Starting phenix.real_space_refine on Mon Aug 25 03:50:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gam_29900/08_2025/8gam_29900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gam_29900/08_2025/8gam_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_2025/8gam_29900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gam_29900/08_2025/8gam_29900.map" model { file = "/net/cci-nas-00/data/ceres_data/8gam_29900/08_2025/8gam_29900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gam_29900/08_2025/8gam_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-2.0-5787/lib/python3.9/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: 5.06, 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: 1.89 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.79 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: 3.83 Time building geometry restraints manager: 2.43 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=" CA ALA A 26 " pdb=" C ALA A 26 " ideal model delta sigma weight residual 1.533 1.523 0.010 5.60e-03 3.19e+04 3.23e+00 bond pdb=" C3' G K 4 " pdb=" O3' G K 4 " ideal model delta sigma weight residual 1.427 1.445 -0.018 1.50e-02 4.44e+03 1.47e+00 bond pdb=" C3' A K 9 " pdb=" O3' A K 9 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.24e+00 bond pdb=" C THR C 118 " pdb=" O THR C 118 " ideal model delta sigma weight residual 1.227 1.236 -0.008 7.80e-03 1.64e+04 1.17e+00 bond pdb=" C THR A 118 " pdb=" O THR A 118 " ideal model delta sigma weight residual 1.227 1.236 -0.008 7.80e-03 1.64e+04 1.09e+00 ... (remaining 26015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 34569 1.28 - 2.56: 701 2.56 - 3.84: 139 3.84 - 5.12: 23 5.12 - 6.40: 13 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=" 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 angle pdb=" C THR C 118 " pdb=" CA THR C 118 " pdb=" CB THR C 118 " ideal model delta sigma weight residual 116.54 110.36 6.18 1.46e+00 4.69e-01 1.79e+01 angle pdb=" C THR B 118 " pdb=" CA THR B 118 " pdb=" CB THR B 118 " ideal model delta sigma weight residual 116.54 110.36 6.18 1.46e+00 4.69e-01 1.79e+01 angle pdb=" C THR D 118 " pdb=" CA THR D 118 " pdb=" CB THR D 118 " ideal model delta sigma weight residual 116.54 110.38 6.16 1.46e+00 4.69e-01 1.78e+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: 3440 0.059 - 0.117: 393 0.117 - 0.176: 16 0.176 - 0.235: 3 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=" C2' C K 34 " pdb=" C3' C K 34 " pdb=" O2' C K 34 " pdb=" C1' C K 34 " both_signs ideal model delta sigma weight residual False -2.52 -2.74 0.22 2.00e-01 2.50e+01 1.24e+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 ... (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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.530 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4606 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= 0.101 Angle : 0.472 6.402 35445 Z= 0.271 Chirality : 0.038 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 aren 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 covalent geometry : bond 0.00173 (26020) covalent geometry : angle 0.47183 (35445) hydrogen bonds : bond 0.12688 ( 901) hydrogen bonds : angle 5.71679 ( 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 : 0.713 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: 0.3931 (p) REVERT: B 226 LEU cc_start: 0.4517 (tp) cc_final: 0.3962 (tt) REVERT: C 54 ILE cc_start: 0.5029 (mt) cc_final: 0.4821 (mt) REVERT: D 60 ASP cc_start: 0.2652 (p0) cc_final: 0.2448 (t70) REVERT: E 49 LYS cc_start: 0.6911 (mttm) cc_final: 0.6678 (tttm) REVERT: E 150 MET cc_start: 0.4004 (ptp) cc_final: 0.2834 (mpp) REVERT: E 172 THR cc_start: 0.6033 (t) cc_final: 0.5793 (t) REVERT: E 247 ILE cc_start: 0.1228 (mm) cc_final: 0.1001 (mm) REVERT: F 4 GLU cc_start: 0.7297 (pp20) cc_final: 0.7093 (pm20) REVERT: F 134 SER cc_start: 0.5896 (m) cc_final: 0.5292 (t) REVERT: G 81 LEU cc_start: 0.8041 (mm) cc_final: 0.7825 (mm) REVERT: G 87 TYR cc_start: 0.4009 (m-80) cc_final: 0.2939 (m-80) REVERT: H 536 ILE cc_start: 0.5485 (tt) cc_final: 0.5022 (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: 0.6596 (t80) REVERT: I 97 GLN cc_start: 0.7850 (mm110) cc_final: 0.7627 (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: 0.5774 (mtm) outliers start: 57 outliers final: 18 residues processed: 843 average time/residue: 0.1678 time to fit residues: 211.8811 Evaluate side-chains 455 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 437 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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: 5.9990 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: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 58 GLN A 187 HIS ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS B 58 GLN B 63 HIS B 81 HIS B 83 GLN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS B 222 ASN C 63 HIS 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 58 GLN D 63 HIS D 181 HIS D 214 HIS ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN E 234 ASN E 248 GLN E 272 ASN F 55 GLN ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN F 83 GLN ** F 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 HIS G 44 GLN G 79 ASN ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN G 156 ASN ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 383 ASN ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 427 GLN H 442 ASN H 465 GLN H 521 ASN ** H 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 538 GLN H 542 HIS 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 J 81 GLN J 94 ASN M 55 GLN ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 GLN N 61 GLN ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.173082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.154246 restraints weight = 71111.667| |-----------------------------------------------------------------------------| r_work (start): 0.4520 rms_B_bonded: 3.57 r_work: 0.4396 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 26020 Z= 0.354 Angle : 0.966 21.871 35445 Z= 0.509 Chirality : 0.053 0.320 3853 Planarity : 0.007 0.092 4393 Dihedral : 17.519 177.433 4375 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 26.93 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.20 % Favored : 89.46 % Rotamer: Outliers : 5.40 % Allowed : 14.27 % Favored : 80.32 % 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 aren not related in a simple way. whole: -2.84 (0.14), residues: 2931 helix: -0.67 (0.16), residues: 953 sheet: -1.16 (0.22), residues: 557 loop : -3.13 (0.14), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 110 TYR 0.036 0.004 TYR J 106 PHE 0.039 0.004 PHE C 188 TRP 0.025 0.004 TRP H 534 HIS 0.013 0.003 HIS G 343 Details of bonding type rmsd covalent geometry : bond 0.00744 (26020) covalent geometry : angle 0.96563 (35445) hydrogen bonds : bond 0.06005 ( 901) hydrogen bonds : angle 5.43548 ( 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 638 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 501 time to evaluate : 0.853 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 35 GLN cc_start: 0.7417 (mm-40) cc_final: 0.6942 (tp40) REVERT: A 200 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6410 (mm-30) REVERT: C 8 ASP cc_start: 0.6779 (t0) cc_final: 0.5998 (t0) REVERT: C 181 HIS cc_start: 0.7354 (m-70) cc_final: 0.5965 (m170) REVERT: C 220 GLN cc_start: 0.6968 (OUTLIER) cc_final: 