final: 0.5361 (mtm) outliers start: 139 outliers final: 77 residues processed: 516 average time/residue: 0.1528 time to fit residues: 125.0005 Evaluate side-chains 438 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 348 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain F residue 134 SER Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 224 VAL Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 325 PHE Chi-restraints excluded: chain G residue 343 HIS Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 398 ILE Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 431 TYR Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain H residue 454 LYS Chi-restraints excluded: chain H residue 460 LEU Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 77 TRP Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 33 ASP Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 35 ARG Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 9.9990 chunk 216 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 227 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS B 145 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 GLN C 63 HIS ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 130 GLN G 186 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 GLN ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 GLN ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.167441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.146770 restraints weight = 68619.998| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 3.73 r_work: 0.4264 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.6716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 26020 Z= 0.266 Angle : 0.780 16.544 35445 Z= 0.410 Chirality : 0.049 0.478 3853 Planarity : 0.005 0.057 4393 Dihedral : 17.200 179.457 4362 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 26.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.36 % Favored : 88.37 % Rotamer: Outliers : 5.17 % Allowed : 19.01 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.14), residues: 2931 helix: -0.33 (0.16), residues: 960 sheet: -1.10 (0.23), residues: 505 loop : -3.03 (0.14), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 259 TYR 0.026 0.003 TYR B 107 PHE 0.032 0.003 PHE C 11 TRP 0.039 0.004 TRP G 82 HIS 0.031 0.002 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.27 (26020) covalent geometry : angle 0.77996 / 0.41 (35445) hydrogen bonds : bond 0.05810 / 3.53 ( 901) hydrogen bonds : angle 5.29336 / 3.76 ( 2614) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 392 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.7855 (t0) cc_final: 0.7552 (t0) REVERT: A 150 MET cc_start: 0.4555 (OUTLIER) cc_final: 0.4294 (mtt) REVERT: A 153 THR cc_start: 0.6775 (OUTLIER) cc_final: 0.6422 (p) REVERT: A 171 PHE cc_start: 0.8533 (m-80) cc_final: 0.8171 (m-80) REVERT: A 200 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6631 (mm-30) REVERT: B 160 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.5554 (mt-10) REVERT: C 56 MET cc_start: 0.6570 (ptp) cc_final: 0.6111 (ptm) REVERT: C 96 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7631 (tp30) REVERT: D 16 GLN cc_start: 0.7436 (mp10) cc_final: 0.6799 (mm-40) REVERT: D 171 PHE cc_start: 0.8169 (m-80) cc_final: 0.7701 (m-80) REVERT: E 5 LYS cc_start: 0.8894 (ptpt) cc_final: 0.8644 (ptpt) REVERT: E 172 THR cc_start: 0.7579 (m) cc_final: 0.6944 (p) REVERT: E 221 MET cc_start: 0.5063 (OUTLIER) cc_final: 0.4339 (mtm) REVERT: E 264 TYR cc_start: 0.4764 (t80) cc_final: 0.4408 (t80) REVERT: F 112 PHE cc_start: 0.7769 (m-10) cc_final: 0.7443 (m-10) REVERT: F 133 PHE cc_start: 0.6474 (t80) cc_final: 0.6064 (t80) REVERT: F 221 MET cc_start: 0.2090 (ptp) cc_final: 0.1118 (ptp) REVERT: G 1 MET cc_start: 0.7729 (ppp) cc_final: 0.7415 (ppp) REVERT: G 80 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6515 (mm) REVERT: G 82 TRP cc_start: 0.7849 (p-90) cc_final: 0.7275 (p-90) REVERT: G 324 LYS cc_start: 0.8217 (ptmm) cc_final: 0.7539 (mmtt) REVERT: H 431 TYR cc_start: 0.6760 (OUTLIER) cc_final: 0.5442 (t80) REVERT: H 454 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6776 (pttm) REVERT: H 536 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7001 (tt) REVERT: H 537 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6518 (mtm-85) REVERT: I 24 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8363 (mm) REVERT: I 97 GLN cc_start: 0.8409 (mm-40) cc_final: 0.8181 (mm-40) REVERT: I 101 PHE cc_start: 0.8251 (t80) cc_final: 0.7963 (t80) REVERT: J 97 GLN cc_start: 0.8354 (mp10) cc_final: 0.8015 (pm20) REVERT: J 110 GLN cc_start: 0.8004 (tp40) cc_final: 0.7558 (tp-100) REVERT: M 53 PHE cc_start: 0.7483 (t80) cc_final: 0.7215 (t80) REVERT: M 265 LEU cc_start: 0.8097 (tt) cc_final: 0.7725 (mt) REVERT: M 280 ARG cc_start: 0.6706 (mpp80) cc_final: 0.6123 (ttp-170) REVERT: N 72 THR cc_start: 0.7437 (p) cc_final: 0.7169 (p) outliers start: 131 outliers final: 80 residues processed: 484 average time/residue: 0.1611 time to fit residues: 123.1947 Evaluate side-chains 430 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 339 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 HIS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 21 ASN Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 250 TYR Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 343 HIS Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 431 TYR Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain H residue 454 LYS Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 481 ILE Chi-restraints excluded: chain H residue 536 ILE Chi-restraints excluded: chain H residue 537 ARG Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 77 TRP Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 35 ARG Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 238 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 289 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 292 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS D 124 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 GLN M 121 ASN ** N 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.168990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.148692 restraints weight = 69724.287| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 3.71 r_work: 0.4289 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.6893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26020 Z= 0.176 Angle : 0.717 12.485 35445 Z= 0.372 Chirality : 0.047 0.440 3853 Planarity : 0.005 0.068 4393 Dihedral : 17.129 179.090 4357 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 24.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.61 % Favored : 89.15 % Rotamer: Outliers : 4.06 % Allowed : 20.94 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.15), residues: 2931 helix: -0.13 (0.17), residues: 940 sheet: -0.89 (0.24), residues: 482 loop : -2.86 (0.14), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 224 TYR 0.030 0.002 TYR C 107 PHE 0.036 0.003 PHE C 11 TRP 0.018 0.002 TRP J 77 HIS 0.011 0.001 HIS G 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (26020) covalent geometry : angle 0.71694 / 0.37 (35445) hydrogen bonds : bond 0.05494 / 3.31 ( 901) hydrogen bonds : angle 5.17189 / 3.65 ( 2614) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 396 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.7974 (t0) cc_final: 0.7646 (t0) REVERT: A 56 MET cc_start: 0.5716 (ttt) cc_final: 0.5067 (tpt) REVERT: A 103 CYS cc_start: 0.8476 (m) cc_final: 0.7733 (m) REVERT: A 150 MET cc_start: 0.4475 (OUTLIER) cc_final: 0.4271 (mtt) REVERT: A 171 PHE cc_start: 0.8489 (m-80) cc_final: 0.7918 (m-80) REVERT: A 200 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6643 (mm-30) REVERT: A 277 LYS cc_start: -0.0419 (OUTLIER) cc_final: -0.0820 (mtpp) REVERT: B 111 THR cc_start: 0.4259 (m) cc_final: 0.4017 (m) REVERT: B 160 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.5574 (mt-10) REVERT: B 194 PHE cc_start: 0.3479 (OUTLIER) cc_final: 0.2549 (m-80) REVERT: C 56 MET cc_start: 0.6113 (ptp) cc_final: 0.5775 (ptm) REVERT: C 96 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7659 (tp30) REVERT: D 16 GLN cc_start: 0.7353 (mp10) cc_final: 0.6731 (mm-40) REVERT: D 124 GLN cc_start: 0.4252 (OUTLIER) cc_final: 0.4029 (mm110) REVERT: D 171 PHE