Starting phenix.real_space_refine on Sat May 24 04:56:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gam_29900/05_2025/8gam_29900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gam_29900/05_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_29900/05_2025/8gam_29900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gam_29900/05_2025/8gam_29900.map" model { file = "/net/cci-nas-00/data/ceres_data/8gam_29900/05_2025/8gam_29900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gam_29900/05_2025/8gam_29900.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.52, per 1000 atoms: 0.61 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: 6.16 Conformation dependent library (CDL) restraints added in 2.8 seconds 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5474 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 29 sheets defined 34.5% alpha, 15.8% beta 14 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 8.05 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: 7.71 Time building geometry restraints manager: 7.16 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: 1.380 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: 0.010 Extract box with map and model: 1.090 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 59.040 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.100 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.640 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.001 TRP G 342 HIS 0.002 0.000 HIS G 343 PHE 0.011 0.001 PHE M 9 TYR 0.010 0.001 TYR G 250 ARG 0.002 0.000 ARG J 16 Details of bonding type rmsd hydrogen bonds : bond 0.12688 ( 901) hydrogen bonds : angle 5.71679 ( 2614) covalent geometry : bond 0.00173 (26020) covalent geometry : angle 0.47183 (35445) *********************** 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 : 3.030 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: 0.4269 time to fit residues: 533.1429 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 : 2.607 ------------------------------------------------------------------------------- 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 252 optimal weight: 0.9980 chunk 226 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 234 optimal weight: 8.9990 chunk 90 optimal weight: 0.2980 chunk 142 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 271 optimal weight: 0.8980 overall best weight: 4.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 83 GLN A 187 HIS A 191 GLN ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 HIS C 83 GLN C 214 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN D 63 HIS D 164 ASN D 181 HIS ** D 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 GLN E 272 ASN F 55 GLN ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 GLN G 79 ASN ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** 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 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 427 GLN H 442 ASN H 465 GLN ** H 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 521 ASN 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 94 ASN M 55 GLN ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.164796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.143800 restraints weight = 69471.834| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 3.61 r_work: 0.4258 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.6826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.109 26020 Z= 0.445 Angle : 1.179 17.442 35445 Z= 0.616 Chirality : 0.060 0.348 3853 Planarity : 0.009 0.114 4393 Dihedral : 17.910 178.566 4375 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 35.16 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.37 % Favored : 89.22 % Rotamer: Outliers : 6.35 % Allowed : 13.88 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.14), residues: 2931 helix: -1.31 (0.15), residues: 1001 sheet: -0.93 (0.25), residues: 423 loop : -3.16 (0.13), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.005 TRP H 534 HIS 0.014 0.003 HIS B 212 PHE 0.045 0.005 PHE C 188 TYR 0.043 0.005 TYR J 106 ARG 0.025 0.002 ARG A 110 Details of bonding type rmsd hydrogen bonds : bond 0.07103 ( 901) hydrogen bonds : angle 6.17808 ( 2614) covalent geometry : bond 0.00967 (26020) covalent geometry : angle 1.17939 (35445) *********************** 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 675 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 514 time to evaluate : 2.718 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: A 21 ASN cc_start: 0.8052 (t0) cc_final: 0.7615 (t0) REVERT: A 28 ASN cc_start: 0.8008 (t0) cc_final: 0.7246 (t0) REVERT: A 42 THR cc_start: 0.9227 (p) cc_final: 0.8990 (p) REVERT: A 103 CYS cc_start: 0.8747 (m) cc_final: 0.7862 (m) REVERT: A 200 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6779 (mm-30) REVERT: A 209 MET cc_start: 0.7313 (ttm) cc_final: 0.6973 (ttp) REVERT: C 8 ASP cc_start: 0.6560 (t0) cc_final: 0.6083 (t0) REVERT: C 181 HIS cc_start: 0.7640 (m-70) cc_final: 0.6551 (m170) REVERT: C 220 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6658 (pt0) REVERT: C 241 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7835 (t0) REVERT: D 16 GLN cc_start: 0.7263 (mp10) cc_final: 0.6615 (mm-40) REVERT: D 56 MET cc_start: 0.6505 (mmm) cc_final: 0.6173 (mmm) REVERT: E 5 LYS cc_start: 0.8873 (mtmt) cc_final: 0.8508 (pttt) REVERT: E 144 GLU cc_start: 0.8540 (tt0) cc_final: 0.8224 (tt0) REVERT: E 221 MET cc_start: 0.5365 (OUTLIER) cc_final: 0.4948 (mtm) REVERT: E 271 LYS cc_start: 0.7989 (mttt) cc_final: 0.7527 (mmtt) REVERT: E 280 ARG cc_start: 0.4555 (ptm160) cc_final: 0.4294 (ptm160) REVERT: F 4 GLU cc_start: 0.7846 (pp20) cc_final: 0.7609 (pm20) REVERT: F 63 HIS cc_start: 0.8255 (m-70) cc_final: 0.8016 (m-70) REVERT: F 93 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7596 (tm-30) REVERT: F 134 SER cc_start: 0.5580 (m) cc_final: 0.4914 (t) REVERT: F 141 MET cc_start: 0.0883 (mpp) cc_final: -0.0403 (tmm) REVERT: G 28 LYS cc_start: 0.8407 (tptt) cc_final: 0.7676 (tptt) REVERT: G 80 LEU cc_start: 0.7691 (mt) cc_final: 0.6882 (mm) REVERT: G 82 TRP cc_start: 0.7594 (p-90) cc_final: 0.7265 (p-90) REVERT: G 218 PRO cc_start: 0.7966 (Cg_exo) cc_final: 0.7696 (Cg_endo) REVERT: G 324 LYS cc_start: 0.8242 (ptmm) cc_final: 0.7493 (mmtt) REVERT: H 411 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8375 (mm) REVERT: H 460 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6775 (tp) REVERT: H 497 TYR cc_start: 0.7163 (m-10) cc_final: 0.6876 (m-80) REVERT: I 71 ARG cc_start: 0.5841 (OUTLIER) cc_final: 0.5491 (ttm170) REVERT: I 97 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8069 (mm-40) REVERT: J 69 GLU cc_start: 0.6492 (mm-30) cc_final: 0.6073 (mm-30) REVERT: J 116 ASP cc_start: 0.6984 (m-30) cc_final: 0.6646 (t0) REVERT: M 33 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6628 (t0) REVERT: M 53 PHE cc_start: 0.7086 (t80) cc_final: 0.6833 (t80) REVERT: M 141 MET cc_start: 0.7656 (ptm) cc_final: 0.6487 (ptm) REVERT: M 266 VAL cc_start: 0.5283 (OUTLIER) cc_final: 0.5057 (p) REVERT: N 127 ARG cc_start: 0.7671 (ptm-80) cc_final: 0.7379 (ptm-80) REVERT: N 193 TYR cc_start: 0.7024 (m-80) cc_final: 0.6815 (m-80) REVERT: N 198 VAL cc_start: 0.6581 (m) cc_final: 0.5093 (m) outliers start: 161 outliers