0.6612 (pt0) REVERT: D 16 GLN cc_start: 0.7149 (mp10) cc_final: 0.6534 (mm-40) REVERT: D 56 MET cc_start: 0.6210 (mmm) cc_final: 0.5776 (mmm) REVERT: D 265 LEU cc_start: 0.7193 (mp) cc_final: 0.6809 (pp) REVERT: E 5 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8502 (pttt) REVERT: E 144 GLU cc_start: 0.8090 (tt0) cc_final: 0.7778 (tt0) REVERT: E 204 GLN cc_start: 0.8075 (tp40) cc_final: 0.7451 (tp-100) REVERT: E 221 MET cc_start: 0.5378 (OUTLIER) cc_final: 0.4878 (mtm) REVERT: E 271 LYS cc_start: 0.7797 (mttt) cc_final: 0.7347 (mmtt) REVERT: E 280 ARG cc_start: 0.4285 (ptm160) cc_final: 0.3985 (ptm160) REVERT: F 93 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7696 (tm-30) REVERT: F 134 SER cc_start: 0.5583 (m) cc_final: 0.5195 (t) REVERT: F 141 MET cc_start: 0.0732 (mpp) cc_final: -0.0508 (tmm) REVERT: F 221 MET cc_start: 0.1065 (ptp) cc_final: 0.0834 (ttp) REVERT: G 44 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8133 (mp10) REVERT: G 80 LEU cc_start: 0.7493 (mt) cc_final: 0.6656 (mm) REVERT: G 218 PRO cc_start: 0.7729 (Cg_exo) cc_final: 0.7459 (Cg_endo) REVERT: G 254 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7879 (tp) REVERT: G 324 LYS cc_start: 0.8111 (ptmm) cc_final: 0.7538 (mmtt) REVERT: I 41 PHE cc_start: 0.7636 (t80) cc_final: 0.7354 (t80) REVERT: I 71 ARG cc_start: 0.5537 (OUTLIER) cc_final: 0.5083 (ttm170) REVERT: I 88 ARG cc_start: 0.6128 (mmp-170) cc_final: 0.5877 (mmp-170) REVERT: I 97 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8068 (mm-40) REVERT: J 57 ARG cc_start: 0.7080 (ttp80) cc_final: 0.6438 (ttm170) REVERT: J 116 ASP cc_start: 0.6509 (m-30) cc_final: 0.6279 (t0) REVERT: M 7 TYR cc_start: 0.7120 (m-80) cc_final: 0.6828 (m-80) REVERT: M 33 ASP cc_start: 0.6562 (OUTLIER) cc_final: 0.6142 (t0) REVERT: N 21 VAL cc_start: 0.8169 (m) cc_final: 0.7949 (m) REVERT: N 38 LEU cc_start: 0.7754 (mt) cc_final: 0.7531 (mt) REVERT: N 171 MET cc_start: 0.4868 (mtm) cc_final: 0.4535 (mtm) REVERT: N 198 VAL cc_start: 0.5463 (m) cc_final: 0.4903 (p) outliers start: 137 outliers final: 67 residues processed: 597 average time/residue: 0.1594 time to fit residues: 146.1162 Evaluate side-chains 449 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 376 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 146 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 LEU 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 150 MET 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 C residue 258 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 E residue 29 LEU Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 272 ASN 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 9 TYR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 44 GLN 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 325 PHE Chi-restraints excluded: chain G residue 337 ILE 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 416 LEU Chi-restraints excluded: chain H residue 429 ILE 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 H residue 549 HIS Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 77 TRP Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 43 SER 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 142 THR Chi-restraints excluded: chain M residue 201 LEU 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 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: 10.0000 chunk 105 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 286 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 182 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 145 HIS B 187 HIS ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 ASN ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 GLN F 231 HIS G 44 GLN ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 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** H 486 ASN ** H 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 GLN ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.171720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.151607 restraints weight = 69964.471| |-----------------------------------------------------------------------------| r_work (start): 0.4463 rms_B_bonded: 3.82 r_work: 0.4334 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26020 Z= 0.181 Angle : 0.698 15.737 35445 Z= 0.364 Chirality : 0.044 0.252 3853 Planarity : 0.005 0.071 4393 Dihedral : 17.172 179.443 4366 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.95 % Favored : 88.71 % Rotamer: Outliers : 3.98 % Allowed : 17.51 % Favored : 78.51 % 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 aren not related in a simple way. whole: -2.41 (0.15), residues: 2931 helix: -0.05 (0.17), residues: 949 sheet: -1.04 (0.24), residues: 497 loop : -2.96 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 340 TYR 0.023 0.002 TYR H 440 PHE 0.035 0.002 PHE D 53 TRP 0.022 0.003 TRP J 77 HIS 0.012 0.002 HIS H 549 Details of bonding type rmsd covalent geometry : bond 0.00399 (26020) covalent geometry : angle 0.69812 (35445) hydrogen bonds : bond 0.04942 ( 901) hydrogen bonds : angle 5.11672 ( 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 516 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 415 time to evaluate : 0.852 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 35 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7216 (tp40) REVERT: A 100 GLN cc_start: 0.7899 (mm110) cc_final: 0.7642 (mm110) REVERT: A 103 CYS cc_start: 0.8661 (m) cc_final: 0.7941 (m) REVERT: A 171 PHE cc_start: 0.8538 (m-80) cc_final: 0.8183 (m-80) REVERT: A 200 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6500 (mm-30) REVERT: B 148 THR cc_start: 0.7970 (p) cc_final: 0.7743 (p) REVERT: C 8 ASP cc_start: 0.7366 (t0) cc_final: 0.6874 (t0) REVERT: C 56 MET cc_start: 0.6049 (ptp) cc_final: 0.5471 (ptm) REVERT: D 16 GLN cc_start: 0.6945 (mp10) cc_final: 0.6482 (mm-40) REVERT: D 56 MET cc_start: 0.6335 (mmm) cc_final: 0.5910 (mmm) REVERT: D 171 PHE cc_start: 0.7968 (m-80) cc_final: 0.7452 (m-80) REVERT: E 132 THR cc_start: 0.6848 (p) cc_final: 0.6599 (t) REVERT: E 221 MET cc_start: 0.4967 (mtp) cc_final: 0.4586 (mtm) REVERT: F 93 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7744 (tm-30) REVERT: F 134 SER cc_start: 0.5071 (m) cc_final: 0.4111 (t) REVERT: F 141 MET cc_start: 0.0848 (mpp) cc_final: -0.0399 (tmm) REVERT: F 221 MET cc_start: 0.2012 (ptp) cc_final: 0.1167 (ttp) REVERT: G 1 MET cc_start: 0.7859 (ppp) cc_final: 0.7459 (ppp) REVERT: G 28 LYS cc_start: 0.8290 (tptt) cc_final: 0.7482 (tptt) REVERT: G 82 TRP cc_start: 0.7223 (p-90) cc_final: 0.6985 (p-90) REVERT: G 111 VAL cc_start: 0.8385 (m) cc_final: 0.8151 (m) REVERT: G 218 PRO cc_start: 0.7816 (Cg_exo) cc_final: 0.7581 (Cg_endo) REVERT: G 324 LYS cc_start: 0.8187 (ptmm) cc_final: 0.7639 (mmtt) REVERT: H 398 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7855 (tt) REVERT: H 497 TYR cc_start: 0.7446 (m-10) cc_final: 0.7192 (m-10) REVERT: I 16 ARG cc_start: 0.7352 (mtm180) cc_final: 0.7144 (ttp-170) REVERT: I 24 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8315 (mm) REVERT: I 88 ARG cc_start: 0.5883 (mmp-170) cc_final: 0.5643 (mmp-170) REVERT: I 97 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8133 (mm-40) REVERT: J 57 ARG cc_start: 0.7334 (ttp80) cc_final: 0.7079 (ttm170) REVERT: J 116 ASP cc_start: 0.6478 (m-30) cc_final: 0.6251 (t0) REVERT: M 7 TYR cc_start: 0.7180 (m-80) cc_final: 0.6939 (m-80) REVERT: N 21 VAL