Starting phenix.real_space_refine on Fri Jan 16 19:32:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yv9_34121/01_2026/7yv9_34121.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yv9_34121/01_2026/7yv9_34121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yv9_34121/01_2026/7yv9_34121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yv9_34121/01_2026/7yv9_34121.map" model { file = "/net/cci-nas-00/data/ceres_data/7yv9_34121/01_2026/7yv9_34121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yv9_34121/01_2026/7yv9_34121.cif" } resolution = 4.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5613 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 254 5.16 5 C 23512 2.51 5 N 6436 2.21 5 O 7308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37510 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8806 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 26, 'TRANS': 1040} Chain breaks: 1 Chain: "B" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1161 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "C" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1161 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "D" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1161 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "E" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1136 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain: "F" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1161 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "G" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1161 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "H" Number of atoms: 8766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8766 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 26, 'TRANS': 1034} Chain breaks: 2 Chain: "I" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1161 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "J" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1161 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "K" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1161 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "L" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1136 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain: "M" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1161 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "N" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1166 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "X" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3036 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 361} Chain breaks: 1 Chain: "Y" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3015 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 358} Chain breaks: 1 Time building chain proxies: 8.54, per 1000 atoms: 0.23 Number of scatterers: 37510 At special positions: 0 Unit cell: (146.864, 248.704, 325.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 254 16.00 O 7308 8.00 N 6436 7.00 C 23512 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: 3.45 Conformation dependent library (CDL) restraints added in 1.5 seconds 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8778 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 28 sheets defined 68.4% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 3.979A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.543A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 186 through 207 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 251 removed outlier: 4.279A pdb=" N VAL A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 removed outlier: 3.982A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 4.719A pdb=" N MET A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 300 through 315 Processing helix chain 'A' and resid 318 through 336 removed outlier: 3.598A pdb=" N GLN A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 376 removed outlier: 4.029A pdb=" N MET A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.510A pdb=" N ILE A 496 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 561 through 569 removed outlier: 4.404A pdb=" N LEU A 565 " --> pdb=" O CYS A 561 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 587 through 593 Processing helix chain 'A' and resid 629 through 633 Processing helix chain 'A' and resid 634 through 652 Processing helix chain 'A' and resid 673 through 685 Processing helix chain 'A' and