Starting phenix.real_space_refine on Sat Jun 21 17:29:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gam_29900/06_2025/8gam_29900.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gam_29900/06_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_29900/06_2025/8gam_29900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gam_29900/06_2025/8gam_29900.map" model { file = "/net/cci-nas-00/data/ceres_data/8gam_29900/06_2025/8gam_29900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gam_29900/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.65, per 1000 atoms: 0.54 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: 5.63 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: 7.74 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: 7.47 Time building geometry restraints manager: 6.68 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 55.610 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.250 ------------------------------------------------------------------------------- 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 : 2.825 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: 0.4359 time to fit residues: 545.9258 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 : 2.539 ------------------------------------------------------------------------------- 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: 0.0570 chunk 142 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 271 optimal weight: 0.8980 overall best weight: 4.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN 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 83 GLN ** 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 187 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.165393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.144706 restraints weight = 69620.024| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 3.59 r_work: 0.4269 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.6676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.109 26020 Z= 0.431 Angle : 1.139 19.865 35445 Z= 0.595 Chirality : 0.059 0.344 3853 Planarity : 0.009 0.110 4393 Dihedral : 17.858 178.752 4375 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 33.86 Ramachandran Plot: Outliers : 0.41 % Allowed : 10.44 % Favored : 89.15 % Rotamer: Outliers : 6.19 % Allowed : 14.12 % Favored : 79.69 % 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: -3.15 (0.14), residues: 2931 helix: -1.25 (0.15), residues: 1001 sheet: -0.89 (0.25), residues: 423 loop : -3.15 (0.13), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP H 534 HIS 0.017 0.003 HIS G 104 PHE 0.044 0.005 PHE C 188 TYR 0.043 0.005 TYR J 106 ARG 0.020 0.002 ARG A 110 Details of bonding type rmsd hydrogen bonds : bond 0.06937 ( 901) hydrogen bonds : angle 6.07822 ( 2614) covalent geometry : bond 0.00933 (26020) covalent geometry : angle 1.13940 (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 667 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 510 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.7900 (t0) cc_final: 0.7147 (t0) REVERT: A 42 THR cc_start: 0.9203 (p) cc_final: 0.8948 (p) REVERT: A 200 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6734 (mm-30) REVERT: A 209 MET cc_start: 0.7278 (ttm) cc_final: 0.6985 (ttp) REVERT: B 11 PHE cc_start: 0.7458 (t80) cc_final: 0.7247 (t80) REVERT: C 8 ASP cc_start: 0.6547 (t0) cc_final: 0.6035 (t0) REVERT: C 181 HIS cc_start: 0.7609 (m-70) cc_final: 0.6497 (m170) REVERT: C 220 GLN cc_start: 0.7019 (OUTLIER) cc_final: 0.6612 (pt0) REVERT: C 241 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7787 (t0) REVERT: D 16 GLN cc_start: 0.7273 (mp10) cc_final: 0.6660 (mm-40) REVERT: D 56 MET cc_start: 0.6461 (mmm) cc_final: 0.6113 (mmm) REVERT: E 5 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8516 (pttt) REVERT: E 131 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7308 (pt) REVERT: E 144 GLU cc_start: 0.8510 (tt0) cc_final: 0.8202 (tt0) REVERT: E 204 GLN cc_start: 0.8413 (tp40) cc_final: 0.7768 (tp-100) REVERT: E 221 MET cc_start: 0.5396 (OUTLIER) cc_final: 0.4317 (mtm) REVERT: E 271 LYS cc_start: 0.7963 (mttt) cc_final: 0.7503 (mmtt) REVERT: E 280 ARG cc_start: 0.4727 (ptm160) cc_final: 0.4380 (ptm160) REVERT: F 4 GLU cc_start: 0.7829 (pp20) cc_final: 0.7599 (pm20) REVERT: F 63 HIS cc_start: 0.8253 (m-70) cc_final: 0.8014 (m-70) REVERT: F 69 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6971 (mm-30) REVERT: F 93 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7598 (tm-30) REVERT: F 134 SER cc_start: 0.5605 (m) cc_final: 0.5232 (t) REVERT: F 141 MET cc_start: 0.0868 (mpp) cc_final: -0.0418 (tmm) REVERT: G 28 LYS cc_start: 0.8395 (tptt) cc_final: 0.7665 (tptt) REVERT: G 80 LEU cc_start: 0.7689 (mt) cc_final: 0.6945 (mm) REVERT: G 82 TRP cc_start: 0.7550 (p-90) cc_final: 0.7234 (p-90) REVERT: G 218 PRO cc_start: 0.7948 (Cg_exo) cc_final: 0.7672 (Cg_endo) REVERT: G 324 LYS cc_start: 0.8229 (ptmm) cc_final: 0.7496 (mmtt) REVERT: H 460 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6413 (tp) REVERT: H 497 TYR cc_start: 0.7159 (m-10) cc_final: 0.6887 (m-10) REVERT: H 546 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.7372 (m-80) REVERT: I 71 ARG cc_start: 0.5858 (OUTLIER) cc_final: 0.5462 (ttm170) REVERT: I 97 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8038 (mm-40) REVERT: J 40 TYR cc_start: 0.8295 (m-80) cc_final: 0.8070 (m-80) REVERT: J 69 GLU cc_start: 0.6469 (mm-30) cc_final: 0.6053 (mm-30) REVERT: J 116 ASP cc_start: 0.6988 (m-30) cc_final: 0.6638 (t0) REVERT: M 33 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6570 (t0) REVERT: M 53 PHE cc_start: 0.6985 (t80) cc_final: 0.6726 (t80) REVERT: N 127 ARG cc_start: 0.7668 (ptm-80) cc_final: 0.7385 (ptm-80) REVERT: N 193 TYR cc_start: 0.6975 (m-80) cc_final: 0.6740 (m-80) outliers start: 157 outliers final: 82 residues processed: 624 average time/residue: 0.4078 time to fit residues: 386.2867 Evaluate side-chains 463 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 373 time to evaluate : 2.585 ------------------------------------------------------------------------------- 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 65 ILE 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 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 131 LEU Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain G residue 9 TYR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 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 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 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 546 PHE 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 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: 0.9980 chunk 93 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 211 optimal weight: 0.7980 chunk 171 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 174 