final: 83 residues processed: 633 average time/residue: 0.3985 time to fit residues: 382.5694 Evaluate side-chains 469 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 378 time to evaluate : 2.673 ------------------------------------------------------------------------------- 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 172 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 231 HIS 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 79 GLU 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 249 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 152 VAL 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 241 ASP 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 111 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 231 HIS Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 116 MET 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 152 VAL Chi-restraints excluded: chain G residue 204 ILE 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 302 ASP Chi-restraints excluded: chain G residue 325 PHE Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 337 ILE Chi-restraints excluded: chain G residue 343 HIS Chi-restraints excluded: chain H residue 411 LEU 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 460 LEU Chi-restraints excluded: chain H residue 474 LEU Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 511 THR 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 J residue 17 LEU 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 126 ARG Chi-restraints excluded: chain M residue 142 THR 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 M residue 241 ASP 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 201 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 0 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 211 optimal weight: 0.7980 chunk 171 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 83 GLN B 124 GLN B 145 HIS ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 HIS ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 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** ** 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 61 HIS ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 GLN ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 166 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.166720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.145468 restraints weight = 68026.807| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 3.74 r_work: 0.4247 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.7100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26020 Z= 0.195 Angle : 0.734 14.957 35445 Z= 0.384 Chirality : 0.046 0.294 3853 Planarity : 0.005 0.096 4393 Dihedral : 17.393 177.564 4361 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 24.11 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.85 % Favored : 88.81 % Rotamer: Outliers : 4.42 % Allowed : 17.74 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.15), residues: 2931 helix: -0.47 (0.16), residues: 960 sheet: -1.17 (0.24), residues: 498 loop : -2.92 (0.14), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP H 534 HIS 0.013 0.002 HIS B 145 PHE 0.045 0.003 PHE A 53 TYR 0.024 0.002 TYR H 497 ARG 0.009 0.001 ARG J 80 Details of bonding type rmsd hydrogen bonds : bond 0.05132 ( 901) hydrogen bonds : angle 5.40426 ( 2614) covalent geometry : bond 0.00430 (26020) covalent geometry : angle 0.73410 (35445) *********************** 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 547 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 435 time to evaluate : 2.844 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 5 LYS cc_start: 0.7104 (mmtt) cc_final: 0.6682 (mmmt) REVERT: A 17 ASP cc_start: 0.7696 (t70) cc_final: 0.7324 (t0) REVERT: A 103 CYS cc_start: 0.8337 (m) cc_final: 0.7732 (m) REVERT: A 171 PHE cc_start: 0.8613 (m-80) cc_final: 0.8335 (m-80) REVERT: A 200 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6696 (mm-30) REVERT: A 277 LYS cc_start: -0.0368 (OUTLIER) cc_final: -0.0785 (mtpp) REVERT: B 110 ARG cc_start: 0.5411 (ptp-170) cc_final: 0.4740 (ptm160) REVERT: B 194 PHE cc_start: 0.3614 (OUTLIER) cc_final: 0.2416 (m-80) REVERT: C 8 ASP cc_start: 0.6931 (t0) cc_final: 0.6628 (t0) REVERT: C 203 TRP cc_start: 0.4579 (OUTLIER) cc_final: 0.1945 (m100) REVERT: C 220 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6081 (pt0) REVERT: D 16 GLN cc_start: 0.7259 (mp10) cc_final: 0.6498 (mm-40) REVERT: D 56 MET cc_start: 0.6505 (mmm) cc_final: 0.6208 (mmm) REVERT: E 191 GLN cc_start: 0.4181 (OUTLIER) cc_final: 0.3846 (pp30) REVERT: E 200 GLU cc_start: 0.8241 (tm-30) cc_final: 0.8038 (tm-30) REVERT: E 221 MET cc_start: 0.5156 (mtp) cc_final: 0.4560 (mtm) REVERT: E 280 ARG cc_start: 0.4760 (ptm160) cc_final: 0.4354 (ptm160) REVERT: F 93 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7580 (tm-30) REVERT: F 134 SER cc_start: 0.5181 (m) cc_final: 0.4832 (t) REVERT: F 141 MET cc_start: 0.0521 (mpp) cc_final: -0.0475 (tmm) REVERT: G 28 LYS cc_start: 0.8426 (tptt) cc_final: 0.7859 (tptt) REVERT: G 62 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.6161 (tp) REVERT: G 82 TRP cc_start: 0.7618 (p-90) cc_final: 0.7257 (p-90) REVERT: G 104 HIS cc_start: 0.7046 (t-90) cc_final: 0.6840 (t-90) REVERT: G 218 PRO cc_start: 0.7968 (Cg_exo) cc_final: 0.7690 (Cg_endo) REVERT: G 324 LYS cc_start: 0.8331 (ptmm) cc_final: 0.7613 (mmtt) REVERT: H 398 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7997 (tt) REVERT: H 460 LEU cc_start: 0.7655 (tp) cc_final: 0.7230 (tp) REVERT: H 497 TYR cc_start: 0.7416 (m-80) cc_final: 0.7106 (m-80) REVERT: I 71 ARG cc_start: 0.5794 (OUTLIER) cc_final: 0.5510 (ttm170) REVERT: I 89 PHE cc_start: 0.5644 (OUTLIER) cc_final: 0.4500 (t80) REVERT: J 27 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7613 (mm-30) REVERT: J 69 GLU cc_start: 0.6271 (mm-30) cc_final: 0.6050 (mm-30) REVERT: J 97 GLN cc_start: 0.8348 (mp10) cc_final: 0.8143 (pm20) REVERT: J 110 GLN cc_start: 0.7948 (tp40) cc_final: 0.7668 (tp-100) REVERT: J 116 ASP cc_start: 0.6771 (m-30) cc_final: 0.6469 (t0) REVERT: M 33 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.7028 (t0) REVERT: M 112 PHE cc_start: 0.7668 (m-80) cc_final: 0.7459 (m-80) REVERT: N 39 MET cc_start: 0.6934 (mtt) cc_final: 0.6569 (mtt) REVERT: N 103 HIS cc_start: 0.4530 (OUTLIER) cc_final: 0.4118 (m170) outliers start: 112 outliers final: 60 residues processed: 516 average time/residue: 0.3885 time to fit residues: 311.1792 Evaluate side-chains 433 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 362 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 101 TYR 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 221 MET Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 203 TRP Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 265 LEU 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 84 HIS Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 250 TYR Chi-restraints excluded: chain G residue 268 ASP 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 471 LEU Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 536 ILE Chi-restraints excluded: chain I residue 71 ARG Chi-restraints excluded: chain I residue 77 TRP Chi-restraints excluded: chain I residue 88 ARG 