resid 685 through 696 removed outlier: 3.665A pdb=" N THR A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 696 " --> pdb=" O ILE A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 710 Processing helix chain 'A' and resid 722 through 735 removed outlier: 3.733A pdb=" N THR A 726 " --> pdb=" O ASP A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 908 Processing helix chain 'A' and resid 914 through 1100 removed outlier: 4.204A pdb=" N TYR A 918 " --> pdb=" O SER A 914 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE A 923 " --> pdb=" O LYS A 919 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY A 924 " --> pdb=" O LYS A 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 21 removed outlier: 3.631A pdb=" N PHE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 45 through 60 removed outlier: 3.999A pdb=" N ASP B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 79 removed outlier: 3.754A pdb=" N ASP B 79 " --> pdb=" O ARG B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.508A pdb=" N ILE B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 139 through 148 Processing helix chain 'C' and resid 6 through 21 Processing helix chain 'C' and resid 29 through 40 Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 103 through 113 Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'C' and resid 139 through 149 Processing helix chain 'D' and resid 6 through 21 Processing helix chain 'D' and resid 30 through 40 Processing helix chain 'D' and resid 45 through 60 Processing helix chain 'D' and resid 65 through 78 Processing helix chain 'D' and resid 82 through 94 removed outlier: 4.232A pdb=" N ILE D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 118 through 129 Processing helix chain 'D' and resid 139 through 149 Processing helix chain 'E' and resid 7 through 21 removed outlier: 3.779A pdb=" N PHE E 20 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 41 removed outlier: 3.790A pdb=" N THR E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 60 Processing helix chain 'E' and resid 66 through 79 Processing helix chain 'E' and resid 82 through 93 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 139 through 149 Processing helix chain 'F' and resid 6 through 21 Processing helix chain 'F' and resid 29 through 41 removed outlier: 4.292A pdb=" N GLY F 41 " --> pdb=" O MET F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 60 Processing helix chain 'F' and resid 65 through 79 removed outlier: 3.616A pdb=" N ASP F 79 " --> pdb=" O ARG F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.712A pdb=" N ILE F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 118 through 130 removed outlier: 3.705A pdb=" N ASP F 130 " --> pdb=" O ILE F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 149 removed outlier: 3.679A pdb=" N LYS F 149 " --> pdb=" O MET F 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 21 Processing helix chain 'G' and resid 29 through 39 removed outlier: 4.003A pdb=" N GLY G 34 " --> pdb=" O THR G 30 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 57 Processing helix chain 'G' and resid 65 through 78 Processing helix chain 'G' and resid 82 through 94 removed outlier: 3.562A pdb=" N ILE G 86 " --> pdb=" O SER G 82 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP G 94 " --> pdb=" O PHE G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 Processing helix chain 'G' and resid 118 through 130 Processing helix chain 'G' and resid 138 through 149 removed outlier: 3.818A pdb=" N PHE G 142 " --> pdb=" O ASN G 138 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET G 145 " --> pdb=" O GLN G 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 95 Processing helix chain 'H' and resid 116 through 119 removed outlier: 4.088A pdb=" N TYR H 119 " --> pdb=" O LEU H 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 116 through 119' Processing helix chain 'H' and resid 120 through 128 Processing helix chain 'H' and resid 138 through 154 Processing helix chain 'H' and resid 168 through 185 removed outlier: 3.658A pdb=" N ARG H 178 " --> pdb=" O LYS H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 208 Proline residue: H 201 - end of helix Processing helix chain 'H' and resid 259 through 268 removed outlier: 4.027A pdb=" N TYR H 263 " --> pdb=" O TYR H 259 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS H 266 " --> pdb=" O PHE H 262 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER H 268 " --> pdb=" O GLN H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 275 removed outlier: 4.043A pdb=" N LYS H 275 " --> pdb=" O PRO H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 284 Processing helix chain 'H' and resid 285 through 290 Processing helix chain 'H' and resid 300 through 316 Processing helix chain 'H' and resid 318 through 335 Processing helix chain 'H' and resid 354 through 365 Processing helix chain 'H' and resid 367 through 375 removed outlier: 3.736A pdb=" N MET H 371 " --> pdb=" O ASP H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 392 through 424 Processing helix chain 'H' and resid 448 through 480 Processing helix chain 'H' and resid 492 through 501 removed outlier: 3.855A pdb=" N ILE H 496 " --> pdb=" O ASN H 492 " (cutoff:3.500A) Processing helix chain 'H' and resid 504 through 515 removed outlier: 3.854A pdb=" N MET H 515 " --> pdb=" O GLU H 511 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 532 removed outlier: 3.602A pdb=" N TRP H 523 " --> pdb=" O THR H 519 " (cutoff:3.500A) Processing helix chain 'H' and resid 561 through 569 removed outlier: 3.643A pdb=" N LYS H 567 " --> pdb=" O GLY H 563 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS H 569 " --> pdb=" O LEU H 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 581 removed outlier: 3.574A pdb=" N ILE H 577 " --> pdb=" O PHE H 573 " (cutoff:3.500A) Processing helix chain 'H' and resid 586 through 593 removed outlier: 3.801A pdb=" N GLU H 590 " --> pdb=" O LYS H 586 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU H 591 " --> pdb=" O MET H 587 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE H 592 " --> pdb=" O LEU H 588 " (cutoff:3.500A) Processing helix chain 'H' and resid 634 through 653 removed outlier: 3.523A pdb=" N ALA H 652 " --> pdb=" O GLU H 648 " (cutoff:3.500A) Processing helix chain 'H' and resid 673 through 684 Processing helix chain 'H' and resid 685 through 696 removed outlier: 3.610A pdb=" N GLY H 696 " --> pdb=" O ILE H 692 " (cutoff:3.500A) Processing helix chain 'H' and resid 703 through 710 Processing helix chain 'H' and resid 722 through 735 Processing helix chain 'H' and resid 752 through 908 removed outlier: 4.675A pdb=" N ALA H 756 " --> pdb=" O ALA H 752 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA H 817 " --> pdb=" O ARG H 813 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU H 852 " --> pdb=" O LEU H 848 " (cutoff:3.500A) Processing helix chain 'H' and resid 915 through 1102 removed outlier: 3.569A pdb=" N ILE H 929 " --> pdb=" O MET H 925 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N MET H 930 " --> pdb=" O GLU H 926 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN H 931 " --> pdb=" O ASN H 927 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU H 932 " --> pdb=" O LYS H 928 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU H 977 " --> pdb=" O LEU H 973 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP H1070 " --> pdb=" O GLN H1066 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 18 removed outlier: 3.884A pdb=" N SER I 18 " --> pdb=" O LYS I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 40 Processing helix chain 'I' and resid 45 through 57 Processing helix chain 'I' and resid 58 through 60 No H-bonds generated for 'chain 'I' and resid 58 through 60' Processing helix chain 'I' and resid 65 through 79 removed outlier: 3.546A pdb=" N ASP I 79 " --> pdb=" O ARG I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 94 removed outlier: 3.588A pdb=" N ILE I 86 " --> pdb=" O SER I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 113 Processing helix chain 'I' and resid 118 through 129 Processing helix chain 'I' and resid 139 through 147 Processing helix chain 'J' and resid 6 through 20 Processing helix chain 'J' and resid 29 through 40 Processing helix chain 'J' and resid 45 through 57 Processing helix chain 'J' and resid 66 through 76 Processing helix chain 'J' and resid 82 through 94 Processing helix chain 'J' and resid 103 through 112 Processing helix chain 'J' and resid 118 through 129 Processing helix chain 'J' and resid 139 through 147 Processing helix chain 'K' and resid 6 through 20 Processing helix chain 'K' and resid 29 through 41 Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 65 through 80 Processing helix chain 'K' and resid 82 through 94 removed outlier: 3.593A pdb=" N ILE K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 