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN 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 D 214 HIS ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** E 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 ASN ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN F 83 GLN ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 531 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.168962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.148015 restraints weight = 68218.554| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 3.80 r_work: 0.4282 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.6855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26020 Z= 0.173 Angle : 0.718 15.100 35445 Z= 0.375 Chirality : 0.045 0.283 3853 Planarity : 0.005 0.092 4393 Dihedral : 17.339 177.892 4361 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.64 % Favored : 89.01 % Rotamer: Outliers : 4.18 % Allowed : 17.55 % Favored : 78.27 % 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: -2.58 (0.15), residues: 2931 helix: -0.41 (0.16), residues: 964 sheet: -1.11 (0.24), residues: 497 loop : -2.94 (0.14), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 534 HIS 0.011 0.002 HIS B 145 PHE 0.043 0.003 PHE A 53 TYR 0.024 0.002 TYR J 106 ARG 0.009 0.001 ARG J 80 Details of bonding type rmsd hydrogen bonds : bond 0.05054 ( 901) hydrogen bonds : angle 5.30985 ( 2614) covalent geometry : bond 0.00384 (26020) covalent geometry : angle 0.71840 (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 544 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 438 time to evaluate : 2.789 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 5 LYS cc_start: 0.7084 (mmtt) cc_final: 0.6716 (mmmt) REVERT: A 17 ASP cc_start: 0.7484 (t70) cc_final: 0.7277 (t0) REVERT: A 103 CYS cc_start: 0.8411 (m) cc_final: 0.7772 (m) REVERT: A 171 PHE cc_start: 0.8583 (m-80) cc_final: 0.8286 (m-80) REVERT: A 183 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7484 (m-80) REVERT: A 200 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6654 (mm-30) REVERT: B 110 ARG cc_start: 0.5007 (ptp-170) cc_final: 0.4051 (ptm160) REVERT: B 194 PHE cc_start: 0.3613 (OUTLIER) cc_final: 0.2639 (m-80) REVERT: C 8 ASP cc_start: 0.6895 (t0) cc_final: 0.6575 (t0) REVERT: D 16 GLN cc_start: 0.7215 (mp10) cc_final: 0.6494 (mm-40) REVERT: D 56 MET cc_start: 0.6604 (mmm) cc_final: 0.6304 (mmm) REVERT: D 124 GLN cc_start: 0.4222 (OUTLIER) cc_final: 0.3881 (tp40) REVERT: E 191 GLN cc_start: 0.4053 (OUTLIER) cc_final: 0.3565 (pp30) REVERT: E 221 MET cc_start: 0.5011 (mtp) cc_final: 0.4439 (mtm) REVERT: F 93 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7639 (tm-30) REVERT: F 134 SER cc_start: 0.5142 (m) cc_final: 0.4268 (t) REVERT: F 141 MET cc_start: 0.0506 (mpp) cc_final: -0.0569 (tmm) REVERT: G 28 LYS cc_start: 0.8370 (tptt) cc_final: 0.7835 (tptt) REVERT: G 62 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.6124 (tp) REVERT: G 82 TRP cc_start: 0.7513 (p-90) cc_final: 0.7188 (p-90) REVERT: G 111 VAL cc_start: 0.8400 (m) cc_final: 0.8166 (m) REVERT: G 218 PRO cc_start: 0.7909 (Cg_exo) cc_final: 0.7648 (Cg_endo) REVERT: G 324 LYS cc_start: 0.8262 (ptmm) cc_final: 0.7567 (mmtt) REVERT: H 398 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8091 (tt) REVERT: H 460 LEU cc_start: 0.7477 (tp) cc_final: 0.7074 (tp) REVERT: H 497 TYR cc_start: 0.7412 (m-80) cc_final: 0.7078 (m-80) REVERT: I 94 ASN cc_start: 0.7956 (t0) cc_final: 0.7724 (t0) REVERT: I 97 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7943 (mm-40) REVERT: I 108 GLU cc_start: 0.7891 (tp30) cc_final: 0.7464 (tp30) REVERT: J 40 TYR cc_start: 0.8474 (m-80) cc_final: 0.8085 (m-80) REVERT: J 69 GLU cc_start: 0.6368 (mm-30) cc_final: 0.6148 (mm-30) REVERT: J 116 ASP cc_start: 0.6836 (m-30) cc_final: 0.6467 (t0) REVERT: M 33 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6865 (t0) REVERT: M 112 PHE cc_start: 0.7722 (m-80) cc_final: 0.7508 (m-80) REVERT: M 273 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7205 (pp) REVERT: M 279 LEU cc_start: 0.7960 (tt) cc_final: 0.7295 (mt) REVERT: N 39 MET cc_start: 0.6808 (mtt) cc_final: 0.6561 (mtt) REVERT: N 74 MET cc_start: 0.5995 (mtp) cc_final: 0.5763 (mtm) REVERT: N 103 HIS cc_start: 0.4501 (OUTLIER) cc_final: 0.4095 (m170) outliers start: 106 outliers final: 52 residues processed: 511 average time/residue: 0.3939 time to fit residues: 314.2174 Evaluate side-chains 419 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 358 time to evaluate : 2.759 ------------------------------------------------------------------------------- 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 183 PHE 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 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 186 THR Chi-restraints excluded: chain C residue 214 HIS 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 124 GLN Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 228 VAL 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 240 PHE Chi-restraints excluded: chain G residue 269 VAL Chi-restraints excluded: chain G residue 325 PHE Chi-restraints excluded: chain G residue 343 HIS Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 398 ILE Chi-restraints excluded: chain H residue 477 VAL 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 15 VAL 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 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 M residue 241 ASP Chi-restraints excluded: chain M residue 273 LEU Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 103 HIS 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: 0.9980 chunk 56 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 192 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS B 191 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN C 124 GLN ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 486 ASN ** H 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.167376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.146286 restraints weight = 68753.841| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 3.82 r_work: 0.4257 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.7208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26020 Z= 0.176 Angle : 0.688 11.437 35445 Z= 0.361 Chirality : 0.045 0.261 3853 Planarity : 0.004 0.071 4393 Dihedral : 17.246 178.299 4356 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 23.69 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.85 % Favored : 88.84 % Rotamer: Outliers : 4.30 % Allowed : 19.05 % Favored : 76.66 % 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: -2.42 (0.15), residues: 2931 helix: -0.26 (0.17), residues: 965 sheet: -0.97 (0.24), residues: 480 loop : -2.86 (0.14), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 77 HIS 0.011 0.001 HIS G 343 PHE 0.049 0.002 PHE A 53 TYR 0.022 0.002 TYR J 106 ARG 0.009 