cc_start: 0.8138 (m) cc_final: 0.7937 (m) outliers start: 101 outliers final: 53 residues processed: 484 average time/residue: 0.1457 time to fit residues: 109.9141 Evaluate side-chains 401 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 346 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 213 ASP Chi-restraints excluded: chain A residue 231 HIS Chi-restraints excluded: chain B residue 15 VAL 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 194 PHE Chi-restraints excluded: chain B residue 199 LEU 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 35 GLN Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 146 SER 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 125 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 231 HIS Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 240 PHE 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 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 477 VAL 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 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 46 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 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: 0.9980 chunk 154 optimal weight: 20.0000 chunk 237 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 270 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 60 optimal weight: 0.0980 chunk 31 optimal weight: 0.0040 chunk 199 optimal weight: 7.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS D 124 GLN D 222 ASN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN F 63 HIS ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 549 HIS I 61 HIS ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.173177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.153585 restraints weight = 69730.557| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 3.74 r_work: 0.4365 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.6365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26020 Z= 0.140 Angle : 0.651 11.936 35445 Z= 0.339 Chirality : 0.043 0.242 3853 Planarity : 0.004 0.068 4393 Dihedral : 17.094 177.926 4361 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.03 % Favored : 89.66 % Rotamer: Outliers : 3.71 % Allowed : 18.22 % Favored : 78.08 % 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 aren not related in a simple way. whole: -2.15 (0.15), residues: 2931 helix: 0.14 (0.17), residues: 952 sheet: -0.90 (0.24), residues: 500 loop : -2.78 (0.14), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 80 TYR 0.022 0.002 TYR J 106 PHE 0.036 0.002 PHE A 53 TRP 0.022 0.002 TRP J 77 HIS 0.009 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00310 (26020) covalent geometry : angle 0.65095 (35445) hydrogen bonds : bond 0.04854 ( 901) hydrogen bonds : angle 4.98711 ( 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 502 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 408 time to evaluate : 0.766 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: A 56 MET cc_start: 0.5859 (tpt) cc_final: 0.4545 (tpt) REVERT: A 100 GLN cc_start: 0.7861 (mm110) cc_final: 0.7560 (mm110) REVERT: A 171 PHE cc_start: 0.8544 (m-80) cc_final: 0.8143 (m-80) REVERT: B 110 ARG cc_start: 0.4484 (OUTLIER) cc_final: 0.3386 (ptm160) REVERT: B 194 PHE cc_start: 0.3120 (OUTLIER) cc_final: 0.2288 (m-80) REVERT: C 8 ASP cc_start: 0.7379 (t0) cc_final: 0.6957 (t0) REVERT: C 280 ARG cc_start: 0.6933 (ptm-80) cc_final: 0.6454 (ptt90) REVERT: D 16 GLN cc_start: 0.6968 (mp10) cc_final: 0.6286 (mm-40) REVERT: D 56 MET cc_start: 0.6341 (mmm) cc_final: 0.5927 (mmm) REVERT: D 124 GLN cc_start: 0.4001 (OUTLIER) cc_final: 0.3365 (tp40) REVERT: D 171 PHE cc_start: 0.8325 (m-80) cc_final: 0.8025 (m-80) REVERT: D 209 MET cc_start: 0.6008 (tpp) cc_final: 0.5461 (tpp) REVERT: E 172 THR cc_start: 0.7677 (OUTLIER) cc_final: 0.7036 (p) REVERT: E 221 MET cc_start: 0.4503 (mtp) cc_final: 0.4222 (mtm) REVERT: F 93 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7774 (tm-30) REVERT: F 134 SER cc_start: 0.4983 (m) cc_final: 0.4109 (t) REVERT: F 141 MET cc_start: 0.0746 (mpp) cc_final: -0.0524 (tmm) REVERT: F 221 MET cc_start: 0.1668 (ptp) cc_final: 0.1119 (ptp) REVERT: G 28 LYS cc_start: 0.8297 (tptt) cc_final: 0.7522 (tptt) REVERT: G 80 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6401 (mm) REVERT: G 218 PRO cc_start: 0.7766 (Cg_exo) cc_final: 0.7524 (Cg_endo) REVERT: G 270 THR cc_start: 0.8397 (m) cc_final: 0.7908 (p) REVERT: G 324 LYS cc_start: 0.8200 (ptmm) cc_final: 0.7636 (mmtt) REVERT: H 398 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7808 (tt) REVERT: H 431 TYR cc_start: 0.6479 (OUTLIER) cc_final: 0.5092 (t80) REVERT: H 497 TYR cc_start: 0.7112 (m-10) cc_final: 0.6893 (m-10) REVERT: I 16 ARG cc_start: 0.7238 (mtm180) cc_final: 0.6951 (ttp-170) REVERT: I 41 PHE cc_start: 0.8036 (t80) cc_final: 0.7751 (t80) REVERT: I 97 GLN cc_start: 0.8264 (mm-40) cc_final: 0.8032 (mm-40) REVERT: J 56 MET cc_start: 0.6824 (mmt) cc_final: 0.6116 (mmp) REVERT: J 110 GLN cc_start: 0.7764 (tp40) cc_final: 0.7488 (tp-100) REVERT: J 116 ASP cc_start: 0.6342 (m-30) cc_final: 0.6139 (t0) REVERT: M 7 TYR cc_start: 0.7036 (m-80) cc_final: 0.6833 (m-80) REVERT: M 33 ASP cc_start: 0.6608 (OUTLIER) cc_final: 0.6271 (t0) REVERT: M 116 MET cc_start: 0.4508 (ptt) cc_final: 0.4204 (ppp) REVERT: N 21 VAL cc_start: 0.8073 (m) cc_final: 0.7863 (m) outliers start: 94 outliers final: 53 residues processed: 475 average time/residue: 0.1431 time to fit residues: 105.9561 Evaluate side-chains 414 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 353 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 172 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 247 ILE 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 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 109 ILE 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 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 172 THR Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 63 HIS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 250 TYR 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 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 471 LEU Chi-restraints excluded: chain I residue 54 THR 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 33 ASP Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 201 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 152 LEU 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: 10.0000 chunk 216 optimal weight: 4.9990 chunk 204 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 227 optimal weight: 0.8980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 HIS ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 ASN F 63 HIS F 181 HIS ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 ASN ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN I 94 ASN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.160282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.140182 restraints weight = 67266.377| |-----------------------------------------------------------------------------| r_work (start): 0.4278 rms_B_bonded: 3.14 r_work: 0.4159 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.7976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 26020 Z= 0.296 Angle : 0.828 12.552 35445 Z= 0.431 Chirality : 0.049 0.295 3853 Planarity : 0.006 0.055 4393 Dihedral : 17.364 178.673 4361 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 30.