cc_start: 0.8179 (m-80) cc_final: 0.7726 (m-80) REVERT: D 183 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.7350 (m-80) REVERT: E 38 GLU cc_start: 0.4837 (pp20) cc_final: 0.4100 (mp0) REVERT: E 146 SER cc_start: 0.8456 (t) cc_final: 0.8254 (t) REVERT: E 172 THR cc_start: 0.7314 (m) cc_final: 0.6673 (p) REVERT: E 221 MET cc_start: 0.4901 (mtp) cc_final: 0.4203 (mtm) REVERT: E 227 TYR cc_start: 0.4906 (m-80) cc_final: 0.4246 (m-80) REVERT: E 264 TYR cc_start: 0.4809 (t80) cc_final: 0.4548 (t80) REVERT: F 112 PHE cc_start: 0.7740 (m-10) cc_final: 0.7373 (m-10) REVERT: F 133 PHE cc_start: 0.6482 (t80) cc_final: 0.6083 (t80) REVERT: F 221 MET cc_start: 0.1782 (ptp) cc_final: 0.0923 (ptp) REVERT: G 80 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6307 (mm) REVERT: G 82 TRP cc_start: 0.7816 (p-90) cc_final: 0.7184 (p-90) REVERT: G 324 LYS cc_start: 0.8223 (ptmm) cc_final: 0.7567 (mmtt) REVERT: H 431 TYR cc_start: 0.6720 (OUTLIER) cc_final: 0.5353 (t80) REVERT: I 24 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8363 (mm) REVERT: I 97 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8320 (mm-40) REVERT: J 89 PHE cc_start: 0.3851 (OUTLIER) cc_final: 0.1761 (t80) REVERT: J 97 GLN cc_start: 0.8254 (mp10) cc_final: 0.8051 (pm20) REVERT: J 110 GLN cc_start: 0.7924 (tp40) cc_final: 0.7491 (tp-100) REVERT: M 21 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7574 (t0) REVERT: M 56 MET cc_start: 0.2509 (mmm) cc_final: 0.2285 (mmt) REVERT: M 265 LEU cc_start: 0.8013 (tt) cc_final: 0.7625 (mt) REVERT: M 266 VAL cc_start: 0.4817 (OUTLIER) cc_final: 0.4552 (p) REVERT: M 280 ARG cc_start: 0.6602 (mpp80) cc_final: 0.6254 (ttp-170) REVERT: N 72 THR cc_start: 0.7313 (OUTLIER) cc_final: 0.7066 (p) outliers start: 103 outliers final: 65 residues processed: 468 average time/residue: 0.1520 time to fit residues: 115.1819 Evaluate side-chains 430 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 351 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 250 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 343 HIS Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 431 TYR Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 77 TRP Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 21 ASN Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 221 MET Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 35 ARG Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 272 optimal weight: 0.0970 chunk 114 optimal weight: 0.0670 chunk 253 optimal weight: 0.7980 chunk 187 optimal weight: 0.0020 chunk 95 optimal weight: 0.3980 chunk 250 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 234 optimal weight: 10.0000 chunk 162 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 203 optimal weight: 10.0000 overall best weight: 0.2724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS D 124 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 ASN ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.170781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.150810 restraints weight = 69489.883| |-----------------------------------------------------------------------------| r_work (start): 0.4448 rms_B_bonded: 3.71 r_work: 0.4321 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.6883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26020 Z= 0.152 Angle : 0.699 15.169 35445 Z= 0.361 Chirality : 0.046 0.425 3853 Planarity : 0.004 0.072 4393 Dihedral : 17.052 179.454 4357 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.47 % Favored : 89.25 % Rotamer: Outliers : 3.90 % Allowed : 21.57 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.15), residues: 2931 helix: -0.16 (0.16), residues: 959 sheet: -0.77 (0.25), residues: 481 loop : -2.79 (0.14), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 80 TYR 0.019 0.002 TYR J 106 PHE 0.046 0.002 PHE A 53 TRP 0.018 0.002 TRP J 77 HIS 0.023 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (26020) covalent geometry : angle 0.69947 / 0.36 (35445) hydrogen bonds : bond 0.05250 / 3.16 ( 901) hydrogen bonds : angle 5.07410 / 3.58 ( 2614) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 380 