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04951 ( 901) hydrogen bonds : angle 5.23054 ( 2614) covalent geometry : bond 0.00391 (26020) covalent geometry : angle 0.68791 (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 496 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 387 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7100 (mmtt) cc_final: 0.6638 (mmmt) REVERT: A 17 ASP cc_start: 0.7533 (t70) cc_final: 0.7258 (t0) REVERT: A 35 GLN cc_start: 0.7874 (tp40) cc_final: 0.7296 (tp40) REVERT: A 103 CYS cc_start: 0.8470 (m) cc_final: 0.7867 (m) REVERT: A 171 PHE cc_start: 0.8607 (m-80) cc_final: 0.8254 (m-80) REVERT: A 200 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6621 (mm-30) REVERT: B 110 ARG cc_start: 0.5228 (ptp-170) cc_final: 0.4391 (ptm160) REVERT: B 194 PHE cc_start: 0.3588 (OUTLIER) cc_final: 0.2443 (m-80) REVERT: B 273 LEU cc_start: 0.7373 (tt) cc_final: 0.7091 (tt) REVERT: C 8 ASP cc_start: 0.7039 (t0) cc_final: 0.6739 (t0) REVERT: C 56 MET cc_start: 0.6609 (ptp) cc_final: 0.6350 (ptm) REVERT: C 203 TRP cc_start: 0.4481 (OUTLIER) cc_final: 0.2032 (m100) REVERT: D 16 GLN cc_start: 0.7332 (mp10) cc_final: 0.6651 (mm-40) REVERT: D 56 MET cc_start: 0.6672 (mmm) cc_final: 0.6412 (mmm) REVERT: D 107 TYR cc_start: 0.4036 (t80) cc_final: 0.3734 (t80) REVERT: D 124 GLN cc_start: 0.4663 (OUTLIER) cc_final: 0.4076 (tp-100) REVERT: D 171 PHE cc_start: 0.8118 (m-80) cc_final: 0.7138 (m-80) REVERT: E 191 GLN cc_start: 0.3781 (OUTLIER) cc_final: 0.3185 (pp30) REVERT: E 221 MET cc_start: 0.5207 (mtp) cc_final: 0.4507 (mtm) REVERT: E 227 TYR cc_start: 0.5128 (m-80) cc_final: 0.4091 (m-80) REVERT: F 93 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7598 (tm-30) REVERT: F 134 SER cc_start: 0.5236 (m) cc_final: 0.4270 (t) REVERT: F 226 LEU cc_start: 0.1925 (tp) cc_final: 0.1263 (pp) REVERT: G 1 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7192 (ppp) REVERT: G 3 LEU cc_start: 0.7216 (mt) cc_final: 0.6665 (mt) REVERT: G 62 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.6076 (tp) REVERT: G 80 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6504 (mm) REVERT: G 218 PRO cc_start: 0.7910 (Cg_exo) cc_final: 0.7657 (Cg_endo) REVERT: G 324 LYS cc_start: 0.8334 (ptmm) cc_final: 0.7638 (mmtt) REVERT: H 398 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7885 (tt) REVERT: H 497 TYR cc_start: 0.7443 (m-80) cc_final: 0.7219 (m-80) REVERT: H 513 MET cc_start: 0.8374 (mmp) cc_final: 0.8142 (mmm) REVERT: I 89 PHE cc_start: 0.5793 (OUTLIER) cc_final: 0.4732 (t80) REVERT: I 109 THR cc_start: 0.7912 (p) cc_final: 0.7705 (p) REVERT: J 27 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7652 (mm-30) REVERT: J 40 TYR cc_start: 0.8589 (m-80) cc_final: 0.8113 (m-80) REVERT: J 69 GLU cc_start: 0.6424 (mm-30) cc_final: 0.6189 (mm-30) REVERT: J 116 ASP cc_start: 0.6719 (m-30) cc_final: 0.6361 (t0) REVERT: M 116 MET cc_start: 0.5221 (ptm) cc_final: 0.4277 (ppp) REVERT: N 39 MET cc_start: 0.6770 (mtt) cc_final: 0.6456 (mtt) REVERT: N 72 THR cc_start: 0.7143 (p) cc_final: 0.6838 (p) REVERT: N 74 MET cc_start: 0.5874 (mtp) cc_final: 0.5420 (mtm) REVERT: N 133 GLN cc_start: 0.7116 (mt0) cc_final: 0.6796 (mt0) outliers start: 109 outliers final: 63 residues processed: 465 average time/residue: 0.3857 time to fit residues: 283.9581 Evaluate side-chains 419 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 347 time to evaluate : 2.617 ------------------------------------------------------------------------------- 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 172 THR 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 54 ILE 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 C residue 15 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 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 15 VAL Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 191 GLN 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 249 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 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 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 397 LEU 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 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 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 172 THR 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 N residue 30 THR Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 65 ILE Chi-restraints excluded: chain N residue 201 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 84 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 0.0980 chunk 278 optimal weight: 3.9990 chunk 228 optimal weight: 10.0000 chunk 164 optimal weight: 0.4980 chunk 273 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 191 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN C 63 HIS ** C 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 187 HIS ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 262 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN I 97 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.160160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.140217 restraints weight = 66772.892| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 3.12 r_work: 0.4166 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.8225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 26020 Z= 0.244 Angle : 0.753 10.558 35445 Z= 0.394 Chirality : 0.047 0.268 3853 Planarity : 0.005 0.090 4393 Dihedral : 17.352 177.574 4356 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 27.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.63 % Favored : 88.13 % Rotamer: Outliers : 4.81 % Allowed : 19.12 % Favored : 76.06 % 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: -2.47 (0.15), residues: 2931 helix: -0.31 (0.16), residues: 986 sheet: -1.30 (0.25), residues: 425 loop : -2.76 (0.14), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP G 342 HIS 0.013 0.002 HIS C 181 PHE 0.036 0.003 PHE A 53 TYR 0.027 0.003 TYR C 107 ARG 0.023 0.001 ARG F 224 Details of bonding type rmsd hydrogen bonds : bond 0.04986 ( 901) hydrogen bonds : angle 5.45913 ( 2614) covalent geometry : bond 0.00538 (26020) covalent geometry : angle 0.75300 (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 510 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 388 time to evaluate : 2.563 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 28 ASN cc_start: 0.7312 (t0) cc_final: 0.6109 (t0) REVERT: A 35 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: A 56 MET cc_start: 0.6513 (tpt) cc_final: 0.5961 (tpt) REVERT: A 84 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5891 (pm20) REVERT: A 103 CYS cc_start: 0.7894 (m) cc_final: 0.7329 (m) REVERT: A 171 PHE cc_start: 0.8440 (m-80) cc_final: 0.8224 (m-80) REVERT: B 251 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7173 (mtpt) REVERT: B 273 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.6007 (tt) REVERT: C 203 TRP cc_start: 0.4992 (OUTLIER) cc_final: 0.2408 (m100) REVERT: D 56 MET cc_start: 0.6699 (mmm) cc_final: 0.6239 (mmm) REVERT: E 191 GLN cc_start: 0.3782 (OUTLIER) cc_final: 0.3376 (pp30) REVERT: E 221 MET cc_start: 0.4924 (OUTLIER) cc_final: 0.3930 (mtm) REVERT: E 264 TYR cc_start: 0.4031 (t80) cc_final: 0.3720 (t80) REVERT: E 271 LYS cc_start: 0.7796 (mttt) cc_final: 0.7417 (mmtt) REVERT: G 28 LYS cc_start: 0.8664 (tptt) cc_final: 0.7831 (tptt) REVERT: G 80 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6597 (mm) REVERT: G 81 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8313 (mm) REVERT: G 82 TRP cc_start: 0.7534 (p-90) cc_final: 0.7110 (p-90) REVERT: G 218 PRO cc_start: 0.7824 (Cg_exo) cc_final: 0.7553 (Cg_endo) REVERT: I 24 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8242 (mm) REVERT: I 89 PHE cc_start: 0.6167 (OUTLIER) cc_final: 0.5094 (t80) REVERT: I 109 THR cc_start: 0.7617 (p) cc_final: 0.7407 (p) REVERT: J 87 GLN cc_start: 0.7632 (pm20) cc_final: 0.7365 (pm20) REVERT: J 110 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7283 (tp-100) REVERT: M 53 PHE cc_start: 0.7772 (t80) cc_final: 0.7534 (t80) outliers start: 122 outliers final: 73 residues processed: 476 average time/residue: 0.3660 time to fit residues: 276.1796 Evaluate side-chains 434 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 349 time to evaluate : 2.619 ------------------------------------------------------------------------------- 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 35 GLN Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 109 ILE 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 15 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 165 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 C residue 15 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 178 TYR Chi-restraints excluded: chain C residue 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 15 VAL 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 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 191 GLN Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain G residue 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 194 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 268 ASP Chi-restraints excluded: chain G residue 269 VAL 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 397 LEU 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 110 GLN 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 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 N residue 30 THR Chi-restraints excluded: chain N residue 42 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 87 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 233 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 257 optimal weight: 0.0010 chunk 246 optimal weight: 3.9990 chunk 286 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 253 optimal weight: 0.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS B 191 GLN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** 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 ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN ** G 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 262 ASN ** 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 I 97 GLN ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.158027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.137935 restraints weight = 66585.509| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 3.08 r_work: 0.4141 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.8789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26020 Z= 0.236 Angle : 0.751 10.639 35445 Z= 0.393 Chirality : 0.047 0.264 3853 Planarity : 0.005 0.071 4393 Dihedral : 17.330 179.850 4353 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 28.04 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.26 % Favored : 88.43 % Rotamer: Outliers : 4.93 % Allowed : 19.99 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (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: -0.64 (0.16), residues: 1022 sheet: -1.53 (0.24), residues: 444 loop : -2.66 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 342 HIS 0.011 0.002 HIS G 343 PHE 0.028 0.003 PHE A 53 TYR 0.031 0.003 TYR B 107 ARG 0.011 0.001 ARG H 421 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 901) hydrogen bonds : angle 5.55736 ( 2614) covalent geometry : bond 0.00522 (26020) covalent geometry : angle 0.75145 (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: 125 poor density : 381 time to evaluate : 2.627 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 28 ASN cc_start: 0.7437 (t0) cc_final: 0.6295 (t0) REVERT: A 53 PHE cc_start: 0.6975 (t80) cc_final: 0.6739 (t80) REVERT: A 56 MET cc_start: 0.6556 (tpt) cc_final: 0.5965 (tpt) REVERT: A 72 ILE cc_start: 0.4693 (mm) cc_final: 0.4268 (tt) REVERT: A 84 GLU cc_start: 0.6227 (OUTLIER) cc_final: 0.5679 (pm20) REVERT: A 103 CYS cc_start: 0.8080 (m) cc_final: 0.7676 (m) REVERT: A 171 PHE cc_start: 0.8457 (m-80) cc_final: 0.8135 (m-80) REVERT: B 76 LEU cc_start: 0.6173 (mt) cc_final: 0.5237 (tp) REVERT: B 179 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6671 (ttm-80) REVERT: B 251 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7177 (mtpt) REVERT: B 273 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5698 (mm) REVERT: C 8 ASP cc_start: 0.6976 (t0) cc_final: 0.6628 (t0) REVERT: C 74 ASN cc_start: 0.6782 (m-40) cc_final: 0.6397 (m110) REVERT: C 203 TRP cc_start: 0.5168 (OUTLIER) cc_final: 0.2582 (m100) REVERT: D 56 MET cc_start: 0.6759 (mmm) cc_final: 0.6428 (mmm) REVERT: D 116 MET cc_start: 0.3249 (ttt) cc_final: 0.2303 (tmm) REVERT: D 209 MET cc_start: 0.7117 (mmm) cc_final: 0.6019 (tpp) REVERT: E 221 MET cc_start: 0.5710 (mtp) cc_final: 0.4402 (mtm) REVERT: E 264 TYR cc_start: 0.4549 (t80) cc_final: 0.4028 (t80) REVERT: E 271 LYS cc_start: 0.7849 (mttt) cc_final: 0.7480 (mmtt) REVERT: G 80 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6475 (mm) REVERT: G 218 PRO cc_start: 0.7684 (Cg_exo) cc_final: 0.7416 (Cg_endo) REVERT: H 416 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8161 (mt) REVERT: H 431 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.5286 (t80) REVERT: H 546 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: I 24 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8302 (mm) REVERT: I 89 PHE cc_start: 0.6210 (OUTLIER) cc_final: 0.5232 (t80) REVERT: I 111 PHE cc_start: 0.7802 (t80) cc_final: 0.7545 (t80) REVERT: J 27 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7439 (mm-30) REVERT: J 69 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6673 (tm-30) REVERT: J 87 GLN cc_start: 0.7707 (pm20) cc_final: 0.7440 (pm20) REVERT: J 89 PHE cc_start: 0.4592 (OUTLIER) cc_final: 0.2725 (t80) REVERT: M 53 PHE cc_start: 0.7547 (t80) cc_final: 0.7145 (t80) REVERT: M 56 MET