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.91 % Favored : 87.85 % Rotamer: Outliers : 5.05 % Allowed : 18.69 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -2.52 (0.15), residues: 2931 helix: -0.46 (0.16), residues: 1021 sheet: -1.27 (0.23), residues: 530 loop : -2.84 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 259 TYR 0.030 0.003 TYR I 12 PHE 0.055 0.003 PHE A 53 TRP 0.033 0.004 TRP G 82 HIS 0.013 0.002 HIS G 343 Details of bonding type rmsd covalent geometry : bond 0.00649 (26020) covalent geometry : angle 0.82822 (35445) hydrogen bonds : bond 0.05377 ( 901) hydrogen bonds : angle 5.48428 ( 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 532 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 404 time to evaluate : 0.959 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: A 56 MET cc_start: 0.6599 (tpt) cc_final: 0.5067 (tpt) REVERT: A 103 CYS cc_start: 0.8318 (m) cc_final: 0.7847 (m) REVERT: A 131 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8325 (mt) REVERT: A 171 PHE cc_start: 0.8508 (m-80) cc_final: 0.8205 (m-80) REVERT: A 277 LYS cc_start: 0.0126 (OUTLIER) cc_final: -0.0160 (ttmm) REVERT: B 179 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6937 (ttm-80) REVERT: B 251 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7509 (mttm) REVERT: C 8 ASP cc_start: 0.6888 (t0) cc_final: 0.6657 (t0) REVERT: C 56 MET cc_start: 0.6309 (ptp) cc_final: 0.6074 (ptm) REVERT: C 82 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6029 (tm-30) REVERT: C 203 TRP cc_start: 0.4690 (OUTLIER) cc_final: 0.2071 (m100) REVERT: C 280 ARG cc_start: 0.7149 (ptm-80) cc_final: 0.6645 (ptt90) REVERT: D 16 GLN cc_start: 0.7306 (mp10) cc_final: 0.6567 (mm-40) REVERT: D 56 MET cc_start: 0.6779 (mmm) cc_final: 0.6435 (mmm) REVERT: D 102 MET cc_start: 0.7568 (tpp) cc_final: 0.7111 (tpp) REVERT: D 116 MET cc_start: 0.3285 (ttt) cc_final: 0.2444 (tmm) REVERT: D 171 PHE cc_start: 0.8464 (m-80) cc_final: 0.7986 (m-80) REVERT: D 220 GLN cc_start: 0.8193 (mt0) cc_final: 0.7904 (tt0) REVERT: E 143 LEU cc_start: 0.5014 (mt) cc_final: 0.4781 (mt) REVERT: E 221 MET cc_start: 0.4841 (OUTLIER) cc_final: 0.4157 (mtm) REVERT: E 271 LYS cc_start: 0.7810 (mttt) cc_final: 0.7405 (mmtt) REVERT: F 63 HIS cc_start: 0.8478 (m90) cc_final: 0.8099 (m170) REVERT: F 177 LEU cc_start: 0.5770 (tt) cc_final: 0.5319 (tt) REVERT: F 221 MET cc_start: 0.1716 (ptp) cc_final: 0.0720 (ptp) REVERT: G 28 LYS cc_start: 0.7954 (tptt) cc_final: 0.7671 (tppt) REVERT: G 80 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6337 (mm) REVERT: G 82 TRP cc_start: 0.7822 (p-90) cc_final: 0.7294 (p-90) REVERT: G 218 PRO cc_start: 0.8004 (Cg_exo) cc_final: 0.7739 (Cg_endo) REVERT: G 247 MET cc_start: 0.8543 (tmm) cc_final: 0.8234 (tmm) REVERT: H 398 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7802 (tt) REVERT: H 431 TYR cc_start: 0.6796 (OUTLIER) cc_final: 0.5214 (t80) REVERT: H 460 LEU cc_start: 0.6732 (tp) cc_final: 0.6335 (tp) REVERT: H 546 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: I 24 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8312 (mm) REVERT: I 108 GLU cc_start: 0.7989 (tp30) cc_final: 0.7467 (tp30) REVERT: I 109 THR cc_start: 0.7729 (p) cc_final: 0.7436 (p) REVERT: I 111 PHE cc_start: 0.7826 (t80) cc_final: 0.7593 (t80) REVERT: J 16 ARG cc_start: 0.6443 (mtp180) cc_final: 0.5720 (mtp180) REVERT: J 56 MET cc_start: 0.7555 (mmt) cc_final: 0.7187 (mmt) REVERT: J 110 GLN cc_start: 0.7848 (tp40) cc_final: 0.7456 (tp-100) REVERT: M 53 PHE cc_start: 0.6794 (t80) cc_final: 0.6552 (t80) REVERT: M 56 MET cc_start: 0.3880 (mmm) cc_final: 0.3623 (mmt) REVERT: M 266 VAL cc_start: 0.5003 (OUTLIER) cc_final: 0.4790 (p) REVERT: M 279 LEU cc_start: 0.7947 (mp) cc_final: 0.7659 (tt) outliers start: 128 outliers final: 74 residues processed: 493 average time/residue: 0.1556 time to fit residues: 119.2614 Evaluate side-chains 438 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 352 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 109 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 179 ARG 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 247 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain C residue 203 TRP Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 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 183 PHE Chi-restraints excluded: chain D residue 184 ILE 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 258 VAL Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 221 MET 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 G residue 2 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 85 TYR 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 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 470 VAL Chi-restraints excluded: chain H residue 481 ILE Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 546 PHE 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 J residue 111 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 44 VAL Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain M residue 221 MET Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 152 LEU 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: 3.9990 chunk 10 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 289 optimal weight: 0.0980 chunk 224 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 223 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 191 GLN D 124 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 HIS ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 GLN ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 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 = 0.4613 r_free = 0.4613 target = 0.162745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.143072 restraints weight = 67289.985| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 3.29 r_work: 0.4205 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.8099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26020 Z= 0.176 Angle : 0.705 13.204 35445 Z= 0.365 Chirality : 0.045 0.261 3853 Planarity : 0.005 0.077 4393 Dihedral : 17.257 178.730 4356 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 25.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.03 % Favored : 89.73 % Rotamer: Outliers : 3.67 % Allowed : 20.58 % Favored : 75.75 % 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 aren not related in a simple way. whole: -2.25 (0.15), residues: 2931 helix: -0.20 (0.17), residues: 988 sheet: -1.11 (0.24), residues: 480 loop : -2.62 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 16 TYR 0.023 0.002 TYR H 440 PHE 0.036 0.003 PHE A 53 TRP 0.021 0.002 TRP G 82 HIS 0.008 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00394 (26020) covalent geometry : angle 0.70475 (35445) hydrogen bonds : bond 0.04792 ( 901) hydrogen bonds : angle 5.25847 ( 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 494 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 401 time to evaluate : 0.934 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 56 MET cc_start: 0.6482 (tpt) cc_final: 0.5407 (tpt) REVERT: A 103 CYS cc_start: 0.8037 (m) cc_final: 0.7537 (m) REVERT: A 131 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.7431 (mp) REVERT: A 171 PHE cc_start: 0.8419 (m-80) cc_final: 0.8134 (m-80) REVERT: B 102 MET cc_start: 0.7712 (tmm) cc_final: 0.7376 (ttp) REVERT: D 16 GLN cc_start: 0.7218 (mp10) cc_final: 0.6783 (mp10) REVERT: D 56 MET cc_start: 