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.7979 (t0) cc_final: 0.7731 (t0) REVERT: A 56 MET cc_start: 0.5178 (ttt) cc_final: 0.4442 (tpt) REVERT: A 103 CYS cc_start: 0.8461 (m) cc_final: 0.7673 (m) REVERT: A 171 PHE cc_start: 0.8260 (m-80) cc_final: 0.7933 (m-80) REVERT: A 200 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6546 (mm-30) REVERT: B 111 THR cc_start: 0.4157 (m) cc_final: 0.3871 (m) REVERT: B 160 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.5568 (mt-10) REVERT: B 194 PHE cc_start: 0.3263 (OUTLIER) cc_final: 0.2439 (m-80) REVERT: C 56 MET cc_start: 0.6398 (ptp) cc_final: 0.6119 (ptm) REVERT: C 82 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6442 (tm-30) REVERT: C 96 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7726 (tp30) REVERT: D 16 GLN cc_start: 0.7283 (mp10) cc_final: 0.6666 (mm-40) REVERT: D 171 PHE cc_start: 0.8271 (m-80) cc_final: 0.7839 (m-80) REVERT: D 183 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7470 (m-80) REVERT: D 209 MET cc_start: 0.6824 (mmm) cc_final: 0.6149 (tpp) REVERT: E 8 ASP cc_start: 0.7315 (p0) cc_final: 0.6979 (m-30) REVERT: E 172 THR cc_start: 0.7116 (m) cc_final: 0.6477 (p) REVERT: E 221 MET cc_start: 0.4415 (mtp) cc_final: 0.3750 (mtm) REVERT: E 227 TYR cc_start: 0.4748 (m-80) cc_final: 0.3979 (m-80) REVERT: F 112 PHE cc_start: 0.7791 (m-10) cc_final: 0.7510 (m-10) REVERT: F 133 PHE cc_start: 0.6398 (t80) cc_final: 0.6069 (t80) REVERT: F 221 MET cc_start: 0.1886 (ptp) cc_final: 0.0516 (ttp) REVERT: G 80 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6298 (mm) REVERT: G 82 TRP cc_start: 0.7762 (p-90) cc_final: 0.7527 (p-90) REVERT: G 324 LYS cc_start: 0.8196 (ptmm) cc_final: 0.7564 (mmtt) REVERT: H 431 TYR cc_start: 0.6640 (OUTLIER) cc_final: 0.5337 (t80) REVERT: H 537 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6502 (mtm-85) REVERT: I 16 ARG cc_start: 0.7383 (mtm180) cc_final: 0.7168 (ttp-170) REVERT: I 24 ILE cc_start: 0.8606 (mm) cc_final: 0.8362 (mm) REVERT: I 97 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8338 (mm-40) REVERT: I 106 TYR cc_start: 0.7548 (m-80) cc_final: 0.7297 (m-80) REVERT: I 108 GLU cc_start: 0.7570 (tp30) cc_final: 0.7200 (tp30) REVERT: J 89 PHE cc_start: 0.3756 (OUTLIER) cc_final: 0.1670 (t80) REVERT: J 97 GLN cc_start: 0.8205 (mp10) cc_final: 0.7989 (pm20) REVERT: J 110 GLN cc_start: 0.7913 (tp40) cc_final: 0.7637 (tp-100) REVERT: M 21 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7526 (t0) REVERT: M 56 MET cc_start: 0.2422 (mmm) cc_final: 0.2081 (mmt) REVERT: M 265 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7535 (mt) REVERT: M 266 VAL cc_start: 0.4680 (OUTLIER) cc_final: 0.4438 (p) REVERT: M 279 LEU cc_start: 0.7528 (tt) cc_final: 0.6504 (pt) REVERT: M 280 ARG cc_start: 0.6452 (mpp80) cc_final: 0.6119 (ttp-170) REVERT: N 5 LEU cc_start: 0.7680 (tt) cc_final: 0.6881 (mm) outliers start: 99 outliers final: 59 residues processed: 452 average time/residue: 0.1559 time to fit residues: 113.3764 Evaluate side-chains 420 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 350 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 197 ASN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 250 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 343 HIS Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 431 TYR Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 537 ARG Chi-restraints excluded: chain H residue 565 GLU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 77 TRP Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 21 ASN Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 121 ASN Chi-restraints excluded: chain M residue 221 MET Chi-restraints excluded: chain M residue 265 LEU Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 235 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 191 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS B 63 HIS B 145 HIS ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.168764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.148451 restraints weight = 69359.908| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 3.71 r_work: 0.4289 