cc_start: 0.5861 (mmt) cc_final: 0.5486 (ttm) REVERT: M 243 LEU cc_start: 0.6348 (mt) cc_final: 0.6118 (mt) REVERT: N 39 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6498 (mtt) outliers start: 125 outliers final: 85 residues processed: 469 average time/residue: 0.3789 time to fit residues: 280.7841 Evaluate side-chains 447 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 348 time to evaluate : 2.612 ------------------------------------------------------------------------------- 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 42 THR 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 109 ILE 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 A residue 258 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 111 THR 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 35 GLN 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 178 TYR 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 15 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 132 THR 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 137 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 84 HIS Chi-restraints excluded: chain G residue 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 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 397 LEU Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 416 LEU Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 431 TYR Chi-restraints excluded: chain H residue 470 VAL Chi-restraints excluded: chain H residue 481 ILE Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 536 ILE Chi-restraints excluded: chain H residue 546 PHE Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 89 PHE Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 110 GLN 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 M residue 241 ASP 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 42 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 134 optimal weight: 7.9990 chunk 283 optimal weight: 4.9990 chunk 186 optimal weight: 8.9990 chunk 281 optimal weight: 0.5980 chunk 144 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.0370 chunk 47 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 overall best weight: 1.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** 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** ** 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 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN M 21 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.158013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.138138 restraints weight = 66720.735| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 3.07 r_work: 0.4140 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.9092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 26020 Z= 0.204 Angle : 0.742 14.385 35445 Z= 0.383 Chirality : 0.047 0.264 3853 Planarity : 0.005 0.072 4393 Dihedral : 17.295 179.596 4352 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 27.31 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.22 % Favored : 88.43 % Rotamer: Outliers : 4.57 % Allowed : 20.58 % 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: -2.60 (0.15), residues: 2931 helix: -0.62 (0.16), residues: 1023 sheet: -1.53 (0.24), residues: 441 loop : -2.65 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 342 HIS 0.011 0.002 HIS C 145 PHE 0.027 0.003 PHE C 9 TYR 0.024 0.002 TYR B 107 ARG 0.011 0.001 ARG F 280 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 901) hydrogen bonds : angle 5.54077 ( 2614) covalent geometry : bond 0.00454 (26020) covalent geometry : angle 0.74233 (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 506 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 390 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.7357 (t0) cc_final: 0.6231 (t0) REVERT: A 53 PHE cc_start: 0.7001 (t80) cc_final: 0.6787 (t80) REVERT: A 56 MET cc_start: 0.6511 (tpt) cc_final: 0.5339 (tpt) REVERT: A 72 ILE cc_start: 0.4740 (mm) cc_final: 0.4527 (tp) REVERT: A 84 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5896 (pm20) REVERT: A 103 CYS cc_start: 0.8108 (m) cc_final: 0.7742 (m) REVERT: A 171 PHE cc_start: 0.8463 (m-80) cc_final: 0.8176 (m-80) REVERT: A 195 SER cc_start: 0.5921 (m) cc_final: 0.5412 (p) REVERT: B 8 ASP cc_start: 0.5880 (t0) cc_final: 0.5642 (t0) REVERT: B 76 LEU cc_start: 0.6454 (mt) cc_final: 0.6135 (tp) REVERT: B 179 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6514 (ttm-80) REVERT: B 251 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7265 (mtpt) REVERT: B 273 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.5455 (mt) REVERT: C 74 ASN cc_start: 0.6769 (m-40) cc_final: 0.6443 (m110) REVERT: C 203 TRP cc_start: 0.5257 (OUTLIER) cc_final: 0.2559 (m100) REVERT: D 56 MET cc_start: 0.6833 (mmm) cc_final: 0.6524 (mmm) REVERT: E 8 ASP cc_start: 0.6790 (m-30) cc_final: 0.6200 (p0) REVERT: E 35 GLN cc_start: 0.7065 (mp10) cc_final: 0.6386 (mt0) REVERT: E 141 MET cc_start: 0.4020 (pmm) cc_final: 0.2216 (ppp) REVERT: E 172 THR cc_start: 0.7641 (m) cc_final: 0.6464 (p) REVERT: E 264 TYR cc_start: 0.4554 (t80) cc_final: 0.4245 (t80) REVERT: E 271 LYS cc_start: 0.7759 (mttt) cc_final: 0.7402 (mmtt) REVERT: F 209 MET cc_start: 0.1060 (tpt) cc_final: 0.0850 (tpt) REVERT: G 80 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6782 (mm) REVERT: G 82 TRP cc_start: 0.7758 (p-90) cc_final: 0.7481 (p-90) REVERT: G 218 PRO cc_start: 0.7722 (Cg_exo) cc_final: 0.7471 (Cg_endo) REVERT: H 431 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.5362 (t80) REVERT: H 471 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7381 (mm) REVERT: H 482 GLN cc_start: 0.6455 (tm-30) cc_final: 0.6239 (tm-30) REVERT: I 24 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8329 (mm) REVERT: I 89 PHE cc_start: 0.6090 (OUTLIER) cc_final: 0.5336 (t80) REVERT: I 111 PHE cc_start: 0.7799 (t80) cc_final: 0.7533 (t80) REVERT: J 27 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7435 (mm-30) REVERT: J 69 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6529 (tm-30) REVERT: J 89 PHE cc_start: 0.4606 (OUTLIER) cc_final: 0.2073 (t80) REVERT: M 53 PHE cc_start: 0.7556 (t80) cc_final: 0.7179 (t80) REVERT: N 39 MET cc_start: 0.6829 (mtt) cc_final: 0.6486 (mtt) REVERT: N 167 ASP cc_start: 0.7400 (p0) cc_final: 0.6968 (p0) outliers start: 116 outliers final: 79 residues processed: 470 average time/residue: 0.3711 time to fit residues: 274.2731 Evaluate side-chains 455 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 364 time to evaluate : 2.556 ------------------------------------------------------------------------------- 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 42 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 258 VAL 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 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 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 35 GLN 