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 41 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 126 ARG 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 103 HIS Chi-restraints excluded: chain N residue 181 ASP 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 44 optimal weight: 2.9990 chunk 267 optimal weight: 5.9990 chunk 202 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 192 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN C 124 GLN ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 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** ** G 236 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.164940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.143743 restraints weight = 68610.970| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 3.77 r_work: 0.4220 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.7548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26020 Z= 0.189 Angle : 0.706 10.966 35445 Z= 0.369 Chirality : 0.045 0.258 3853 Planarity : 0.005 0.075 4393 Dihedral : 17.317 177.569 4357 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 24.74 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.88 % Favored : 88.81 % Rotamer: Outliers : 4.77 % Allowed : 18.69 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.15), residues: 2931 helix: -0.30 (0.16), residues: 958 sheet: -1.03 (0.24), residues: 478 loop : -2.82 (0.14), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 534 HIS 0.018 0.002 HIS C 214 PHE 0.051 0.003 PHE A 53 TYR 0.022 0.002 TYR J 106 ARG 0.008 0.001 ARG G 340 Details of bonding type rmsd hydrogen bonds : bond 0.05012 ( 901) hydrogen bonds : angle 5.27141 ( 2614) covalent geometry : bond 0.00416 (26020) covalent geometry : angle 0.70570 (35445) *********************** 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 512 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 391 time to evaluate : 2.777 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 35 GLN cc_start: 0.7725 (tp40) cc_final: 0.7521 (tt0) REVERT: A 56 MET cc_start: 0.6384 (tpt) cc_final: 0.5297 (tpt) REVERT: A 103 CYS cc_start: 0.8396 (m) cc_final: 0.7801 (m) REVERT: A 131 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8304 (mt) REVERT: A 171 PHE cc_start: 0.8602 (m-80) cc_final: 0.8312 (m-80) REVERT: A 200 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6700 (mm-30) REVERT: A 277 LYS cc_start: -0.0006 (OUTLIER) cc_final: -0.0330 (ttmm) REVERT: B 251 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7317 (mttm) REVERT: B 273 LEU cc_start: 0.7436 (tt) cc_final: 0.6929 (mm) REVERT: C 8 ASP cc_start: 0.7097 (t0) cc_final: 0.6781 (t0) REVERT: C 56 MET cc_start: 0.6736 (ptp) cc_final: 0.6396 (ptm) REVERT: C 75 ASN cc_start: 0.6471 (m-40) cc_final: 0.6159 (t0) REVERT: C 203 TRP cc_start: 0.4578 (OUTLIER) cc_final: 0.2061 (m100) REVERT: D 16 GLN cc_start: 0.7344 (mp10) cc_final: 0.6702 (mm-40) REVERT: D 56 MET cc_start: 0.6591 (mmm) cc_final: 0.6329 (mmm) REVERT: E 116 MET cc_start: 0.4552 (mpp) cc_final: 0.4195 (pmm) REVERT: E 191 GLN cc_start: 0.4108 (OUTLIER) cc_final: 0.3595 (pp30) REVERT: E 200 GLU cc_start: 0.8276 (tm-30) cc_final: 0.8021 (tm-30) REVERT: E 221 MET cc_start: 0.5216 (mtp) cc_final: 0.4590 (mtm) REVERT: E 264 TYR cc_start: 0.4686 (OUTLIER) cc_final: 0.4296 (t80) REVERT: E 271 LYS cc_start: 0.7843 (mttt) cc_final: 0.7438 (mmtt) REVERT: F 93 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7600 (tm-30) REVERT: F 134 SER cc_start: 0.5171 (m) cc_final: 0.4889 (t) REVERT: G 1 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.6889 (ppp) REVERT: G 80 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6438 (mm) REVERT: G 104 HIS cc_start: 0.6922 (t-90) cc_final: 0.6677 (t70) REVERT: G 218 PRO cc_start: 0.7956 (Cg_exo) cc_final: 0.7702 (Cg_endo) REVERT: G 324 LYS cc_start: 0.8406 (ptmm) cc_final: 0.7675 (mmtt) REVERT: G 326 TYR cc_start: 0.5469 (p90) cc_final: 0.4893 (p90) REVERT: H 398 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7881 (tt) REVERT: H 513 MET cc_start: 0.8471 (mmp) cc_final: 0.8253 (mmm) REVERT: I 24 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8308 (mm) REVERT: I 89 PHE cc_start: 0.5887 (OUTLIER) cc_final: 0.4701 (t80) REVERT: I 109 THR cc_start: 0.7916 (p) cc_final: 0.7702 (p) REVERT: J 69 GLU cc_start: 0.6480 (mm-30) cc_final: 0.6248 (mm-30) REVERT: J 110 GLN cc_start: 0.8031 (tp40) cc_final: 0.7719 (tp-100) REVERT: J 116 ASP cc_start: 0.6762 (m-30) cc_final: 0.6447 (t0) REVERT: M 279 LEU cc_start: 0.7883 (tt) cc_final: 0.7578 (mt) REVERT: N 39 MET cc_start: 0.6856 (mtt) cc_final: 0.6495 (mtt) REVERT: N 47 ILE cc_start: 0.6527 (OUTLIER) cc_final: 0.6298 (mm) REVERT: N 72 THR cc_start: 0.7514 (p) cc_final: 0.7247 (p) REVERT: N 100 TYR cc_start: 0.7558 (m-80) cc_final: 0.7347 (m-10) REVERT: N 127 ARG cc_start: 0.7162 (ptm-80) cc_final: 0.6943 (ptm-80) outliers start: 121 outliers final: 70 residues processed: 475 average time/residue: 0.3657 time to fit residues: 272.2640 Evaluate side-chains 427 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 345 time to evaluate : 2.684 ------------------------------------------------------------------------------- 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 131 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 199 LEU 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 186 THR Chi-restraints excluded: chain C residue 203 TRP Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 264 TYR Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 81 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 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 G residue 344 GLU 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 470 VAL Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 481 ILE Chi-restraints excluded: chain H residue 536 ILE 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 75 LEU 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 50 VAL Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 172 THR 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 30 THR Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 181 ASP 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 84 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 0.0980 chunk 278 optimal weight: 0.7980 chunk 228 optimal weight: 6.9990 chunk 164 optimal weight: 0.9990 chunk 273 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN B 191 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 ASN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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 486 ASN ** H 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN I 97 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.161744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.141705 restraints weight = 67109.266| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 3.27 r_work: 0.4181 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.8081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26020 Z= 0.204 Angle : 0.715 10.385 35445 Z= 0.373 Chirality : 0.046 0.259 3853 Planarity : 0.005 0.068 4393 Dihedral : 17.290 179.876 4357 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.92 % Favored : 88.81 % Rotamer: Outliers : 4.69 % Allowed : 19.