112 Processing helix chain 'K' and resid 118 through 130 Processing helix chain 'K' and resid 139 through 149 removed outlier: 3.717A pdb=" N ALA K 148 " --> pdb=" O GLN K 144 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS K 149 " --> pdb=" O MET K 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 21 Processing helix chain 'L' and resid 30 through 40 Processing helix chain 'L' and resid 45 through 57 Processing helix chain 'L' and resid 58 through 60 No H-bonds generated for 'chain 'L' and resid 58 through 60' Processing helix chain 'L' and resid 65 through 80 Processing helix chain 'L' and resid 82 through 94 removed outlier: 3.632A pdb=" N ILE L 86 " --> pdb=" O SER L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 113 Processing helix chain 'L' and resid 118 through 130 Processing helix chain 'L' and resid 139 through 149 Processing helix chain 'M' and resid 6 through 21 Processing helix chain 'M' and resid 30 through 41 removed outlier: 3.581A pdb=" N THR M 35 " --> pdb=" O LYS M 31 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY M 41 " --> pdb=" O MET M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 60 Processing helix chain 'M' and resid 65 through 77 Processing helix chain 'M' and resid 82 through 94 removed outlier: 3.789A pdb=" N ILE M 86 " --> pdb=" O SER M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 113 removed outlier: 4.074A pdb=" N LEU M 113 " --> pdb=" O VAL M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 118 through 127 Processing helix chain 'M' and resid 138 through 148 removed outlier: 3.723A pdb=" N PHE M 142 " --> pdb=" O ASN M 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 21 Processing helix chain 'N' and resid 29 through 40 Processing helix chain 'N' and resid 45 through 60 removed outlier: 3.687A pdb=" N ASP N 59 " --> pdb=" O GLU N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 78 removed outlier: 3.723A pdb=" N PHE N 69 " --> pdb=" O ASP N 65 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS N 78 " --> pdb=" O ALA N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 90 Processing helix chain 'N' and resid 91 through 94 Processing helix chain 'N' and resid 102 through 113 removed outlier: 3.666A pdb=" N LEU N 106 " --> pdb=" O SER N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 130 removed outlier: 3.799A pdb=" N ASP N 130 " --> pdb=" O ILE N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 149 removed outlier: 3.600A pdb=" N MET N 145 " --> pdb=" O GLN N 141 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS N 149 " --> pdb=" O MET N 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 1456 through 1465 Processing helix chain 'X' and resid 1472 through 1478 removed outlier: 4.116A pdb=" N ILE X1478 " --> pdb=" O ALA X1474 " (cutoff:3.500A) Processing helix chain 'X' and resid 1480 through 1497 Processing helix chain 'X' and resid 1498 through 1520 Processing helix chain 'X' and resid 1523 through 1545 Processing helix chain 'X' and resid 1547 through 1552 Processing helix chain 'X' and resid 1555 through 1560 Processing helix chain 'X' and resid 1568 through 1603 Proline residue: X1596 - end of helix removed outlier: 4.586A pdb=" N VAL X1599 " --> pdb=" O GLN X1595 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER X1600 " --> pdb=" O PRO X1596 " (cutoff:3.500A) Processing helix chain 'X' and resid 1633 through 1652 Processing helix chain 'X' and resid 1654 through 1680 Processing helix chain 'X' and resid 1685 through 1707 removed outlier: 4.175A pdb=" N MET X1690 " --> pdb=" O TRP X1686 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN X1691 " --> pdb=" O SER X1687 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS X1706 " --> pdb=" O TRP X1702 " (cutoff:3.500A) Processing helix chain 'X' and resid 1712 through 1729 Proline residue: X1719 - end of helix Processing helix chain 'X' and resid 1733 through 1744 removed outlier: 3.769A pdb=" N ALA X1739 " --> pdb=" O ASP X1735 " (cutoff:3.500A) Processing helix chain 'X' and resid 1748 through 1758 Processing helix chain 'X' and resid 1770 through 1781 Processing helix chain 'X' and resid 1782 through 1785 Processing helix chain 'Y' and resid 1453 through 1465 removed outlier: 4.380A pdb=" N GLN Y1458 " --> pdb=" O ARG Y1454 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYS Y1459 " --> pdb=" O GLU Y1455 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1472 through 1478 removed