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 178 TYR 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 C residue 280 ARG Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 227 TYR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 231 HIS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 80 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 268 ASP Chi-restraints excluded: chain G residue 269 VAL 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 397 LEU 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 471 LEU Chi-restraints excluded: chain H residue 536 ILE 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 J residue 110 GLN 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 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 241 ASP 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 65 ILE 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: 1.9990 chunk 23 optimal weight: 0.0060 chunk 235 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 264 optimal weight: 0.7980 chunk 234 optimal weight: 0.8980 chunk 188 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS ** C 154 ASN ** 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 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 234 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** ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 531 GLN ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN ** I 92 HIS ** 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** J 91 ASN J 110 GLN N 36 ASN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.160032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.140274 restraints weight = 66702.430| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 3.20 r_work: 0.4174 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.9105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26020 Z= 0.163 Angle : 0.720 11.140 35445 Z= 0.371 Chirality : 0.045 0.239 3853 Planarity : 0.005 0.076 4393 Dihedral : 17.227 179.979 4351 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 26.48 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.54 % Favored : 89.12 % Rotamer: Outliers : 3.75 % Allowed : 21.81 % Favored : 74.45 % 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: -0.46 (0.16), residues: 1013 sheet: -1.38 (0.26), residues: 404 loop : -2.58 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 342 HIS 0.020 0.002 HIS I 92 PHE 0.036 0.003 PHE H 558 TYR 0.032 0.002 TYR A 107 ARG 0.018 0.001 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.04654 ( 901) hydrogen bonds : angle 5.40917 ( 2614) covalent geometry : bond 0.00365 (26020) covalent geometry : angle 0.72037 (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 491 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 396 time to evaluate : 2.745 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 56 MET cc_start: 0.6189 (tpt) cc_final: 0.5495 (tpt) REVERT: A 72 ILE cc_start: 0.4944 (mm) cc_final: 0.4661 (tp) REVERT: A 103 CYS cc_start: 0.7793 (m) cc_final: 0.7191 (m) REVERT: A 155 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6967 (mm-30) REVERT: A 171 PHE cc_start: 0.8433 (m-80) cc_final: 0.8222 (m-80) REVERT: A 195 SER cc_start: 0.5620 (m) cc_final: 0.5184 (p) REVERT: B 6 ARG cc_start: 0.5964 (tmm-80) cc_final: 0.5407 (tmm160) REVERT: B 76 LEU cc_start: 0.6428 (mt) cc_final: 0.5947 (tp) REVERT: B 116 MET cc_start: 0.7565 (mpp) cc_final: 0.6878 (mpp) REVERT: B 179 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6032 (ttm-80) REVERT: B 251 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7090 (mtpt) REVERT: B 273 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.5467 (mt) REVERT: C 74 ASN cc_start: 0.6824 (m-40) cc_final: 0.6569 (m110) REVERT: D 56 MET cc_start: 0.6977 (mmm) cc_final: 0.6685 (mmm) REVERT: D 116 MET cc_start: 0.2931 (ttt) cc_final: 0.2463 (tmm) REVERT: D 209 MET cc_start: 0.6464 (mmm) cc_final: 0.6161 (mmm) REVERT: E 8 ASP cc_start: 0.6925 (m-30) cc_final: 0.6203 (p0) REVERT: E 35 GLN cc_start: 0.6775 (mp10) cc_final: 0.6535 (mt0) REVERT: E 141 MET cc_start: 0.4201 (pmm) cc_final: 0.2467 (ppp) REVERT: E 172 THR cc_start: 0.7302 (m) cc_final: 0.6503 (p) REVERT: E 221 MET cc_start: 0.4990 (mtp) cc_final: 0.4514 (mtm) REVERT: E 264 TYR cc_start: 0.5049 (t80) cc_final: 0.4832 (t80) REVERT: E 271 LYS cc_start: 0.7743 (mttt) cc_final: 0.7392 (mmtt) REVERT: G 48 THR cc_start: 0.6395 (p) cc_final: 0.5057 (p) REVERT: G 59 ARG cc_start: 0.7370 (mmt180) cc_final: 0.7086 (mmt180) REVERT: G 80 LEU cc_start: 0.7105 (mt) cc_final: 0.6729 (mm) REVERT: G 218 PRO cc_start: 0.7853 (Cg_exo) cc_final: 0.7645 (Cg_endo) REVERT: G 247 MET cc_start: 0.7988 (tmm) cc_final: 0.7666 (tmm) REVERT: G 270 THR cc_start: 0.8774 (m) cc_final: 0.8178 (p) REVERT: G 326 TYR cc_start: 0.6435 (p90) cc_final: 0.5463 (p90) REVERT: H 397 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.6771 (tp) REVERT: H 403 ASP cc_start: 0.7384 (t0) cc_final: 0.6593 (t0) REVERT: H 431 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.5207 (t80) REVERT: H 471 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7528 (mm) REVERT: I 20 VAL cc_start: 0.8666 (t) cc_final: 0.8464 (m) REVERT: I 24 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8224 (mm) REVERT: J 69 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6433 (tm-30) REVERT: J 89 PHE cc_start: 0.4448 (OUTLIER) cc_final: 0.2536 (t80) REVERT: M 56 MET cc_start: 0.5139 (mmt) cc_final: 0.4675 (ttm) REVERT: N 93 MET cc_start: 0.7051 (mtm) cc_final: 0.6757 (ptt) REVERT: N 100 TYR cc_start: 0.7203 (m-80) cc_final: 0.6995 (m-10) REVERT: N 167 ASP cc_start: 0.7317 (p0) cc_final: 0.6900 (p0) outliers start: 95 outliers final: 58 residues processed: 458 average time/residue: 0.3826 time to fit residues: 274.6444 Evaluate side-chains 436 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 368 time to evaluate : 2.665 ------------------------------------------------------------------------------- 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 155 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 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 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 227 TYR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain 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 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 397 LEU 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 471 LEU Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 536 ILE Chi-restraints excluded: chain H residue 566 THR 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 89 PHE Chi-restraints excluded: chain J residue 110 GLN 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 201 LEU Chi-restraints excluded: chain M residue 221 MET Chi-restraints excluded: chain M residue 241 ASP 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 65 ILE 