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.7111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 26020 Z= 0.182 Angle : 0.713 15.264 35445 Z= 0.370 Chirality : 0.047 0.435 3853 Planarity : 0.004 0.062 4393 Dihedral : 17.042 179.212 4356 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.47 % Favored : 89.25 % Rotamer: Outliers : 3.63 % Allowed : 22.20 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.15), residues: 2931 helix: -0.08 (0.17), residues: 950 sheet: -0.73 (0.25), residues: 481 loop : -2.76 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 88 TYR 0.029 0.002 TYR H 497 PHE 0.040 0.002 PHE A 53 TRP 0.019 0.002 TRP J 77 HIS 0.022 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (26020) covalent geometry : angle 0.71252 / 0.37 (35445) hydrogen bonds : bond 0.05232 / 3.17 ( 901) hydrogen bonds : angle 5.08579 / 3.57 ( 2614) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 359 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.7982 (t0) cc_final: 0.7685 (t0) REVERT: A 56 MET cc_start: 0.5126 (ttt) cc_final: 0.4337 (tpt) REVERT: A 103 CYS cc_start: 0.8429 (m) cc_final: 0.7789 (m) REVERT: A 155 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7270 (mm-30) REVERT: A 171 PHE cc_start: 0.8265 (m-80) cc_final: 0.7988 (m-80) REVERT: A 200 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6574 (mm-30) REVERT: B 111 THR cc_start: 0.4332 (m) cc_final: 0.4048 (m) REVERT: B 194 PHE cc_start: 0.3530 (OUTLIER) cc_final: 0.2636 (m-80) REVERT: C 56 MET cc_start: 0.6455 (ptp) cc_final: 0.6227 (ptm) REVERT: C 82 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6483 (tm-30) REVERT: C 96 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: D 9 PHE cc_start: 0.4929 (p90) cc_final: 0.4603 (p90) REVERT: D 16 GLN cc_start: 0.7353 (mp10) cc_final: 0.6686 (mm-40) REVERT: D 171 PHE cc_start: 0.8308 (m-80) cc_final: 0.7875 (m-80) REVERT: D 209 MET cc_start: 0.6768 (mmm) cc_final: 0.6120 (mmm) REVERT: E 35 GLN cc_start: 0.6557 (mp10) cc_final: 0.5761 (mt0) REVERT: E 38 GLU cc_start: 0.4870 (pp20) cc_final: 0.4114 (mp0) REVERT: E 169 ARG cc_start: 0.7529 (mmm160) cc_final: 0.7272 (mmm-85) REVERT: E 171 PHE cc_start: 0.7279 (m-80) cc_final: 0.6665 (m-10) REVERT: E 172 THR cc_start: 0.7052 (m) cc_final: 0.6356 (p) REVERT: E 221 MET cc_start: 0.4463 (mtp) cc_final: 0.3696 (mtm) REVERT: E 227 TYR cc_start: 0.4718 (m-80) cc_final: 0.3740 (m-80) REVERT: F 112 PHE cc_start: 0.7913 (m-10) cc_final: 0.7587 (m-10) REVERT: F 133 PHE cc_start: 0.6205 (t80) cc_final: 0.5899 (t80) REVERT: F 221 MET cc_start: 0.1424 (ptp) cc_final: 0.0390 (ttp) REVERT: G 80 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6301 (mm) REVERT: G 82 TRP cc_start: 0.7787 (p-90) cc_final: 0.7101 (p-90) REVERT: G 324 LYS cc_start: 0.8215 (ptmm) cc_final: 0.7537 (mmtt) REVERT: H 431 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.5408 (t80) REVERT: H 537 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6450 (mtm-85) REVERT: I 16 ARG cc_start: 0.7430 (mtm180) cc_final: 0.7112 (ttp-170) REVERT: I 20 VAL cc_start: 0.8692 (t) cc_final: 0.8440 (m) REVERT: I 24 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8375 (mm) REVERT: I 108 GLU cc_start: 0.7619 (tp30) cc_final: 0.7079 (tp30) REVERT: J 89 PHE cc_start: 0.3943 (OUTLIER) cc_final: 0.1749 (t80) REVERT: J 97 GLN cc_start: 0.8253 (mp10) cc_final: 0.7580 (pm20) REVERT: J 110 GLN cc_start: 0.7946 (tp40) cc_final: 0.7707 (tp-100) REVERT: M 21 ASN cc_start: 0.7750 (OUTLIER) cc_final: 0.7482 (t0) REVERT: M 56 MET cc_start: 0.2823 (mmm) cc_final: 0.2513 (mmt) REVERT: M 265 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7468 (mt) REVERT: M 266 VAL cc_start: 0.4710 (OUTLIER) cc_final: 0.4486 (p) REVERT: M 279 LEU cc_start: 0.7680 (tt) cc_final: 0.6778 (pt) REVERT: M 280 ARG cc_start: 0.6514 (mpp80) cc_final: 0.6111 (mtm-85) REVERT: N 5 LEU cc_start: 0.7767 (tt) cc_final: 0.6917 (mm) REVERT: N 171 MET cc_start: 0.5158 (mtp) cc_final: 0.4504 (mtm) outliers start: 92 outliers final: 67 residues processed: 425 average time/residue: 0.1509 time to fit residues: 103.3663 Evaluate side-chains 421 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 343 