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.15), residues: 2931 helix: -0.41 (0.16), residues: 995 sheet: -1.24 (0.24), residues: 481 loop : -2.70 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 342 HIS 0.012 0.002 HIS C 181 PHE 0.060 0.003 PHE A 53 TYR 0.023 0.002 TYR J 40 ARG 0.013 0.001 ARG H 421 Details of bonding type rmsd hydrogen bonds : bond 0.04862 ( 901) hydrogen bonds : angle 5.31379 ( 2614) covalent geometry : bond 0.00450 (26020) covalent geometry : angle 0.71545 (35445) *********************** 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 497 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 378 time to evaluate : 2.970 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: A 56 MET cc_start: 0.6402 (tpt) cc_final: 0.5373 (tpt) REVERT: A 84 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5924 (pm20) REVERT: A 103 CYS cc_start: 0.8171 (m) cc_final: 0.7637 (m) REVERT: A 131 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7366 (mp) REVERT: A 171 PHE cc_start: 0.8498 (m-80) cc_final: 0.8253 (m-80) REVERT: B 251 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7443 (mttm) REVERT: B 273 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5837 (mm) REVERT: C 56 MET cc_start: 0.6377 (ptp) cc_final: 0.6084 (ptm) REVERT: C 72 ILE cc_start: 0.6291 (mm) cc_final: 0.5316 (mm) REVERT: C 74 ASN cc_start: 0.6541 (m-40) cc_final: 0.6293 (m-40) REVERT: C 203 TRP cc_start: 0.4915 (OUTLIER) cc_final: 0.2289 (m100) REVERT: D 16 GLN cc_start: 0.7238 (mp10) cc_final: 0.6391 (mm-40) REVERT: D 56 MET cc_start: 0.6762 (mmm) cc_final: 0.6307 (mmm) REVERT: D 221 MET cc_start: 0.7848 (mmm) cc_final: 0.7516 (tpp) REVERT: E 191 GLN cc_start: 0.3838 (OUTLIER) cc_final: 0.3430 (pp30) REVERT: E 200 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8086 (tm-30) REVERT: E 211 ASP cc_start: 0.8078 (m-30) cc_final: 0.7837 (t0) REVERT: E 221 MET cc_start: 0.4670 (OUTLIER) cc_final: 0.3873 (mtm) REVERT: E 271 LYS cc_start: 0.7794 (mttt) cc_final: 0.7386 (mmtt) REVERT: F 50 VAL cc_start: 0.7874 (t) cc_final: 0.7550 (p) REVERT: F 93 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7558 (tm-30) REVERT: F 134 SER cc_start: 0.5842 (m) cc_final: 0.5240 (t) REVERT: G 28 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7336 (tptt) REVERT: G 80 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6609 (mm) REVERT: G 81 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8310 (mm) REVERT: G 82 TRP cc_start: 0.7621 (p-90) cc_final: 0.7182 (p-90) REVERT: G 111 VAL cc_start: 0.8399 (m) cc_final: 0.8186 (m) REVERT: G 218 PRO cc_start: 0.8139 (Cg_exo) cc_final: 0.7879 (Cg_endo) REVERT: H 398 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7873 (tt) REVERT: H 431 TYR cc_start: 0.6878 (OUTLIER) cc_final: 0.5124 (t80) REVERT: H 493 ILE cc_start: 0.7883 (mp) cc_final: 0.7590 (mp) REVERT: I 24 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8318 (mm) REVERT: I 89 PHE cc_start: 0.6076 (OUTLIER) cc_final: 0.5058 (t80) REVERT: I 109 THR cc_start: 0.7703 (p) cc_final: 0.7486 (p) REVERT: J 110 GLN cc_start: 0.7980 (tp40) cc_final: 0.7629 (tp-100) REVERT: J 116 ASP cc_start: 0.6703 (m-30) cc_final: 0.6450 (t0) REVERT: M 53 PHE cc_start: 0.7706 (t80) cc_final: 0.7427 (t80) REVERT: M 112 PHE cc_start: 0.7861 (m-80) cc_final: 0.7543 (m-80) REVERT: N 72 THR cc_start: 0.7621 (p) cc_final: 0.7409 (p) REVERT: N 74 MET cc_start: 0.5734 (mtp) cc_final: 0.5467 (mtm) outliers start: 119 outliers final: 71 residues processed: 463 average time/residue: 0.3587 time to fit residues: 263.2213 Evaluate side-chains 433 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 348 time to evaluate : 3.065 ------------------------------------------------------------------------------- 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 84 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 227 TYR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 111 THR 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 251 LYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 203 TRP Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 84 HIS 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 268 ASP 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 471 LEU Chi-restraints excluded: chain H residue 481 ILE Chi-restraints excluded: chain H residue 536 ILE 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 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 46 LEU 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 172 THR 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 30 THR Chi-restraints excluded: chain N residue 181 ASP 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 87 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 chunk 233 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 246 optimal weight: 4.9990 chunk 286 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 253 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 181 HIS ** 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 236 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 554 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.158103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.137977 restraints weight = 66360.587| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 3.08 r_work: 0.4139 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.8765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26020 Z= 0.236 Angle : 0.749 12.802 35445 Z= 0.390 Chirality : 0.047 0.269 3853 Planarity : 0.005 0.072 4393 Dihedral : 17.311 179.194 4354 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 28.60 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.16 % Favored : 88.54 % Rotamer: Outliers : 4.81 % Allowed : 20.35 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.15), residues: 2931 helix: -0.51 (0.16), residues: 1029 sheet: -1.39 (0.25), residues: 435 loop : -2.70 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 342 HIS 0.011 0.002 HIS C 181 PHE 0.065 0.003 PHE A 53 TYR 0.023 0.002 TYR B 107 ARG 0.012 0.001 ARG H 421 Details of bonding type rmsd hydrogen bonds : bond 0.04955 ( 901) hydrogen bonds : angle 5.47635 ( 2614) covalent geometry : bond 0.00515 (26020) covalent geometry : angle 0.74925 (35445) *********************** 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 506 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 384 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.7784 (t0) cc_final: 0.7317 (t0) REVERT: A 28 ASN cc_start: 0.7446 (t0) cc_final: 0.6299 (t0) REVERT: A 56 MET cc_start: 0.6252 (tpt) cc_final: 0.5313 (tpt) REVERT: A 84 GLU cc_start: 0.6086 (OUTLIER) cc_final: 0.5624 (pm20) REVERT: A 103 CYS cc_start: 0.7867 (m) cc_final: 0.7446 (m) REVERT: A 131 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7246 (mp) REVERT: A 171 PHE cc_start: 0.8472 (m-80) cc_final: 0.8182 (m-80) REVERT: B 14 ASP cc_start: 0.6544 (p0) cc_final: 0.6280 (p0) REVERT: B 76 LEU cc_start: 0.6356 (mt) cc_final: 0.6039 (tp) REVERT: B 141 MET cc_start: 0.7179 (mpp) cc_final: 0.6055 (mpp) REVERT: B 150 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7762 (mtm) REVERT: B 179 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6463 (ttm-80) REVERT: B 251 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7622 (mttm) REVERT: B 273 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5656 (mm) REVERT: C 203 TRP cc_start: 0.5288 (OUTLIER) cc_final: 0.2585 (m100) REVERT: D 16 GLN cc_start: 0.7091 (mp10) cc_final: 0.6794 (mp10) REVERT: D 56 MET cc_start: 0.6625 (mmm) cc_final: 0.6263 (mmm) REVERT: D 183 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7358 (m-80) REVERT: D 220 GLN cc_start: 0.8194 (mt0) cc_final: 0.7945 (mt0) REVERT: E 200 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8056 (tm-30) REVERT: E 221 MET cc_start: 0.5417 (OUTLIER) cc_final: 0.4240 (mtm) REVERT: E 271 LYS cc_start: 0.7809 (mttt) cc_final: 0.7365 (mmtt) REVERT: E 280 ARG cc_start: 0.4023 (ptm160) cc_final: 0.3546 (ptm160) REVERT: F 41 VAL cc_start: 0.7404 (t) cc_final: 0.7170 (t) REVERT: F 134 SER cc_start: 0.6122 (m) cc_final: 0.5447 (t) REVERT: G 80 LEU cc_start: 0.7002 (mt) cc_final: 0.6468 (mm) REVERT: G 81 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8441 (mm) REVERT: G 218 PRO cc_start: 0.7735 (Cg_exo) cc_final: 0.7481 (Cg_endo) REVERT: G 326 TYR cc_start: 0.6330 (p90) cc_final: 0.5327 (p90) REVERT: H 398 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7813 (tt) REVERT: H 431 TYR cc_start: 0.6865 (OUTLIER) cc_final: 0.5224 (t80) REVERT: I 89 PHE cc_start: 0.6209 (OUTLIER) cc_final: 0.5248 (t80) REVERT: I 109 THR cc_start: 0.7576 (p) cc_final: 0.7332 (p) REVERT: J 89 PHE cc_start: 0.4509 (OUTLIER) cc_final: 0.2769 (t80) REVERT: J 96 GLU cc_start: 0.7943 (tp30) cc_final: 0.7615 (tp30) REVERT: J 110 GLN cc_start: 0.7925 (tp40) cc_final: 0.7717 (tp-100) REVERT: M 53 PHE cc_start: 0.7547 (t80) cc_final: 0.7211 (t80) REVERT: M 56 MET cc_start: 0.5376 (mmt) cc_final: 0.5138 (ttm) REVERT: N 100 TYR cc_start: 0.7268 (m-10) cc_final: 0.6891 (m-10) outliers start: 122 outliers final: 75 residues processed: 468 average time/residue: 0.3841 time to fit residues: 277.7168 Evaluate side-chains 426 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 337 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 150 MET 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 247 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 THR 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 150 MET Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 203 TRP Chi-restraints excluded: chain C residue 229 PHE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 229 PHE 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 266 VAL Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 81 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 254 LEU Chi-restraints excluded: chain G residue 268 ASP 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 471 LEU Chi-restraints excluded: chain H residue 481 ILE Chi-restraints excluded: chain H residue 566 THR 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 69 GLU 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 46 LEU 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 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 39 MET Chi-restraints excluded: chain N residue 181 ASP 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 134 optimal weight: 6.9990 chunk 283 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 281 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 63 HIS ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN D 204 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 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 ** 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 400 GLN ** 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** M 21 ASN ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.157834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.137791 restraints weight = 66704.237| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 3.07 r_work: 0.4136 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.9078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 26020 Z= 0.210 Angle : 0.736 10.570 35445 Z= 0.382 Chirality : 0.046 0.314 3853 Planarity : 0.005 0.077 4393 Dihedral : 17.279 178.932 4353 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 28.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.16 % Favored : 88.54 % Rotamer: Outliers : 4.38 % Allowed : 21.57 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.15), residues: 2931 helix: -0.52 (0.16), residues: 1022 sheet: -1.41 (0.25), residues: 433 loop : -2.71 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 82 HIS 0.009 0.001 HIS G 343 PHE 0.063 0.003 PHE A 53 TYR 0.026 0.002 TYR J 40 ARG 0.011 0.001 ARG H 421 Details of bonding type rmsd hydrogen bonds : bond 0.04846 ( 901) hydrogen bonds : angle 5.48232 ( 2614) covalent geometry : bond 0.00472 (26020) covalent geometry : angle 0.73603 (35445) *********************** 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 499 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 388 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.7823 (t0) cc_final: 0.7404 (t0) REVERT: A 56 MET cc_start: 0.6056 (tpt) cc_final: 0.5379 (tpt) REVERT: A 72 ILE cc_start: 0.4762 (mm) cc_final: 0.4546 (tp) REVERT: A 84 GLU cc_start: 0.6138 (OUTLIER) cc_final: 0.5858 (pm20) REVERT: A 103 CYS cc_start: 0.7772 (m) cc_final: 0.7506 (m) REVERT: A 131 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7086 (mp) REVERT: A 141 MET cc_start: 0.6136 (mmt) cc_final: 0.5820 (mmt) REVERT: A 171 PHE cc_start: 0.8470 (m-80) cc_final: 0.8188 (m-80) REVERT: A 195 SER cc_start: 0.5710 (m) cc_final: 0.5235 (p) REVERT: B 68 ARG cc_start: 0.6954 (tmm-80) cc_final: 0.6746 (ptt180) REVERT: B 76 LEU cc_start: 0.6478 (mt) cc_final: 0.5961 (tp) REVERT: B 150 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7557 (mtm) REVERT: B 179 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.6370 (ttm-80) REVERT: B 251 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7215 (mtpt) REVERT: B 273 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.5602 (mt) REVERT: C 108 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8449 (t70) REVERT: C 203 TRP cc_start: 0.5576 (OUTLIER) cc_final: 0.2786 (m100) REVERT: D 16 GLN cc_start: 0.7219 (mp10) cc_final: 0.6860 (mp10) REVERT: D 56 MET cc_start: 0.6559 (mmm) cc_final: 0.6230 (mmm) REVERT: E 8 ASP cc_start: 0.6876 (m-30) cc_final: 0.6221 (p0) REVERT: E 172 THR cc_start: 0.7618 (m) cc_final: 0.6815 (p) REVERT: E 221 MET cc_start: 0.5458 (OUTLIER) cc_final: 0.4092 (mtm) REVERT: E 271 LYS cc_start: 0.7734 (mttt) cc_final: 0.7222 (tppt) REVERT: F 93 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7703 (pp20) REVERT: F 134 SER cc_start: 0.6374 (m) cc_final: 0.5830 (t) REVERT: G 1 MET cc_start: 0.6783 (ppp) cc_final: 0.6475 (ppp) REVERT: G 80 LEU cc_start: 0.6901 (mt) cc_final: 0.6472 (mm) REVERT: G 81 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8394 (mm) REVERT: G 82 TRP cc_start: 0.7828 (p-90) cc_final: 0.7560 (p-90) REVERT: G 218 PRO cc_start: 0.7699 (Cg_exo) cc_final: 0.7447 (Cg_endo) REVERT: G 326 TYR cc_start: 0.6058 (p90) cc_final: 0.5504 (p90) REVERT: H 398 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7782 (tt) REVERT: H 431 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.5271 (t80) REVERT: H 474 LEU cc_start: 0.8936 (tp) cc_final: 0.8456 (tp) REVERT: H 482 GLN cc_start: 0.6441 (tm-30) cc_final: 0.6229 (tm-30) REVERT: I 16 ARG cc_start: 0.7197 (ttp-170) cc_final: 0.6979 (ttp-110) REVERT: I 89 