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: 0.5980 chunk 15 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 48 optimal weight: 0.0980 chunk 49 optimal weight: 8.9990 chunk 195 optimal weight: 0.0770 chunk 214 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 202 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 55 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** 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 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 HIS ** 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 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 383 ASN ** H 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** M 19 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.161763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.142400 restraints weight = 67234.214| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 3.22 r_work: 0.4202 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.9079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26020 Z= 0.150 Angle : 0.714 10.833 35445 Z= 0.367 Chirality : 0.044 0.233 3853 Planarity : 0.005 0.125 4393 Dihedral : 17.148 178.787 4350 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 25.12 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.27 % Favored : 89.39 % Rotamer: Outliers : 2.96 % Allowed : 22.48 % Favored : 74.57 % 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: -2.39 (0.15), residues: 2931 helix: -0.37 (0.16), residues: 1007 sheet: -1.49 (0.25), residues: 433 loop : -2.55 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 342 HIS 0.012 0.001 HIS I 92 PHE 0.059 0.002 PHE A 53 TYR 0.028 0.002 TYR A 107 ARG 0.016 0.001 ARG H 409 Details of bonding type rmsd hydrogen bonds : bond 0.04579 ( 901) hydrogen bonds : angle 5.27919 ( 2614) covalent geometry : bond 0.00336 (26020) covalent geometry : angle 0.71357 (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 478 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 403 time to evaluate : 2.577 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 56 MET cc_start: 0.6016 (tpt) cc_final: 0.5127 (tpt) REVERT: A 103 CYS cc_start: 0.7714 (m) cc_final: 0.7113 (m) REVERT: A 155 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6913 (mm-30) REVERT: A 183 PHE cc_start: 0.7564 (m-80) cc_final: 0.7352 (m-80) REVERT: B 6 ARG cc_start: 0.5898 (tmm-80) cc_final: 0.5519 (tmm160) REVERT: B 7 TYR cc_start: 0.6500 (m-80) cc_final: 0.6215 (m-80) REVERT: B 76 LEU cc_start: 0.6362 (mt) cc_final: 0.5983 (tp) REVERT: B 116 MET cc_start: 0.7481 (mpp) cc_final: 0.7000 (mpp) REVERT: B 170 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8045 (ttmm) REVERT: B 179 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.5834 (ttm-80) REVERT: B 194 PHE cc_start: 0.4015 (OUTLIER) cc_final: 0.3783 (m-80) REVERT: B 210 PHE cc_start: 0.7832 (m-80) cc_final: 0.7512 (m-80) REVERT: B 251 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7469 (mtpt) REVERT: B 273 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.5410 (mt) REVERT: C 108 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8256 (t70) REVERT: D 111 THR cc_start: 0.6688 (m) cc_final: 0.6184 (m) REVERT: D 171 PHE cc_start: 0.8309 (m-80) cc_final: 0.7351 (m-80) REVERT: D 209 MET cc_start: 0.6706 (mmm) cc_final: 0.6045 (mmm) REVERT: E 8 ASP cc_start: 0.6851 (m-30) cc_final: 0.6191 (p0) REVERT: E 141 MET cc_start: 0.4224 (pmm) cc_final: 0.2755 (ppp) REVERT: E 150 MET cc_start: 0.4371 (mpp) cc_final: 0.3160 (pmm) REVERT: E 221 MET cc_start: 0.4574 (mtp) cc_final: 0.4103 (mtm) REVERT: E 227 TYR cc_start: 0.5117 (m-80) cc_final: 0.4642 (m-80) REVERT: E 264 TYR cc_start: 0.4492 (t80) cc_final: 0.4048 (t80) REVERT: E 271 LYS cc_start: 0.7664 (mttt) cc_final: 0.7323 (mmtt) REVERT: F 102 MET cc_start: 0.3507 (mmm) cc_final: 0.3195 (mmp) REVERT: F 133 PHE cc_start: 0.6846 (t80) cc_final: 0.6396 (t80) REVERT: F 220 GLN cc_start: 0.7183 (tm-30) cc_final: 0.6653 (tt0) REVERT: G 80 LEU cc_start: 0.7104 (mt) cc_final: 0.6727 (mm) REVERT: G 82 TRP cc_start: 0.7681 (p-90) cc_final: 0.7390 (p-90) REVERT: G 103 GLN cc_start: 0.7777 (mt0) cc_final: 0.7294 (mt0) REVERT: G 218 PRO cc_start: 0.7692 (Cg_exo) cc_final: 0.7443 (Cg_endo) REVERT: G 326 TYR cc_start: 0.6285 (p90) cc_final: 0.5415 (p90) REVERT: H 380 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7942 (tt) REVERT: H 397 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6695 (tp) REVERT: H 431 TYR cc_start: 0.6738 (OUTLIER) cc_final: 0.5320 (t80) REVERT: H 471 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7429 (mm) REVERT: H 497 TYR cc_start: 0.6965 (m-80) cc_final: 0.6686 (m-80) REVERT: I 89 PHE cc_start: 0.4566 (OUTLIER) cc_final: 0.2375 (t80) REVERT: J 69 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6377 (tm-30) REVERT: J 89 PHE cc_start: 0.4814 (OUTLIER) cc_final: 0.2540 (t80) REVERT: M 56 MET cc_start: 0.5319 (mmt) cc_final: 0.4724 (ttm) REVERT: M 263 ASP cc_start: 0.7590 (t0) cc_final: 0.7366 (t0) REVERT: M 279 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7194 (mt) REVERT: N 93 MET cc_start: 0.6939 (mtm) cc_final: 0.6657 (ptt) REVERT: N 100 TYR cc_start: 0.7055 (m-80) cc_final: 0.6850 (m-10) REVERT: N 167 ASP cc_start: 0.7221 (p0) cc_final: 0.6824 (p0) outliers start: 75 outliers final: 48 residues processed: 453 average time/residue: 0.3800 time to fit residues: 268.5002 Evaluate side-chains 435 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 373 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 14 ASP 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 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 186 THR Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 227 TYR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 PHE Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 272 ASN Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain F residue 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 344 GLU Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 385 VAL Chi-restraints excluded: chain H residue 397 LEU Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 431 TYR Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain 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 51 VAL Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 110 GLN 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 201 LEU Chi-restraints excluded: chain M residue 241 ASP 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 42 LEU Chi-restraints excluded: chain N residue 65 ILE 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: 3.9990 chunk 74 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 11 optimal weight: 0.4980 chunk 223 optimal weight: 0.7980 chunk 157 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 HIS ** 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** ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 GLN N 36 