0.6824 (mmm) cc_final: 0.6601 (mmm) REVERT: D 102 MET cc_start: 0.7669 (tpp) cc_final: 0.7259 (tpp) REVERT: D 116 MET cc_start: 0.3269 (ttt) cc_final: 0.2060 (tmm) REVERT: D 171 PHE cc_start: 0.8209 (m-80) cc_final: 0.7327 (m-80) REVERT: D 209 MET cc_start: 0.6992 (tpp) cc_final: 0.6725 (tpp) REVERT: E 171 PHE cc_start: 0.7406 (m-80) cc_final: 0.6926 (m-10) REVERT: E 172 THR cc_start: 0.7424 (m) cc_final: 0.6562 (p) REVERT: E 209 MET cc_start: 0.6651 (tpp) cc_final: 0.5187 (mmm) REVERT: E 221 MET cc_start: 0.4746 (mtp) cc_final: 0.4073 (mtm) REVERT: F 63 HIS cc_start: 0.8331 (m90) cc_final: 0.8064 (m-70) REVERT: F 65 ILE cc_start: 0.1902 (OUTLIER) cc_final: 0.1455 (mp) REVERT: F 133 PHE cc_start: 0.6283 (t80) cc_final: 0.5995 (t80) REVERT: F 177 LEU cc_start: 0.5810 (tt) cc_final: 0.5328 (tt) REVERT: F 221 MET cc_start: 0.1916 (ptp) cc_final: 0.1004 (ptm) REVERT: G 28 LYS cc_start: 0.7909 (tptt) cc_final: 0.7511 (tptp) REVERT: G 80 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6538 (mm) REVERT: G 218 PRO cc_start: 0.7785 (Cg_exo) cc_final: 0.7501 (Cg_endo) REVERT: G 236 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.6354 (tm-30) REVERT: G 324 LYS cc_start: 0.8121 (ptmm) cc_final: 0.7392 (mmtt) REVERT: G 326 TYR cc_start: 0.5278 (p90) cc_final: 0.4750 (p90) REVERT: H 398 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7850 (tt) REVERT: H 431 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.5140 (t80) REVERT: H 451 LYS cc_start: 0.7565 (pptt) cc_final: 0.7181 (pttm) REVERT: H 460 LEU cc_start: 0.6871 (tp) cc_final: 0.6490 (tp) REVERT: H 471 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7393 (mm) REVERT: H 537 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6728 (mtm-85) REVERT: H 546 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7703 (m-80) REVERT: I 16 ARG cc_start: 0.7585 (mtp-110) cc_final: 0.7223 (mtm-85) REVERT: I 24 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8311 (mm) REVERT: I 41 PHE cc_start: 0.8185 (t80) cc_final: 0.7940 (t80) REVERT: I 108 GLU cc_start: 0.8016 (tp30) cc_final: 0.7658 (tp30) REVERT: J 110 GLN cc_start: 0.7918 (tp40) cc_final: 0.7639 (tp-100) REVERT: M 112 PHE cc_start: 0.7862 (m-80) cc_final: 0.7486 (m-80) REVERT: M 132 THR cc_start: 0.7439 (OUTLIER) cc_final: 0.7004 (m) REVERT: M 279 LEU cc_start: 0.7951 (mp) cc_final: 0.7588 (tt) REVERT: N 39 MET cc_start: 0.6576 (mpp) cc_final: 0.6290 (mmm) outliers start: 93 outliers final: 59 residues processed: 467 average time/residue: 0.1665 time to fit residues: 122.8033 Evaluate side-chains 429 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 359 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 107 TYR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 LEU 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 111 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 LEU 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 146 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 227 TYR 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 147 ILE Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 236 GLN 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 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 470 VAL Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 537 ARG Chi-restraints excluded: chain H residue 546 PHE 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 J residue 89 PHE Chi-restraints excluded: chain M residue 33 ASP Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 221 MET Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 65 ILE 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: 2.9990 chunk 114 optimal weight: 0.7980 chunk 253 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 250 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 234 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 203 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 ASN F 181 HIS ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 531 GLN I 81 GLN I 97 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 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 = 0.4633 r_free = 0.4633 target = 0.164060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.144724 restraints weight = 66704.627| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 3.27 r_work: 0.4232 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.8198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26020 Z= 0.158 Angle : 0.701 13.642 35445 Z= 0.359 Chirality : 0.045 0.257 3853 Planarity : 0.004 0.075 4393 Dihedral : 17.195 177.269 4352 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 24.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.75 % Favored : 89.01 % Rotamer: Outliers : 3.12 % Allowed : 21.53 % Favored : 75.35 % 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 aren not related in a simple way. whole: -2.17 (0.15), residues: 2931 helix: -0.19 (0.17), residues: 1004 sheet: -1.05 (0.25), residues: 421 loop : -2.52 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 105 TYR 0.035 0.002 TYR H 440 PHE 0.030 0.002 PHE A 53 TRP 0.024 0.002 TRP G 82 HIS 0.008 0.001 HIS G 343 Details of bonding type rmsd covalent geometry : bond 0.00350 (26020) covalent geometry : angle 0.70055 (35445) hydrogen bonds : bond 0.04663 ( 901) hydrogen bonds : angle 5.14404 ( 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 493 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 414 time to evaluate : 0.957 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 19 ASN cc_start: 0.8242 (t0) cc_final: 0.7876 (p0) REVERT: A 56 MET cc_start: 0.6345 (tpt) cc_final: 0.4454 (tpt) REVERT: A 103 CYS cc_start: 0.7813 (m) cc_final: 0.7208 (m) REVERT: A 171 PHE cc_start: 0.8459 (m-80) cc_final: 0.8221 (m-80) REVERT: B 8 ASP cc_start: 0.5745 (t0) cc_final: 0.5468 (t0) REVERT: B 102 MET cc_start: 0.7517 (tmm) cc_final: 0.7292 (ttp) REVERT: B 210 PHE cc_start: 0.6920 (m-10) cc_final: 0.6358 (m-80) REVERT: B 261 PHE cc_start: 0.6545 (t80) cc_final: 0.6075 (t80) REVERT: C 8 ASP cc_start: 0.7232 (t0) cc_final: 0.7006 (m-30) REVERT: C 103 CYS cc_start: 0.8050 (m) cc_final: 0.7151 (p) REVERT: C 167 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.6388 (tpp) REVERT: C 201 LEU cc_start: 0.6284 (tt) cc_final: 0.6072 (tp) REVERT: D 16 GLN cc_start: 0.6918 (mp10) cc_final: 0.6647 (mp10) REVERT: D 56 MET cc_start: 0.7038 (mmm) cc_final: 0.6496 (mmm) REVERT: D 102 MET cc_start: 0.7507 (tpp) cc_final: 0.6965 (tpp) REVERT: D 105 ARG cc_start: 0.5897 (tpt170) cc_final: 0.5497 (tpt90) REVERT: D 116 MET cc_start: 0.3710 (ttt) cc_final: 0.2932 (tmm) REVERT: D 171 PHE cc_start: 0.8251 (m-80) cc_final: 0.7386 (m-80) REVERT: D 220 GLN cc_start: 0.7636 (mt0) cc_final: 0.7377 (mt0) REVERT: E 102 MET cc_start: 0.6101 (mmt) cc_final: 0.5791 (mmp) REVERT: E 172 THR cc_start: 0.6994 (m) cc_final: 0.6193 (p) REVERT: E 209 MET cc_start: 0.6382 (tpp) cc_final: 0.5380 (mmm) REVERT: E 211 ASP cc_start: 0.8225 (m-30) cc_final: 0.7978 (t0) REVERT: E 221 MET cc_start: 0.5118 (mtp) cc_final: 0.4212 (mtm) REVERT: F 63 HIS cc_start: 0.8317 (m90) cc_final: 0.8013 (m-70) REVERT: F 133 PHE cc_start: 0.6351 (t80) cc_final: 0.6070 (t80) REVERT: F 177 LEU cc_start: 0.5745 (tt) cc_final: 0.5224 (tt) REVERT: F 221 MET cc_start: 0.1545 (ptp) cc_final: 0.1194 (ptm) REVERT: G 28 LYS cc_start: 0.7910 (tptt) cc_final: 0.7527 (tptp) REVERT: G 59 ARG cc_start: 0.7309 (mmt180) cc_final: 0.7040 (mmt180) REVERT: G 80 LEU cc_start: 0.6921 (mt) cc_final: 0.6390 (mm) REVERT: G 218 PRO cc_start: 0.7676 (Cg_exo) cc_final: 0.7402 (Cg_endo) REVERT: G 270 THR cc_start: 0.8401 (m) cc_final: 0.8036 (p) REVERT: G 324 LYS cc_start: 0.8211 (ptmm) cc_final: 0.7559 (mmtt) REVERT: G 326 TYR cc_start: 0.5216 (p90) cc_final: 0.4786 (p90) REVERT: H 398 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7774 (tt) REVERT: H 431 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.5355 (t80) REVERT: H 451 LYS cc_start: 0.7275 (pptt) cc_final: 0.6899 (pttm) REVERT: H 460 LEU cc_start: 0.6860 (tp) cc_final: 0.6414 (tp) REVERT: H 471 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7268 (mm) REVERT: H 513 MET cc_start: 0.8369 (mmp) cc_final: 0.7902 (mmm) REVERT: H 537 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6688 (mtm-85) REVERT: H 546 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: I 16 ARG cc_start: 0.7531 (mtp-110) cc_final: 0.7252 (mtm-85) REVERT: I 24 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8233 (mm) REVERT: I 41 PHE cc_start: 0.8089 (t80) cc_final: 0.7866 (t80) REVERT: I 71 ARG cc_start: 0.6223 (ttm170) cc_final: 0.5993 (ttm170) REVERT: I 108 GLU cc_start: 0.7999 (tp30) cc_final: 0.7508 (tp30) REVERT: J 110 GLN cc_start: 0.7863 (tp40) cc_final: 0.7661 (tp-100) REVERT: M 112 PHE cc_start: 0.7846 (m-80) cc_final: 0.7474 (m-80) REVERT: M 132 THR cc_start: 0.7459 (OUTLIER) cc_final: 0.6964 (m) REVERT: M 279 LEU cc_start: 0.7657 (mp) cc_final: 0.7349 (mp) REVERT: N 39 MET cc_start: 0.6479 (mpp) cc_final: 0.6229 (mmm) REVERT: N 100 TYR cc_start: 0.7365 (m-80) cc_final: 0.7096 (m-10) REVERT: N 167 ASP cc_start: 0.7009 (p0) cc_final: 0.6798 (p0) outliers start: 79 outliers final: 49 residues processed: 472 average time/residue: 0.1689 time to fit residues: 126.6725 Evaluate side-chains 434 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 377 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 172 THR 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 249 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 227 TYR 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 111 THR Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 249 VAL 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 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 546 PHE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 89 PHE 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 132 THR Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 221 MET Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 152 LEU 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: 0.6980 chunk 227 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 HIS F 234 ASN ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 GLN ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.164822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.145527 restraints weight = 67177.182| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 3.28 r_work: 0.4244 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.8276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26020 Z= 0.149 Angle : 0.692 12.011 35445 Z= 0.357 Chirality : 0.045 0.254 3853 Planarity : 0.004 0.075 4393 Dihedral : 17.158 176.182 4352 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 24.66 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.96 % Favored : 89.70 % Rotamer: Outliers : 3.00 % Allowed : 21.77 % Favored : 75.24 % 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 aren not related in a simple way. whole: -2.19 (0.15), residues: 2931 helix: -0.21 (0.16), residues: 1007 sheet: -1.06 (0.26), residues: 420 loop : -2.53 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 48 TYR 0.032 0.002 TYR I 12 PHE 0.056 0.002 PHE A 53 TRP 0.029 0.002 TRP F 203 HIS 0.007 0.001 HIS G 343 Details of bonding type rmsd covalent geometry : bond 0.00336 (26020) covalent geometry : angle 0.69247 (35445) hydrogen bonds : bond 0.04628 ( 901) hydrogen bonds : angle 5.09807 ( 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 484 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 408 time to evaluate : 1.144 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 56 MET cc_start: 0.6009 (tpt) cc_final: 0.4750 (tpt) REVERT: A 103 CYS cc_start: 0.8079 (m) cc_final: 0.7443 (m) REVERT: A 171 PHE cc_start: 0.8417 (m-80) cc_final: 0.8139 (m-80) REVERT: A 220 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7907 (tp40) REVERT: B 8 ASP cc_start: 0.5395 (t0) cc_final: 0.5144 (t0) REVERT: B 102 MET cc_start: 0.7605 (tmm) cc_final: 0.7206 (ttp) REVERT: B 261 PHE cc_start: 0.6454 (t80) cc_final: 0.6126 (t80) REVERT: C 8 ASP cc_start: 0.7147 (t0) cc_final: 0.6771 (t0) REVERT: C 103 CYS cc_start: 0.8055 (m) cc_final: 0.7261 (p) REVERT: C 167 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6042 (tpp) REVERT: D 16 GLN cc_start: 0.6952 (mp10) cc_final: 0.6665 (mp10) REVERT: D 56 MET cc_start: 0.6911 (mmm) cc_final: 0.6590 (mmm) REVERT: D 102 MET cc_start: 0.7555 (tpp) cc_final: 0.7240 (tpp) REVERT: D 116 MET cc_start: 0.3527 (ttt) cc_final: 0.2846 (tmm) REVERT: D 171 PHE cc_start: 0.8440 (m-80) cc_final: 0.7891 (m-80) REVERT: D 220 GLN cc_start: 0.7995 (mt0) cc_final: 0.7775 (mt0) REVERT: E 102 MET cc_start: 0.6141 (mmt) cc_final: 0.5710 (mmp) REVERT: E 172 THR cc_start: 0.6869 (m) cc_final: 0.6087 (p) REVERT: E 209 MET cc_start: 0.6251 (tpp) cc_final: 0.5298 (mmm) REVERT: E 211 ASP cc_start: 0.8305 (m-30) cc_final: 0.7898 (t0) REVERT: E 221 MET cc_start: 0.5055 (OUTLIER) cc_final: 0.4194 (mtm) REVERT: E 227 TYR cc_start: 0.4026 (m-80) cc_final: 0.3720 (m-80) REVERT: F 63 HIS cc_start: 0.8327 (m90) cc_final: 0.7948 (m-70) REVERT: F 133 PHE cc_start: 0.6321 (t80) cc_final: 0.6105 (t80) REVERT: F 177 LEU cc_start: 0.5662 (tt) cc_final: 0.5132 (tt) REVERT: G 28 LYS cc_start: 0.8027 (tptt) cc_final: 0.7747 (tppt) REVERT: G 59 ARG cc_start: 0.7321 (mmt180) cc_final: 0.7044 (mmt180) REVERT: G 80 LEU cc_start: 0.6893 (mt) cc_final: 0.6374 (mm) REVERT: G 218 PRO cc_start: 0.7585 (Cg_exo) cc_final: 0.7326 (Cg_endo) REVERT: G 270 THR cc_start: 0.8315 (m) cc_final: 0.7944 (p) REVERT: G 324 LYS cc_start: 0.8238 (ptmm) cc_final: 0.7611 (mmtt) REVERT: G 326 TYR cc_start: 0.5358 (p90) cc_final: 0.4855 (p90) REVERT: H 398 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7651 (tt) REVERT: H 431 TYR cc_start: 0.6883 (OUTLIER) cc_final: 0.5356 (t80) REVERT: H 451 LYS cc_start: 0.7275 (pptt) cc_final: 0.6836 (pttm) REVERT: H 460 LEU cc_start: 0.6960 (tp) cc_final: 0.6681 (tp) REVERT: H 471 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7192 (mm) REVERT: H 513 MET cc_start: 0.8227 (mmp) cc_final: 0.7773 (mmm) REVERT: H 537 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6706 (mtm-85) REVERT: I 16 ARG cc_start: 0.7563 (mtp-110) cc_final: 0.7221 (mtm-85) REVERT: I 24 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8224 (mm) REVERT: I 41 PHE cc_start: 0.8172 (t80) cc_final: 0.7936 (t80) REVERT: I 108 GLU cc_start: 0.8017 (tp30) cc_final: 0.7713 (tp30) REVERT: J 65 LYS cc_start: 0.7359 (pttp) cc_final: 0.6817 (ptpt) REVERT: J 110 GLN cc_start: 0.7747 (tp40) cc_final: 0.7428 (tp-100) REVERT: M 56 MET cc_start: 0.3104 (mmm) cc_final: 0.2874 (mmt) REVERT: M 132 THR cc_start: 0.7402 (OUTLIER) cc_final: 0.6890 (m) REVERT: M 279 LEU cc_start: 0.7549 (mp) cc_final: 0.7260 (mp) REVERT: N 35 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7477 (ttm-80) REVERT: N 39 MET cc_start: 0.6567 (mpp) cc_final: 0.6362 (mmm) outliers start: 76 outliers final: 54 residues processed: 460 average time/residue: 0.1584 time to fit residues: 116.1933 Evaluate side-chains 443 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 380 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 107 TYR Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 LEU 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 141 MET Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 227 TYR 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 15 VAL Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 221 MET 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 249 VAL 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 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 I residue 24 ILE Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain M residue 21 ASN Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain N residue 30 THR 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: 9.9990 chunk 35 optimal weight: 1.9990 chunk 79 optimal weight: 0.0000 chunk 82 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 136 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 HIS ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN ** N 133 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 = 0.4585 r_free = 0.4585 target = 0.160400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.140308 restraints weight = 67045.006| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 3.26 r_work: 0.4167 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.8782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 26020 Z= 0.204 Angle : 0.761 16.567 35445 Z= 0.391 Chirality : 0.047 0.359 3853 Planarity : 0.005 0.059 4393 Dihedral : 17.169 178.193 4352 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 26.97 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.71 % Favored : 88.95 % Rotamer: Outliers : 3.15 % Allowed : 22.24 % Favored : 74.61 % 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 aren not related in a simple way. whole: -2.32 (0.15), residues: 2931 helix: -0.41 (0.16), residues: 1031 sheet: -1.23 (0.25), residues: 446 loop : -2.54 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 165 TYR 0.038 0.003 TYR H 497 PHE 0.056 0.003 PHE A 53 TRP 0.026 0.003 TRP N 49 HIS 0.011 0.001 HIS G 343 Details of bonding type rmsd covalent geometry : bond 0.00457 (26020) covalent geometry : angle 0.76123 (35445) hydrogen bonds : bond 0.04807 ( 901) hydrogen bonds : angle 5.19198 ( 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 468 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 388 time to evaluate : 0.994 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: A 103 CYS cc_start: 0.7788 (m) cc_final: 0.7309 (m) REVERT: A 220 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7954 (tp40) REVERT: B 8 ASP cc_start: 0.5648 (t0) cc_final: 0.5412 (t0) REVERT: B 261 PHE cc_start: 0.6306 (t80) cc_final: 0.6032 (t80) REVERT: C 74 ASN cc_start: 0.6844 (m-40) cc_final: 0.6563 (m110) REVERT: C 201 LEU cc_start: 0.6550 (tt) cc_final: 0.6229 (tp) REVERT: D 16 GLN cc_start: 0.7345 (mp10) cc_final: 0.6956 (mp10) REVERT: D 56 MET cc_start: 0.7089 (mmm) cc_final: 0.6583 (mmm) REVERT: D 102 MET cc_start: 0.7641 (tpp) cc_final: 0.7104 (tpp) REVERT: D 116 MET cc_start: 0.4185 (ttt) cc_final: 0.3037 (tmm) REVERT: D 220 GLN cc_start: 0.8020 (mt0) cc_final: 0.7714 (tt0) REVERT: E 8 ASP cc_start: 0.6635 (m-30) cc_final: 0.6404 (m-30) REVERT: E 209 MET cc_start: 0.6260 (tpp) cc_final: 0.5164 (mmm) REVERT: E 211 ASP cc_start: 0.8226 (m-30) cc_final: 0.7874 (t0) REVERT: E 221 MET cc_start: 0.4973 (OUTLIER) cc_final: 0.3745 (mtm) REVERT: E 227 TYR cc_start: 0.4278 (m-80) cc_final: 0.4018 (m-80) REVERT: E 271 LYS cc_start: 0.7672 (mttt) cc_final: 0.7287 (mmtt) REVERT: F 63 HIS cc_start: 0.8378 (m90) cc_final: 0.8028 (m-70) REVERT: F 102 MET cc_start: 0.3617 (mmm) cc_final: 0.3048 (mmt) REVERT: F 116 MET cc_start: 0.5484 (pmm) cc_final: 0.5260 (pmm) REVERT: F 133 PHE cc_start: 0.6214 (t80) cc_final: 0.6005 (t80) REVERT: F 177 LEU cc_start: 0.5658 (tt) cc_final: 0.5072 (tt) REVERT: F 220 GLN cc_start: 0.7113 (tm-30) cc_final: 0.6863 (tt0) REVERT: G 3 LEU cc_start: 0.7745 (mt) cc_final: 0.7245 (mt) REVERT: G 28 LYS cc_start: 0.8054 (tptt) cc_final: 0.7757 (tppt) REVERT: G 80 LEU cc_start: 0.6787 (mt) cc_final: 0.6285 (mm) REVERT: G 82 TRP cc_start: 0.7619 (p-90) cc_final: 0.7225 (p-90) REVERT: G 218 PRO cc_start: 0.7693 (Cg_exo) cc_final: 0.7443 (Cg_endo) REVERT: G 326 TYR cc_start: 0.5745 (p90) cc_final: 0.5261 (p90) REVERT: H 398 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7471 (tt) REVERT: H 431 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.5280 (t80) REVERT: H 451 LYS cc_start: 0.7453 (pptt) cc_final: 0.7030 (pttm) REVERT: H 460 LEU cc_start: 0.6980 (tp) cc_final: 0.6696 (tp) REVERT: H 513 MET cc_start: 0.8732 (mmp) cc_final: 0.8387 (mmm) REVERT: H 537 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.7005 (mtm-85) REVERT: I 16 ARG cc_start: 0.7697 (mtp-110) cc_final: 0.7373 (mtm-85) REVERT: I 24 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8439 (mm) REVERT: I 40 TYR cc_start: 0.7142 (m-80) cc_final: 0.6928 (m-80) REVERT: I 101 PHE cc_start: 0.8465 (t80) cc_final: 0.8178 (t80) REVERT: I 108 GLU cc_start: 0.8114 (tp30) cc_final: 0.7865 (tp30) REVERT: J 110 GLN cc_start: 0.7894 (tp40) cc_final: 0.7408 (tp-100) REVERT: M 279 LEU cc_start: 0.7850 (mp) cc_final: 0.7590 (mp) REVERT: M 280 ARG cc_start: 0.6366 (mtm-85) cc_final: 0.5894 (ttp-170) REVERT: N 72 THR cc_start: 0.7127 (p) cc_final: 0.6897 (p) REVERT: N 167 ASP cc_start: 0.7446 (p0) cc_final: 0.7167 (p0) outliers start: 80 outliers final: 58 residues processed: 439 average time/residue: 0.1638 time to fit residues: 113.4137 Evaluate side-chains 430 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 366 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 150 MET Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 265 LEU 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 178 TYR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 196 GLU 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 111 THR Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 228 VAL 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 249 VAL Chi-restraints excluded: chain G residue 62 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 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 I residue 24 ILE Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain M residue 21 ASN Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 110 ARG Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 221 MET Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 30 THR 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: 0.0980 chunk 261 optimal weight: 0.0270 chunk 271 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 232 optimal weight: 8.9990 chunk 268 optimal weight: 0.9980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN F 181 HIS ** F 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN N 36 ASN ** N 133 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 = 0.4610 r_free = 0.4610 target = 0.162256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.142538 restraints weight = 67299.970| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 3.28 r_work: 0.4203 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.8835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26020 Z= 0.163 Angle : 0.740 15.942 35445 Z= 0.378 Chirality : 0.046 0.244 3853 Planarity : 0.005 0.078 4393 Dihedral : 17.147 178.419 4351 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 25.