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.5371 (t80) REVERT: J 27 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7430 (mm-30) REVERT: J 89 PHE cc_start: 0.4486 (OUTLIER) cc_final: 0.2121 (t80) REVERT: J 110 GLN cc_start: 0.7934 (tp40) cc_final: 0.7709 (tp-100) REVERT: M 53 PHE cc_start: 0.7532 (t80) cc_final: 0.7149 (t80) REVERT: M 56 MET cc_start: 0.5498 (mmt) cc_final: 0.5186 (ttp) REVERT: M 279 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7229 (mt) REVERT: N 100 TYR cc_start: 0.7324 (m-80) cc_final: 0.7061 (m-10) outliers start: 111 outliers final: 70 residues processed: 465 average time/residue: 0.3820 time to fit residues: 277.1598 Evaluate side-chains 438 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 353 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 THR 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 249 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain B residue 150 MET 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 249 VAL Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 108 ASP 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 186 THR 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 33 ASP Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 229 PHE 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 273 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 81 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 254 LEU Chi-restraints excluded: chain G residue 268 ASP 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 471 LEU Chi-restraints excluded: chain H residue 536 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 69 GLU 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 46 LEU 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 201 LEU Chi-restraints excluded: chain M residue 221 MET Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain M residue 279 LEU Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 181 ASP 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 295 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 0.0270 chunk 235 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 264 optimal weight: 3.9990 chunk 234 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 HIS ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 ASN M 35 GLN ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 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 = 0.4492 r_free = 0.4492 target = 0.152914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.132418 restraints weight = 66277.929| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 3.02 r_work: 0.4057 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.9800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 26020 Z= 0.274 Angle : 0.814 10.757 35445 Z= 0.422 Chirality : 0.049 0.349 3853 Planarity : 0.005 0.067 4393 Dihedral : 17.314 179.026 4352 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 32.21 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.74 % Favored : 87.89 % Rotamer: Outliers : 4.69 % Allowed : 22.08 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.15), residues: 2931 helix: -0.74 (0.16), residues: 1025 sheet: -1.48 (0.25), residues: 436 loop : -2.78 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP N 43 HIS 0.011 0.002 HIS A 63 PHE 0.070 0.003 PHE A 53 TYR 0.028 0.003 TYR J 40 ARG 0.012 0.001 ARG H 421 Details of bonding type rmsd hydrogen bonds : bond 0.05163 ( 901) hydrogen bonds : angle 5.72761 ( 2614) covalent geometry : bond 0.00603 (26020) covalent geometry : angle 0.81433 (35445) *********************** 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 502 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 383 time to evaluate : 3.117 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: A 8 ASP cc_start: 0.7291 (t0) cc_final: 0.6976 (m-30) REVERT: A 28 ASN cc_start: 0.7343 (t0) cc_final: 0.6591 (t0) REVERT: A 35 GLN cc_start: 0.7754 (tp40) cc_final: 0.7418 (mm-40) REVERT: A 56 MET cc_start: 0.6188 (tpt) cc_final: 0.5610 (tpt) REVERT: A 72 ILE cc_start: 0.4745 (mm) cc_final: 0.4504 (tp) REVERT: A 103 CYS cc_start: 0.7703 (m) cc_final: 0.7495 (m) REVERT: A 131 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.6953 (mp) REVERT: A 150 MET cc_start: 0.4821 (ptp) cc_final: 0.4037 (ptp) REVERT: A 171 PHE cc_start: 0.8399 (m-80) cc_final: 0.8149 (m-80) REVERT: B 76 LEU cc_start: 0.6922 (mt) cc_final: 0.5939 (tp) REVERT: B 90 GLU cc_start: 0.7004 (tp30) cc_final: 0.6609 (tm-30) REVERT: B 150 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7482 (mtm) REVERT: B 167 MET cc_start: 0.7081 (mmm) cc_final: 0.6872 (tpp) REVERT: B 173 VAL cc_start: 0.8630 (t) cc_final: 0.8391 (m) REVERT: B 179 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6673 (ttm-80) REVERT: B 251 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7341 (mtpt) REVERT: B 273 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.5552 (mt) REVERT: C 63 HIS cc_start: 0.7294 (m-70) cc_final: 0.7027 (m170) REVERT: C 201 LEU cc_start: 0.7331 (tt) cc_final: 0.6629 (mt) REVERT: D 56 MET cc_start: 0.6954 (mmm) cc_final: 0.6583 (mmm) REVERT: D 116 MET cc_start: 0.4231 (ttt) cc_final: 0.3597 (tmm) REVERT: E 35 GLN cc_start: 0.5915 (mt0) cc_final: 0.5625 (mp10) REVERT: E 141 MET cc_start: 0.3377 (pmm) cc_final: 0.1657 (ppp) REVERT: E 271 LYS cc_start: 0.7803 (mttt) cc_final: 0.7426 (mmtt) REVERT: E 280 ARG cc_start: 0.4898 (ptm160) cc_final: 0.4563 (ptm160) REVERT: F 134 SER cc_start: 0.6447 (m) cc_final: 0.5815 (t) REVERT: G 28 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7711 (tptt) REVERT: G 80 LEU cc_start: 0.7048 (mt) cc_final: 0.6711 (mm) REVERT: G 82 TRP cc_start: 0.7862 (p-90) cc_final: 0.7583 (p-90) REVERT: G 104 HIS cc_start: 0.6178 (t70) cc_final: 0.5940 (t70) REVERT: G 218 PRO cc_start: 0.7637 (Cg_exo) cc_final: 0.7415 (Cg_endo) REVERT: G 326 TYR cc_start: 0.6157 (p90) cc_final: 0.5492 (p90) REVERT: H 431 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.5627 (t80) REVERT: H 482 GLN cc_start: 0.6630 (tm-30) cc_final: 0.6363 (tm-30) REVERT: H 537 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6600 (mtm-85) REVERT: I 16 ARG cc_start: 0.7190 (ttp-170) cc_final: 0.6911 (ttp-110) REVERT: J 27 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7442 (mm-30) REVERT: J 65 LYS cc_start: 0.7285 (pttp) cc_final: 0.7023 (ptmm) REVERT: J 69 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6072 (tm-30) REVERT: J 89 PHE cc_start: 0.5325 (OUTLIER) cc_final: 0.3102 (t80) REVERT: J 95 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8586 (mm) REVERT: M 53 PHE cc_start: 0.7664 (t80) cc_final: 0.7287 (t80) REVERT: M 56 MET cc_start: 0.5920 (mmt) cc_final: 0.5529 (ttp) REVERT: N 39 MET cc_start: 0.6687 (mpp) cc_final: 0.6346 (mmm) REVERT: N 100 TYR cc_start: 0.7486 (m-80) cc_final: 0.7278 (m-80) REVERT: N 135 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.7485 (t80) outliers start: 119 outliers final: 81 residues processed: 466 average time/residue: 0.3757 time to fit residues: 273.6906 Evaluate side-chains 451 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 358 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 213 ASP 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 42 THR Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 150 MET 