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 250 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 343 HIS Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 398 ILE Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 431 TYR Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 537 ARG Chi-restraints excluded: chain H residue 565 GLU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 77 TRP Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 21 ASN Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 221 MET Chi-restraints excluded: chain M residue 265 LEU Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 98 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 190 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 185 optimal weight: 0.2980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.168615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.148257 restraints weight = 69597.603| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 3.72 r_work: 0.4286 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.7263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 26020 Z= 0.171 Angle : 0.714 15.218 35445 Z= 0.369 Chirality : 0.047 0.436 3853 Planarity : 0.005 0.115 4393 Dihedral : 17.047 179.127 4356 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 24.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.10 % Favored : 89.63 % Rotamer: Outliers : 3.39 % Allowed : 22.63 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.15), residues: 2931 helix: -0.26 (0.16), residues: 980 sheet: -0.78 (0.25), residues: 488 loop : -2.66 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 421 TYR 0.021 0.002 TYR B 107 PHE 0.062 0.002 PHE A 53 TRP 0.019 0.002 TRP J 77 HIS 0.018 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (26020) covalent geometry : angle 0.71398 / 0.37 (35445) hydrogen bonds : bond 0.05245 / 3.18 ( 901) hydrogen bonds : angle 5.08505 / 3.57 ( 2614) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 367 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.7973 (t0) cc_final: 0.7698 (t0) REVERT: A 56 MET cc_start: 0.5194 (ttt) cc_final: 0.4350 (tpt) REVERT: A 103 CYS cc_start: 0.8381 (m) cc_final: 0.7797 (m) REVERT: A 131 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8323 (mt) REVERT: A 171 PHE cc_start: 0.8317 (m-80) cc_final: 0.8015 (m-80) REVERT: A 200 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6606 (mm-30) REVERT: B 111 THR cc_start: 0.4363 (m) cc_final: 0.4069 (m) REVERT: B 194 PHE cc_start: 0.3559 (OUTLIER) cc_final: 0.2694 (m-80) REVERT: C 56 MET cc_start: 0.6476 (ptp) cc_final: 0.6104 (ptm) REVERT: C 82 GLU cc_start: 0.7621 (mt-10) cc_final: 0.6313 (tm-30) REVERT: C 96 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7770 (tp30) REVERT: D 16 GLN cc_start: 0.7344 (mp10) cc_final: 0.6720 (mm-40) REVERT: D 171 PHE cc_start: 0.8307 (m-80) cc_final: 0.7855 (m-80) REVERT: D 209 MET cc_start: 0.6723 (mmm) cc_final: 0.6135 (mmm) REVERT: E 8 ASP cc_start: 0.7398 (p0) cc_final: 0.7039 (m-30) REVERT: E 38 GLU cc_start: 0.4851 (pp20) cc_final: 0.4088 (mp0) REVERT: E 171 PHE cc_start: 0.7232 (m-80) cc_final: 0.6700 (m-10) REVERT: E 172 THR cc_start: 0.6728 (m) cc_final: 0.6080 (p) REVERT: E 221 MET cc_start: 0.4421 (mtp) cc_final: 0.3618 (mtm) REVERT: E 227 TYR cc_start: 0.4814 (m-80) cc_final: 0.3802 (m-80) REVERT: F 133 PHE cc_start: 0.6199 (t80) cc_final: 0.5925 (t80) REVERT: F 221 MET cc_start: 0.1512 (ptp) cc_final: 0.0337 (ttp) REVERT: G 80 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6329 (mm) REVERT: G 82 TRP cc_start: 0.7840 (p-90) cc_final: 0.7126 (p-90) REVERT: G 324 LYS cc_start: 0.8311 (ptmm) cc_final: 0.7628 (mmtt) REVERT: H 431 TYR cc_start: 0.6698 (OUTLIER) cc_final: 0.5057 (t80) REVERT: H 537 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6871 (mtm-85) REVERT: I 16 ARG cc_start: 0.7443 (mtm180) cc_final: 0.7127 (ttp-170) REVERT: I 24 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8373 (mm) REVERT: I 106 TYR cc_start: 0.7238 (m-80) cc_final: 0.6881 (m-80) REVERT: I 108 GLU cc_start: 0.7689 (tp30) cc_final: 0.7103 (tp30) REVERT: J 89 PHE cc_start: 0.3974 (OUTLIER) cc_final: 0.1757 (t80) REVERT: J 