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.20 % Favored : 89.49 % Rotamer: Outliers : 2.60 % Allowed : 23.03 % Favored : 74.37 % 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 aren not related in a simple way. whole: -2.23 (0.15), residues: 2931 helix: -0.32 (0.16), residues: 1005 sheet: -1.24 (0.25), residues: 441 loop : -2.45 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG H 421 TYR 0.034 0.002 TYR N 100 PHE 0.049 0.002 PHE A 53 TRP 0.024 0.002 TRP G 82 HIS 0.009 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00372 (26020) covalent geometry : angle 0.74045 (35445) hydrogen bonds : bond 0.04677 ( 901) hydrogen bonds : angle 5.17743 ( 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 472 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 406 time to evaluate : 1.108 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: A 28 ASN cc_start: 0.7349 (t0) cc_final: 0.6602 (t0) REVERT: A 56 MET cc_start: 0.5806 (tpt) cc_final: 0.5193 (tpt) REVERT: A 103 CYS cc_start: 0.7496 (m) cc_final: 0.7124 (m) REVERT: A 131 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7125 (mp) REVERT: A 220 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7834 (tp40) REVERT: B 107 TYR cc_start: 0.3565 (t80) cc_final: 0.3310 (t80) REVERT: B 261 PHE cc_start: 0.6533 (t80) cc_final: 0.6221 (t80) REVERT: C 74 ASN cc_start: 0.6677 (m-40) cc_final: 0.6418 (m110) REVERT: C 201 LEU cc_start: 0.6456 (tt) cc_final: 0.6162 (tp) REVERT: D 16 GLN cc_start: 0.7332 (mp10) cc_final: 0.6988 (mp10) REVERT: D 56 MET cc_start: 0.6937 (mmm) cc_final: 0.6687 (mmm) REVERT: D 102 MET cc_start: 0.7729 (tpp) cc_final: 0.7387 (tpp) REVERT: D 116 MET cc_start: 0.3619 (ttt) cc_final: 0.2920 (tmm) REVERT: D 171 PHE cc_start: 0.8431 (m-80) cc_final: 0.7609 (m-80) REVERT: D 220 GLN cc_start: 0.8010 (mt0) cc_final: 0.7755 (tt0) REVERT: E 8 ASP cc_start: 0.6753 (m-30) cc_final: 0.6362 (p0) REVERT: E 150 MET cc_start: 0.4010 (mpp) cc_final: 0.2950 (pmm) REVERT: E 209 MET cc_start: 0.6390 (tpp) cc_final: 0.5880 (tpp) REVERT: E 211 ASP cc_start: 0.8284 (m-30) cc_final: 0.7916 (t0) REVERT: E 221 MET cc_start: 0.4947 (OUTLIER) cc_final: 0.3785 (mtm) REVERT: E 271 LYS cc_start: 0.7619 (mttt) cc_final: 0.7248 (mmtt) REVERT: F 63 HIS cc_start: 0.8369 (m90) cc_final: 0.8008 (m-70) REVERT: F 102 MET cc_start: 0.3053 (mmm) cc_final: 0.2757 (mmt) REVERT: F 133 PHE cc_start: 0.6114 (t80) cc_final: 0.5891 (t80) REVERT: F 177 LEU cc_start: 0.5627 (tt) cc_final: 0.5041 (tt) REVERT: F 209 MET cc_start: 0.1031 (tpt) cc_final: 0.0808 (tpt) REVERT: F 220 GLN cc_start: 0.7008 (tm-30) cc_final: 0.6802 (tt0) REVERT: G 28 LYS cc_start: 0.8061 (tptt) cc_final: 0.7768 (tppt) REVERT: G 80 LEU cc_start: 0.6723 (mt) cc_final: 0.6216 (mm) REVERT: G 82 TRP cc_start: 0.7622 (p-90) cc_final: 0.7214 (p-90) REVERT: G 218 PRO cc_start: 0.7626 (Cg_exo) cc_final: 0.7379 (Cg_endo) REVERT: G 247 MET cc_start: 0.8109 (tmm) cc_final: 0.7640 (tmm) REVERT: G 270 THR cc_start: 0.8403 (m) cc_final: 0.8057 (p) REVERT: G 326 TYR cc_start: 0.5661 (p90) cc_final: 0.5342 (p90) REVERT: H 398 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7406 (tt) REVERT: H 431 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.5172 (t80) REVERT: H 513 MET cc_start: 0.8583 (mmp) cc_final: 0.8262 (mmm) REVERT: H 537 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6719 (mtm-85) REVERT: I 16 ARG cc_start: 0.7644 (mtp-110) cc_final: 0.7276 (mtm-85) REVERT: I 24 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8390 (mm) REVERT: I 40 TYR cc_start: 0.7356 (m-80) cc_final: 0.7139 (m-80) REVERT: I 108 GLU cc_start: 0.8193 (tp30) cc_final: 0.7725 (tp30) REVERT: J 110 GLN cc_start: 0.7879 (tp40) cc_final: 0.7575 (tp-100) REVERT: M 21 ASN cc_start: 0.7274 (OUTLIER) cc_final: 0.6900 (t0) REVERT: M 132 THR cc_start: 0.7430 (OUTLIER) cc_final: 0.6916 (m) REVERT: M 280 ARG cc_start: 0.6364 (mtm-85) cc_final: 0.6000 (ttp-170) REVERT: N 35 ARG cc_start: 0.7718 (ttm110) cc_final: 0.7475 (ttm-80) REVERT: N 72 THR cc_start: 0.7020 (p) cc_final: 0.6814 (p) REVERT: N 93 MET cc_start: 0.7340 (mtm) cc_final: 0.6999 (ptt) REVERT: N 100 TYR cc_start: 0.6358 (m-10) cc_final: 0.6078 (m-10) REVERT: N 167 ASP cc_start: 0.7420 (p0) cc_final: 0.7129 (p0) outliers start: 66 outliers final: 50 residues processed: 446 average time/residue: 0.1692 time to fit residues: 119.4696 Evaluate side-chains 438 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 379 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 131 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 265 LEU 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 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 196 GLU 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 221 MET Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 181 HIS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain G residue 62 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 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 I residue 24 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 79 ILE Chi-restraints excluded: chain M residue 21 ASN Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 110 ARG Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 221 MET Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 42 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 196 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 256 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 281 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN C 214 HIS ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 HIS F 181 HIS ** F 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 554 GLN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 ASN ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN N 36 ASN ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.158085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.138236 restraints weight = 67024.409| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 3.11 r_work: 0.4151 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.9308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 26020 Z= 0.224 Angle : 0.785 15.207 35445 Z= 0.404 Chirality : 0.047 0.274 3853 Planarity : 0.005 0.074 4393 Dihedral : 17.165 179.784 4351 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 29.03 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.22 % Favored : 88.47 % Rotamer: Outliers : 2.76 % Allowed : 22.83 % Favored : 74.41 % 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 aren not related in a simple way. whole: -2.40 (0.15), residues: 2931 helix: -0.49 (0.16), residues: 1021 sheet: -1.61 (0.23), residues: 501 loop : -2.44 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG H 421 TYR 0.033 0.003 TYR I 106 PHE 0.052 0.003 PHE A 53 TRP 0.033 0.003 TRP N 43 HIS 0.018 0.002 HIS F 181 Details of bonding type rmsd covalent geometry : bond 0.00504 (26020) covalent geometry : angle 0.78486 (35445) hydrogen bonds : bond 0.04892 ( 901) hydrogen bonds : angle 5.41679 ( 2614) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5886.67 seconds wall clock time: 102 minutes 4.56 seconds (6124.56 seconds total)