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.155030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.134395 restraints weight = 66809.992| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 3.21 r_work: 0.4084 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.9711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 26020 Z= 0.244 Angle : 0.801 12.847 35445 Z= 0.413 Chirality : 0.048 0.262 3853 Planarity : 0.006 0.087 4393 Dihedral : 17.204 178.161 4350 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 30.00 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.67 % Favored : 87.99 % Rotamer: Outliers : 3.27 % Allowed : 22.59 % Favored : 74.13 % 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: -2.48 (0.15), residues: 2931 helix: -0.54 (0.16), residues: 1015 sheet: -1.39 (0.24), residues: 440 loop : -2.58 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP N 43 HIS 0.012 0.002 HIS G 343 PHE 0.071 0.003 PHE A 53 TYR 0.031 0.003 TYR J 40 ARG 0.018 0.001 ARG H 409 Details of bonding type rmsd hydrogen bonds : bond 0.04970 ( 901) hydrogen bonds : angle 5.52931 ( 2614) covalent geometry : bond 0.00546 (26020) covalent geometry : angle 0.80086 (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 459 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 376 time to evaluate : 2.793 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: 0.7633 (t0) cc_final: 0.7296 (m-30) REVERT: A 28 ASN cc_start: 0.8371 (t0) cc_final: 0.7719 (t0) REVERT: A 56 MET cc_start: 0.5820 (tpt) cc_final: 0.5089 (tpt) REVERT: A 103 CYS cc_start: 0.7825 (m) cc_final: 0.7572 (m) REVERT: B 76 LEU cc_start: 0.6625 (mt) cc_final: 0.6359 (tp) REVERT: B 116 MET cc_start: 0.7594 (mpp) cc_final: 0.7078 (mpp) REVERT: B 179 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6124 (ttm-80) REVERT: B 194 PHE cc_start: 0.4725 (OUTLIER) cc_final: 0.4290 (m-80) REVERT: B 273 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.5737 (mt) REVERT: C 103 CYS cc_start: 0.8357 (m) cc_final: 0.8143 (m) REVERT: C 108 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8364 (t70) REVERT: C 116 MET cc_start: 0.6462 (ppp) cc_final: 0.6218 (ppp) REVERT: D 111 THR cc_start: 0.7095 (m) cc_final: 0.6659 (m) REVERT: D 171 PHE cc_start: 0.8396 (m-80) cc_final: 0.7208 (m-80) REVERT: E 141 MET cc_start: 0.4288 (pmm) cc_final: 0.2558 (ppp) REVERT: E 221 MET cc_start: 0.4988 (mtp) cc_final: 0.4167 (mtm) REVERT: E 264 TYR cc_start: 0.4447 (t80) cc_final: 0.3845 (t80) REVERT: E 271 LYS cc_start: 0.7910 (mttt) cc_final: 0.7369 (tppt) REVERT: F 102 MET cc_start: 0.4589 (mmm) cc_final: 0.4220 (mmt) REVERT: F 220 GLN cc_start: 0.7286 (tm-30) cc_final: 0.5708 (mp10) REVERT: G 56 LYS cc_start: 0.5055 (mmtt) cc_final: 0.4708 (mmtm) REVERT: G 80 LEU cc_start: 0.7078 (mt) cc_final: 0.6706 (mm) REVERT: G 95 LYS cc_start: 0.3655 (tttt) cc_final: 0.3143 (tttt) REVERT: G 218 PRO cc_start: 0.7525 (Cg_exo) cc_final: 0.7307 (Cg_endo) REVERT: H 411 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8353 (mm) REVERT: H 431 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.5265 (t80) REVERT: H 497 TYR cc_start: 0.7179 (m-80) cc_final: 0.6970 (m-80) REVERT: I 89 PHE cc_start: 0.5182 (OUTLIER) cc_final: 0.2780 (t80) REVERT: I 92 HIS cc_start: 0.5943 (t-90) cc_final: 0.5701 (t-90) REVERT: J 69 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6341 (tm-30) REVERT: J 87 GLN cc_start: 0.7746 (pm20) cc_final: 0.7486 (pm20) REVERT: J 89 PHE cc_start: 0.4975 (OUTLIER) cc_final: 0.2998 (t80) REVERT: M 55 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7083 (mp10) REVERT: M 56 MET cc_start: 0.5870 (mmt) cc_final: 0.5343 (ttm) REVERT: N 167 ASP cc_start: 0.7501 (p0) cc_final: 0.7110 (p0) outliers start: 83 outliers final: 58 residues processed: 437 average time/residue: 0.3811 time to fit residues: 263.3095 Evaluate side-chains 418 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 350 time to evaluate : 2.844 ------------------------------------------------------------------------------- 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 153 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 66 PHE 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 265 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 35 GLN 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 178 TYR Chi-restraints excluded: chain C residue 214 HIS Chi-restraints excluded: chain C residue 250 VAL 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 D residue 258 VAL Chi-restraints excluded: chain E residue 132 THR 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 397 LEU Chi-restraints excluded: chain H residue 402 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 431 TYR Chi-restraints excluded: chain H residue 471 LEU Chi-restraints excluded: chain H residue 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 51 VAL Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 89 PHE Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 111 PHE Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 55 GLN Chi-restraints excluded: chain M residue 112 PHE Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 227 TYR Chi-restraints excluded: chain M residue 241 ASP Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 30 THR 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: 5.9990 chunk 36 optimal weight: 0.1980 chunk 72 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 HIS ** 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** ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 ASN ** M 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.155357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.135350 restraints weight = 66290.297| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 3.03 r_work: 0.4103 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.9742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.288 26020 Z= 0.304 Angle : 0.938 59.163 35445 Z= 0.510 Chirality : 0.048 0.342 3853 Planarity : 0.006 0.147 4393 Dihedral : 17.205 178.112 4350 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 34.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.91 % Favored : 87.82 % Rotamer: Outliers : 3.19 % Allowed : 23.34 % Favored : 73.46 % Cbeta Deviations : 0.04 % 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: -2.49 (0.15), residues: 2931 helix: -0.55 (0.16), residues: 1015 sheet: -1.39 (0.24), residues: 442 loop : -2.59 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP N 43 HIS 0.017 0.002 HIS B 63 PHE 0.061 0.003 PHE A 53 TYR 0.029 0.003 TYR H 440 ARG 0.029 0.001 ARG J 88 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 901) hydrogen bonds : angle 5.53193 ( 2614) covalent geometry : bond 0.00697 (26020) covalent geometry : angle 0.93808 (35445) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13336.97 seconds wall clock time: 229 minutes 20.90 seconds (13760.90 seconds total)