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 249 VAL Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 108 ASP 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 203 TRP Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 187 HIS 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 E residue 111 THR Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain G residue 62 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 254 LEU Chi-restraints excluded: chain G residue 268 ASP 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 402 THR 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 536 ILE Chi-restraints excluded: chain H residue 537 ARG Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain I residue 10 ILE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 95 LEU 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 46 LEU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 221 MET Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 42 LEU Chi-restraints excluded: chain N residue 135 PHE Chi-restraints excluded: chain N residue 181 ASP 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 97 optimal weight: 0.0670 chunk 15 optimal weight: 0.4980 chunk 158 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 195 optimal weight: 9.9990 chunk 214 optimal weight: 0.6980 chunk 134 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 ASN ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** 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 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 531 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 194 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.157989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.138245 restraints weight = 66729.884| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 3.17 r_work: 0.4149 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.9618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26020 Z= 0.164 Angle : 0.753 17.181 35445 Z= 0.386 Chirality : 0.046 0.242 3853 Planarity : 0.005 0.089 4393 Dihedral : 17.232 179.080 4352 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 28.18 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.34 % Favored : 89.29 % Rotamer: Outliers : 3.63 % Allowed : 23.30 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.15), residues: 2931 helix: -0.67 (0.16), residues: 1019 sheet: -1.39 (0.26), residues: 390 loop : -2.67 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 43 HIS 0.010 0.002 HIS C 181 PHE 0.036 0.003 PHE H 558 TYR 0.029 0.002 TYR J 40 ARG 0.012 0.001 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.04745 ( 901) hydrogen bonds : angle 5.53847 ( 2614) covalent geometry : bond 0.00372 (26020) covalent geometry : angle 0.75319 (35445) *********************** 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 507 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 415 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.7726 (t0) cc_final: 0.7392 (m-30) REVERT: A 28 ASN cc_start: 0.7393 (t0) cc_final: 0.6106 (t0) REVERT: A 103 CYS cc_start: 0.7436 (m) cc_final: 0.6616 (m) REVERT: A 131 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.6981 (mp) REVERT: A 171 PHE cc_start: 0.8367 (m-80) cc_final: 0.8145 (m-80) REVERT: B 8 ASP cc_start: 0.6144 (t0) cc_final: 0.5900 (t0) REVERT: B 68 ARG cc_start: 0.7440 (tmm-80) cc_final: 0.7166 (ptt180) REVERT: B 93 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8084 (mp0) REVERT: B 150 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7021 (mtm) REVERT: B 179 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6349 (ttm-80) REVERT: B 210 PHE cc_start: 0.7663 (m-80) cc_final: 0.6893 (m-80) REVERT: B 221 MET cc_start: 0.7179 (mmm) cc_final: 0.6959 (mmt) REVERT: B 251 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7358 (mtpt) REVERT: B 261 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: B 273 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.5644 (mt) REVERT: C 63 HIS cc_start: 0.6882 (m-70) cc_final: 0.6570 (m170) REVERT: C 108 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8462 (t0) REVERT: C 201 LEU cc_start: 0.7079 (tt) cc_final: 0.6395 (mt) REVERT: D 111 THR cc_start: 0.6917 (m) cc_final: 0.6489 (m) REVERT: D 116 MET cc_start: 0.4136 (ttt) cc_final: 0.3593 (tmm) REVERT: D 252 LYS cc_start: 0.5341 (OUTLIER) cc_final: 0.4741 (ptpp) REVERT: D 255 VAL cc_start: 0.3154 (OUTLIER) cc_final: 0.2684 (t) REVERT: E 35 GLN cc_start: 0.6016 (mt0) cc_final: 0.5283 (mp10) REVERT: E 141 MET cc_start: 0.4480 (pmm) cc_final: 0.2824 (ppp) REVERT: E 271 LYS cc_start: 0.7689 (mttt) cc_final: 0.7285 (mmtt) REVERT: F 134 SER cc_start: 0.6439 (m) cc_final: 0.6134 (t) REVERT: G 56 LYS cc_start: 0.5032 (mmtt) cc_final: 0.4636 (mmtm) REVERT: G 80 LEU cc_start: 0.7134 (mt) cc_final: 0.6772 (mm) REVERT: G 218 PRO cc_start: 0.7534 (Cg_exo) cc_final: 0.7306 (Cg_endo) REVERT: G 247 MET cc_start: 0.7844 (tmm) cc_final: 0.7457 (tmm) REVERT: G 326 TYR cc_start: 0.6356 (p90) cc_final: 0.6118 (p90) REVERT: H 431 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.5129 (t80) REVERT: H 460 LEU cc_start: 0.8466 (tp) cc_final: 0.8248 (tp) REVERT: H 482 GLN cc_start: 0.6764 (tm-30) cc_final: 0.6397 (tm-30) REVERT: H 537 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6650 (mtm-85) REVERT: I 12 TYR cc_start: 0.8412 (t80) cc_final: 0.8031 (t80) REVERT: I 16 ARG cc_start: 0.7256 (ttp-170) cc_final: 0.6958 (ttp-110) REVERT: I 89 PHE cc_start: 0.3907 (OUTLIER) cc_final: 0.1839 (t80) REVERT: J 27 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7457 (mm-30) REVERT: J 65 LYS cc_start: 0.7013 (pttp) cc_final: 0.6807 (ptmm) REVERT: J 87 GLN cc_start: 0.7847 (pm20) cc_final: 0.7606 (pm20) REVERT: J 89 PHE cc_start: 0.4670 (OUTLIER) cc_final: 0.2654 (t80) REVERT: M 53 PHE cc_start: 0.7379 (t80) cc_final: 0.7171 (t80) REVERT: M 56 MET cc_start: 0.5835 (mmt) cc_final: 0.5150 (ttm) REVERT: M 279 LEU cc_start: 0.7454 (tt) cc_final: 0.7250 (mt) REVERT: N 39 MET cc_start: 0.6714 (mpp) cc_final: 0.6424 (mmm) REVERT: N 100 TYR cc_start: 0.7302 (m-80) cc_final: 0.7012 (m-10) REVERT: N 135 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7540 (t80) REVERT: N 167 ASP cc_start: 0.7206 (p0) cc_final: 0.6981 (p0) outliers start: 92 outliers final: 56 residues processed: 482 average time/residue: 0.3825 time to fit residues: 287.8579 Evaluate side-chains 442 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 372 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 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 42 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 261 PHE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 108 ASP 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 214 HIS Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 252 LYS Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 226 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 343 HIS Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 431 TYR Chi-restraints excluded: chain H residue 454 LYS Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 536 ILE Chi-restraints excluded: chain H residue 537 ARG Chi-restraints excluded: chain H residue 566 THR Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 221 MET Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 