110 GLN cc_start: 0.7954 (tp40) cc_final: 0.7514 (tp-100) REVERT: M 21 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7445 (t0) REVERT: M 56 MET cc_start: 0.2914 (mmm) cc_final: 0.2591 (mmt) REVERT: M 148 THR cc_start: 0.8324 (p) cc_final: 0.8060 (p) REVERT: M 265 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7449 (mt) REVERT: M 266 VAL cc_start: 0.4721 (OUTLIER) cc_final: 0.4485 (p) REVERT: M 279 LEU cc_start: 0.7665 (tt) cc_final: 0.6599 (pt) REVERT: M 280 ARG cc_start: 0.6491 (mpp80) cc_final: 0.6125 (ttp-170) REVERT: N 5 LEU cc_start: 0.7656 (tt) cc_final: 0.6968 (mm) REVERT: N 47 ILE cc_start: 0.6448 (OUTLIER) cc_final: 0.6243 (mm) REVERT: N 171 MET cc_start: 0.4769 (mtp) cc_final: 0.3968 (mtm) outliers start: 86 outliers final: 67 residues processed: 429 average time/residue: 0.1395 time to fit residues: 97.0668 Evaluate side-chains 422 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 343 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 250 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 325 PHE Chi-restraints excluded: chain G residue 343 HIS Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 398 ILE Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 431 TYR Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 537 ARG Chi-restraints excluded: chain H residue 565 GLU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 77 TRP Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 21 ASN Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 221 MET Chi-restraints excluded: chain M residue 265 LEU Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 152 LEU Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 282 optimal weight: 3.9990 chunk 261 optimal weight: 0.5980 chunk 271 optimal weight: 3.9990 chunk 190 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 268 optimal weight: 4.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 HIS ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.167209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.146586 restraints weight = 69251.290| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 3.73 r_work: 0.4263 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.7541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26020 Z= 0.184 Angle : 0.738 15.247 35445 Z= 0.381 Chirality : 0.047 0.443 3853 Planarity : 0.005 0.071 4393 Dihedral : 17.056 178.851 4356 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 24.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.51 % Favored : 89.18 % Rotamer: Outliers : 3.43 % Allowed : 22.67 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.15), residues: 2931 helix: -0.24 (0.17), residues: 979 sheet: -0.72 (0.25), residues: 482 loop : -2.67 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 421 TYR 0.021 0.002 TYR B 107 PHE 0.057 0.003 PHE A 53 TRP 0.019 0.002 TRP J 77 HIS 0.034 0.002 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (26020) covalent geometry : angle 0.73771 / 0.38 (35445) hydrogen bonds : bond 0.05277 / 3.20 ( 901) hydrogen bonds : angle 5.12601 / 3.61 ( 2614) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 364 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.8027 (t0) cc_final: 0.7779 (t0) REVERT: A 56 MET cc_start: 0.5234 (ttt) cc_final: 0.4329 (tpt) REVERT: A 103 CYS cc_start: 0.8538 (m) cc_final: 0.7941 (m) REVERT: A 171 PHE cc_start: 0.8124 (m-80) cc_final: 0.7666 (m-80) REVERT: A 200 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6603 (mm-30) REVERT: C 56 MET cc_start: 0.6538 (ptp) cc_final: 0.6169 (ptm) REVERT: C 82 GLU cc_start: 0.7701 (mt-10) cc_final: 0.6406 (tm-30) REVERT: C 96 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7796 (tp30) REVERT: D 16 GLN cc_start: 0.7307 (mp10) cc_final: 0.6640 (mm-40) REVERT: D 171 PHE cc_start: 0.8339 (m-80) cc_final: 0.7897 (m-80) REVERT: D 209 MET cc_start: 0.6869 (mmm) cc_final: 0.6262 (mmm) REVERT: E 8 ASP cc_start: 0.7378 (p0) cc_final: 0.6875 (m-30) REVERT: E 38 GLU cc_start: 0.4934 (pp20) cc_final: 0.4282 (mp0) REVERT: E 221 MET cc_start: 0.4414 (mtp) cc_final: 0.3565 (mtm) REVERT: E 227 TYR cc_start: 0.4546 (m-80) cc_final: 0.3939 (m-80) REVERT: F 