135 PHE Chi-restraints excluded: chain N residue 181 ASP 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 31 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 160 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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** ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 HIS ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN I 97 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 ASN ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 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 = 0.4498 r_free = 0.4498 target = 0.153418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.133132 restraints weight = 66695.854| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 3.02 r_work: 0.4069 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 1.0035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26020 Z= 0.245 Angle : 0.813 12.724 35445 Z= 0.418 Chirality : 0.048 0.279 3853 Planarity : 0.005 0.071 4393 Dihedral : 17.245 178.590 4352 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 32.18 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.84 % Favored : 87.82 % Rotamer: Outliers : 3.35 % Allowed : 24.01 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.15), residues: 2931 helix: -0.78 (0.16), residues: 1028 sheet: -1.53 (0.25), residues: 419 loop : -2.73 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP N 43 HIS 0.010 0.002 HIS B 181 PHE 0.053 0.003 PHE A 53 TYR 0.052 0.003 TYR B 107 ARG 0.011 0.001 ARG H 421 Details of bonding type rmsd hydrogen bonds : bond 0.05014 ( 901) hydrogen bonds : angle 5.57685 ( 2614) covalent geometry : bond 0.00550 (26020) covalent geometry : angle 0.81273 (35445) ********************** 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 453 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 368 time to evaluate : 2.759 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: A 8 ASP cc_start: 0.7326 (t0) cc_final: 0.7052 (m-30) REVERT: A 103 CYS cc_start: 0.7822 (m) cc_final: 0.7175 (m) REVERT: A 131 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.6898 (mp) REVERT: A 171 PHE cc_start: 0.8389 (m-80) cc_final: 0.8171 (m-80) REVERT: B 8 ASP cc_start: 0.6029 (t0) cc_final: 0.5781 (t0) REVERT: B 150 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7132 (mtm) REVERT: B 173 VAL cc_start: 0.8703 (t) cc_final: 0.8469 (m) REVERT: B 179 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6545 (ttm-80) REVERT: B 251 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7390 (mtpt) REVERT: B 273 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.5496 (mt) REVERT: D 7 TYR cc_start: 0.6348 (m-80) cc_final: 0.6064 (m-80) REVERT: D 56 MET cc_start: 0.6600 (mmm) cc_final: 0.6307 (tpt) REVERT: D 105 ARG cc_start: 0.5973 (tpt170) cc_final: 0.5741 (tpt90) REVERT: D 111 THR cc_start: 0.7274 (OUTLIER) cc_final: 0.6832 (m) REVERT: D 116 MET cc_start: 0.4981 (ttt) cc_final: 0.4059 (tmm) REVERT: E 141 MET cc_start: 0.4697 (pmm) cc_final: 0.3026 (ppp) REVERT: E 271 LYS cc_start: 0.7786 (mttt) cc_final: 0.7248 (tppt) REVERT: E 280 ARG cc_start: 0.5132 (ptm160) cc_final: 0.4756 (ptm160) REVERT: F 134 SER cc_start: 0.6450 (m) cc_final: 0.6147 (t) REVERT: G 80 LEU cc_start: 0.7005 (mt) cc_final: 0.6699 (mm) REVERT: G 218 PRO cc_start: 0.7517 (Cg_exo) cc_final: 0.7294 (Cg_endo) REVERT: G 326 TYR cc_start: 0.6159 (p90) cc_final: 0.5875 (p90) REVERT: H 431 TYR cc_start: 0.7026 (OUTLIER) cc_final: 0.5790 (t80) REVERT: H 497 TYR cc_start: 0.6983 (m-80) cc_final: 0.6485 (m-80) REVERT: H 537 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6398 (mtm-85) REVERT: I 16 ARG cc_start: 0.7193 (ttp-170) cc_final: 0.6905 (ttp-110) REVERT: I 23 LYS cc_start: 0.7687 (tmtt) cc_final: 0.7432 (tmtt) REVERT: I 89 PHE cc_start: 0.5409 (OUTLIER) cc_final: 0.3100 (t80) REVERT: I 94 ASN cc_start: 0.8229 (t0) cc_final: 0.7868 (p0) REVERT: J 69 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.5953 (tm-30) REVERT: J 89 PHE cc_start: 0.5137 (OUTLIER) cc_final: 0.2991 (t80) REVERT: J 106 TYR cc_start: 0.8183 (m-80) cc_final: 0.7831 (t80) REVERT: J 116 ASP cc_start: 0.6771 (t0) cc_final: 0.6322 (m-30) REVERT: M 53 PHE cc_start: 0.7570 (t80) cc_final: 0.7189 (t80) REVERT: M 56 MET cc_start: 0.5734 (mmt) cc_final: 0.5409 (ttp) REVERT: M 115 VAL cc_start: 0.3803 (OUTLIER) cc_final: 0.2346 (p) REVERT: N 39 MET cc_start: 0.6534 (mpp) cc_final: 0.6276 (mmm) REVERT: N 55 GLU cc_start: 0.6367 (tt0) cc_final: 0.6160 (tt0) REVERT: N 135 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7427 (t80) outliers start: 85 outliers final: 58 residues processed: 429 average time/residue: 0.3655 time to fit residues: 245.6644 Evaluate side-chains 424 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 353 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 THR 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 42 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 229 PHE Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 226 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 343 HIS Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 431 TYR Chi-restraints excluded: chain H residue 454 LYS 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 566 THR Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 101 TYR Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 221 MET Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 135 PHE Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 181 ASP 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 169 optimal weight: 6.9990 chunk 36 optimal weight: 0.2980 chunk 72 optimal weight: 4.9990 chunk 116 optimal weight: 0.2980 chunk 109 optimal weight: 5.9990 chunk 203 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 173 optimal weight: 0.3980 chunk 174 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 HIS ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 383 ASN ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 HIS ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.157630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.137973 restraints weight = 66295.420| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 3.13 r_work: 0.4144 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.9925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26020 Z= 0.167 Angle : 0.766 13.816 35445 Z= 0.391 Chirality : 0.046 0.244 3853 Planarity : 0.005 0.086 4393 Dihedral : 17.233 179.211 4352 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 28.46 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.54 % Favored : 89.15 % Rotamer: Outliers : 2.60 % Allowed : 24.84 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.15), residues: 2931 helix: -0.63 (0.16), residues: 997 sheet: -1.31 (0.27), residues: 377 loop : -2.69 (0.14), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 43 HIS 0.017 0.002 HIS I 92 PHE 0.046 0.003 PHE A 53 TYR 0.023 0.002 TYR J 105 ARG 0.010 0.001 ARG M 218 Details of bonding type rmsd hydrogen bonds : bond 0.04800 ( 901) hydrogen bonds : angle 5.49065 ( 2614) covalent geometry : bond 0.00378 (26020) covalent geometry : angle 0.76564 (35445) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12796.35 seconds wall clock time: 222 minutes 50.73 seconds (13370.73 seconds total)