93 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7967 (pp20) REVERT: F 221 MET cc_start: 0.1559 (ptp) cc_final: 0.0754 (ttp) REVERT: G 80 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6142 (mm) REVERT: G 82 TRP cc_start: 0.7829 (p-90) cc_final: 0.7544 (p-90) REVERT: G 324 LYS cc_start: 0.8346 (ptmm) cc_final: 0.7589 (mmtt) REVERT: H 431 TYR cc_start: 0.6888 (OUTLIER) cc_final: 0.5039 (t80) REVERT: H 438 LYS cc_start: 0.6230 (OUTLIER) cc_final: 0.5661 (pptt) REVERT: H 497 TYR cc_start: 0.7412 (m-10) cc_final: 0.7174 (m-10) REVERT: H 537 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6825 (mtm-85) REVERT: I 16 ARG cc_start: 0.7370 (mtm180) cc_final: 0.7119 (ttp-170) REVERT: I 24 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8375 (mm) REVERT: I 108 GLU cc_start: 0.7794 (tp30) cc_final: 0.7174 (tp30) REVERT: J 89 PHE cc_start: 0.4158 (OUTLIER) cc_final: 0.1884 (t80) REVERT: J 110 GLN cc_start: 0.7958 (tp40) cc_final: 0.7498 (tp-100) REVERT: M 21 ASN cc_start: 0.7682 (OUTLIER) cc_final: 0.7423 (t0) REVERT: M 56 MET cc_start: 0.3468 (mmm) cc_final: 0.3143 (mmt) REVERT: M 148 THR cc_start: 0.8355 (p) cc_final: 0.8052 (p) REVERT: M 265 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7382 (mt) REVERT: M 266 VAL cc_start: 0.4755 (OUTLIER) cc_final: 0.4526 (p) REVERT: M 279 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.6645 (pt) REVERT: M 280 ARG cc_start: 0.6486 (mpp80) cc_final: 0.6121 (ttp-170) REVERT: N 5 LEU cc_start: 0.7676 (tt) cc_final: 0.6988 (mm) REVERT: N 47 ILE cc_start: 0.6567 (OUTLIER) cc_final: 0.6349 (mm) REVERT: N 171 MET cc_start: 0.4799 (mtp) cc_final: 0.3983 (mtm) outliers start: 87 outliers final: 63 residues processed: 426 average time/residue: 0.1629 time to fit residues: 110.9203 Evaluate side-chains 418 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 343 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 250 TYR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 311 LEU Chi-restraints excluded: chain G residue 343 HIS Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 398 ILE Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 431 TYR Chi-restraints excluded: chain H residue 438 LYS Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 537 ARG Chi-restraints excluded: chain H residue 565 GLU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 21 ASN Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 221 MET Chi-restraints excluded: chain M residue 265 LEU Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 196 optimal weight: 0.6980 chunk 181 optimal weight: 10.0000 chunk 256 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 245 optimal weight: 0.0980 chunk 189 optimal weight: 0.9990 chunk 261 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 281 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 HIS F 181 HIS ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.168625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.148463 restraints weight = 69251.579| |-----------------------------------------------------------------------------| r_work (start): 0.4415 rms_B_bonded: 3.69 r_work: 0.4290 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.7596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26020 Z= 0.154 Angle : 0.725 14.862 35445 Z= 0.373 Chirality : 0.046 0.434 3853 Planarity : 0.005 0.081 4393 Dihedral : 17.029 178.842 4356 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.27 % Favored : 89.42 % Rotamer: Outliers : 2.88 % Allowed : 23.62 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.15), residues: 2931 helix: -0.20 (0.17), residues: 974 sheet: -0.71 (0.25), residues: 472 loop : -2.64 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG I 88 TYR 0.024 0.002 TYR I 106 PHE 0.060 0.003 PHE A 53 TRP 0.016 0.002 TRP J 77 HIS 0.008 0.001 HIS I 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (26020) covalent geometry : angle 0.72495 / 0.37 (35445) hydrogen bonds : bond 0.05228 / 3.14 ( 901) hydrogen bonds : angle 5.08479 / 3.57 ( 2614) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6066.35 seconds wall clock time: 104 minutes 58.28 seconds (6298.28 seconds total)