outlier: 3.681A pdb=" N ASN Y1476 " --> pdb=" O GLY Y1472 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE Y1478 " --> pdb=" O ALA Y1474 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1480 through 1497 Processing helix chain 'Y' and resid 1498 through 1521 Processing helix chain 'Y' and resid 1523 through 1544 Processing helix chain 'Y' and resid 1555 through 1561 Processing helix chain 'Y' and resid 1568 through 1603 Proline residue: Y1596 - end of helix removed outlier: 3.735A pdb=" N VAL Y1599 " --> pdb=" O GLN Y1595 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER Y1600 " --> pdb=" O PRO Y1596 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU Y1603 " --> pdb=" O VAL Y1599 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1633 through 1651 Processing helix chain 'Y' and resid 1654 through 1680 Processing helix chain 'Y' and resid 1685 through 1706 Processing helix chain 'Y' and resid 1708 through 1711 Processing helix chain 'Y' and resid 1712 through 1727 removed outlier: 3.836A pdb=" N THR Y1716 " --> pdb=" O GLY Y1712 " (cutoff:3.500A) Proline residue: Y1719 - end of helix Processing helix chain 'Y' and resid 1733 through 1744 Processing helix chain 'Y' and resid 1748 through 1758 Processing helix chain 'Y' and resid 1770 through 1782 Processing helix chain 'Y' and resid 1783 through 1785 No H-bonds generated for 'chain 'Y' and resid 1783 through 1785' Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 16 removed outlier: 3.858A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.400A pdb=" N LEU A 107 " --> pdb=" O ARG A 659 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE A 661 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA A 109 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS A 660 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 209 removed outlier: 3.530A pdb=" N SER A 217 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA6, first strand: chain 'A' and resid 699 through 702 removed outlier: 3.694A pdb=" N SER A 699 " --> pdb=" O PHE A 750 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA9, first strand: chain 'D' and resid 28 through 29 Processing sheet with id=AB1, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AB2, first strand: chain 'E' and resid 27 through 29 Processing sheet with id=AB3, first strand: chain 'E' and resid 100 through 101 Processing sheet with id=AB4, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 16 removed outlier: 3.573A pdb=" N ALA H 11 " --> pdb=" O LEU H 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 100 through 103 removed outlier: 6.356A pdb=" N LEU H 107 " --> pdb=" O ARG H 659 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE H 661 " --> pdb=" O LEU H 107 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA H 109 " --> pdb=" O ILE H 661 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN H 157 " --> pdb=" O GLY H 434 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU H 436 " --> pdb=" O GLN H 157 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE H 159 " --> pdb=" O LEU H 436 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS H 222 " --> pdb=" O ASP H 437 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLY H 221 " --> pdb=" O THR H 241 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR H 241 " --> pdb=" O GLY H 221 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR H 223 " --> pdb=" O MET H 239 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET H 239 " --> pdb=" O TYR H 223 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU H 225 " --> pdb=" O ALA H 237 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA H 237 " --> pdb=" O GLU H 225 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY H 227 " --> pdb=" O ILE H 235 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 377 through 381 Processing sheet with id=AB8, first strand: chain 'H' and resid 538 through 539 removed outlier: 3.558A pdb=" N GLU H 539 " --> pdb=" O ILE H 549 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 699 through 702 Processing sheet with id=AC1, first strand: chain 'I' and resid 100 through 101 Processing sheet with id=AC2, first strand: chain 'J' and resid 27 through 28 Processing sheet with id=AC3, first strand: chain 'J' and resid 100 through 102 Processing sheet with id=AC4, first strand: chain 'K' and resid 100 through 101 removed outlier: 4.041A pdb=" N ILE K 101 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL K 137 " --> pdb=" O ILE K 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'L' and resid 28 through 29 removed outlier: 3.797A pdb=" N ILE L 28 " --> pdb=" O ILE L 64 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 100 through 102 Processing sheet with id=AC7, first strand: chain 'M' and resid 28 through 29 removed outlier: 3.690A pdb=" N ILE M 28 " --> pdb=" O ILE M 64 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 101 through 102 removed outlier: 3.910A pdb=" N ILE M 101 " --> pdb=" O VAL M 137 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 100 through 101 Processing sheet with id=AD1, first strand: chain 'X' and resid 1449 through 1451 2427 hydrogen bonds defined for protein. 7194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.91 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8102 1.33 - 1.45: 8081 1.45 - 1.57: 21453 1.57 - 1.70: 0 1.70 - 1.82: 451 Bond restraints: 38087 Sorted by residual: bond pdb=" N ILE Y1439 " pdb=" CA ILE Y1439 " ideal model delta sigma weight residual 1.456 1.494 -0.038 8.60e-03 1.35e+04 2.00e+01 bond pdb=" C ILE X1439 " pdb=" N PRO X1440 " ideal model delta sigma weight residual 1.335 1.368 -0.033 8.70e-03 1.32e+04 1.40e+01 bond pdb=" N VAL Y1437 " pdb=" CA VAL Y1437 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.65e+00 bond pdb=" N ILE Y1434 " pdb=" CA ILE Y1434 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.20e+00 bond pdb=" N ILE X1434 " pdb=" CA ILE X1434 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 8.09e+00 ... (remaining 38082 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 50610 2.21 - 4.42: 468 4.42 - 6.63: 89 6.63 - 8.84: 18 8.84 - 11.06: 6 Bond angle restraints: 51191 Sorted by residual: angle pdb=" C GLN J 144 " pdb=" N MET J 145 " pdb=" CA MET J 145 " ideal model delta sigma weight residual 122.06 112.85 9.21 1.86e+00 2.89e-01 2.45e+01 angle pdb=" N PHE N 66 " pdb=" CA PHE N 66 " pdb=" C PHE N 66 " ideal model delta sigma weight residual 109.81 118.53 -8.72 2.21e+00 2.05e-01 1.56e+01 angle pdb=" CB MET A 827 " pdb=" CG MET A 827 " pdb=" SD MET A 827 " ideal model delta sigma weight residual 112.70 123.76 -11.06 3.00e+00 1.11e-01 1.36e+01 angle pdb=" CB MET D 125 " pdb=" CG MET D 125 " pdb=" SD MET D 125 " ideal model delta sigma weight residual 112.70 101.90 10.80 3.00e+00 1.11e-01 1.30e+01 angle pdb=" C GLN C 144 " pdb=" N MET C 145 " pdb=" CA MET C 145 " ideal model delta sigma weight residual 121.58 114.59 6.99 1.95e+00 2.63e-01 1.29e+01 ... (remaining 51186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 21205 17.42 - 34.83: 1800 34.83 - 52.25: 371 52.25 - 69.67: 74 69.67 - 87.08: 25 Dihedral angle restraints: 23475 sinusoidal: 9934 harmonic: 13541 Sorted by residual: dihedral pdb=" CA GLN K 42 " pdb=" C GLN K 42 " pdb=" N ASN K 43 " pdb=" CA ASN K 43 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA MET D 72 " pdb=" C MET D 72 " pdb=" N MET D 73 " pdb=" CA MET D 73 " ideal model delta harmonic sigma weight residual 180.00 158.25 21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA MET L 72 " pdb=" C MET L 72 " pdb=" N MET L 73 " pdb=" CA MET L 73 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 23472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 4555 0.046 - 0.093: 859 0.093 - 0.139: 174 0.139 - 0.185: 14 0.185 - 0.232: 5 Chirality restraints: 5607 Sorted by residual: chirality pdb=" CA ILE X1434 " pdb=" N ILE X1434 " pdb=" C ILE X1434 " pdb=" CB ILE X1434 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ILE Y1434 " pdb=" N ILE Y1434 " pdb=" C ILE Y1434 " pdb=" CB ILE Y1434 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE X1439 " pdb=" N ILE X1439 " pdb=" C ILE X1439 " pdb=" CB ILE X1439 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 5604 not shown) Planarity restraints: 6720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 43 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO C 44 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 44 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 44 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 90 " 0.013 2.00e-02 2.50e+03 1.39e-02 3.38e+00 pdb=" CG PHE N 90 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE N 90 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE N 90 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE N 90 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE N 90 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE N 90 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 200 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 201 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 201 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 201 " 0.025 5.00e-02 4.00e+02 ... (remaining 6717 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 563 2.65 - 3.21: 38062 3.21 - 3.78: 64136 3.78 - 4.34: 84277 4.34 - 4.90: 129456 Nonbonded interactions: 316494 Sorted by model distance: nonbonded pdb=" OH TYR H 703 " pdb=" O GLY H 744 " model vdw 2.089 3.040 nonbonded pdb=" O PHE A 470 " pdb=" NE2 GLN A 474 " model vdw 2.099 3.120 nonbonded pdb=" OH TYR A 703 " pdb=" O GLY A 744 " model vdw 2.124 3.040 nonbonded pdb=" O PHE H 220 " pdb=" OH TYR H 439 " model vdw 2.159 3.040 nonbonded pdb=" O ALA A 282 " pdb=" OG1 THR A 288 " model vdw 2.161 3.040 ... (remaining 316489 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 4 through 532 or resid 537 through 596 or resid 631 throug \ h 1100)) selection = (chain 'H' and resid 4 through 1100) } ncs_group { reference = (chain 'B' and resid 6 through 149) selection = (chain 'C' and resid 6 through 149) selection = (chain 'D' and resid 6 through 149) selection = chain 'E' selection = (chain 'F' and resid 6 through 149) selection = (chain 'G' and resid 6 through 149) selection = (chain 'I' and resid 6 through 149) selection = (chain 'J' and resid 6 through 149) selection = (chain 'K' and resid 6 through 149) selection = chain 'L' selection = (chain 'M' and resid 6 through 149) selection = (chain 'N' and resid 6 through 149) } ncs_group { reference = (chain 'X' and (resid 1433 through 1607 or resid 1631 through 1828)) selection = chain 'Y' } 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 group one per residue 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: 21.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 33.200 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.003 0.045 38087 Z= 0.144 Angle : 0.584 11.056 51191 Z= 0.336 Chirality : 0.038 0.232 5607 Planarity : 0.003 0.047 6720 Dihedral : 13.753 87.083 14697 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.17 % Allowed : 0.27 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.12), residues: 4594 helix: 2.15 (0.09), residues: 2986 sheet: -0.59 (0.34), residues: 214 loop : 0.29 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 127 TYR 0.022 0.001 TYR H 918 PHE 0.032 0.001 PHE N 90 TRP 0.016 0.002 TRP Y1702 HIS 0.010 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00263 (38087) covalent geometry : angle 0.58372 (51191) hydrogen bonds : bond 0.11423 ( 2427) hydrogen bonds : angle 5.14290 ( 7194) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 248 time to evaluate : 1.606 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 239 MET cc_start: 0.8361 (mmp) cc_final: 0.8040 (mmm) REVERT: A 295 MET cc_start: 0.7989 (mmp) cc_final: 0.7771 (mmp) REVERT: A 307 HIS cc_start: 0.9069 (m-70) cc_final: 0.8591 (m90) REVERT: A 647 MET cc_start: 0.9597 (mmm) cc_final: 0.8984 (mmm) REVERT: A 714 MET cc_start: 0.8027 (tpt) cc_final: 0.7379 (tpp) REVERT: A 886 MET cc_start: 0.8727 (mpp) cc_final: 0.8166 (mpp) REVERT: D 145 MET cc_start: 0.7028 (ptt) cc_final: 0.6761 (ptt) REVERT: F 72 MET cc_start: 0.7883 (ptp) cc_final: 0.7464 (ptp) REVERT: H 107 LEU cc_start: 0.9039 (tp) cc_final: 0.8595 (tp) REVERT: H 478 MET cc_start: 0.9187 (ptp) cc_final: 0.8973 (ptt) REVERT: H 647 MET cc_start: 0.9046 (mmp) cc_final: 0.8541 (mmm) REVERT: H 900 MET cc_start: 0.6672 (ptp) cc_final: 0.6408 (ptm) REVERT: H 925 MET cc_start: 0.7120 (mtp) cc_final: 0.6834 (ttt) REVERT: H 930 MET cc_start: 0.8423 (mpp) cc_final: 0.7604 (mpp) REVERT: J 125 MET cc_start: 0.8831 (mpp) cc_final: 0.8549 (mpp) REVERT: K 110 MET cc_start: 0.7860 (tpt) cc_final: 0.7448 (tpp) REVERT: L 54 ASN cc_start: 0.8717 (m-40) cc_final: 0.8225 (p0) REVERT: M 61 ASN cc_start: 0.8648 (m110) cc_final: 0.8072 (t0) REVERT: M 110 MET cc_start: 0.8145 (tmm) cc_final: 0.7784 (tpp) REVERT: X 1488 MET cc_start: 0.7573 (tpt) cc_final: 0.7354 (tpp) REVERT: X 1597 MET cc_start: 0.7480 (tpt) cc_final: 0.7042 (tpt) REVERT: X 1648 MET cc_start: 0.9360 (mpp) cc_final: 0.9063 (mpp) REVERT: Y 1449 MET cc_start: 0.8105 (mmp) cc_final: 0.7089 (mmp) REVERT: Y 1488 MET cc_start: 0.7891 (mmt) cc_final: 0.7552 (mmt) REVERT: Y 1648 MET cc_start: 0.9573 (ttt) cc_final: 0.9245 (ttt) REVERT: Y 1653 MET cc_start: 0.8984 (mmp) cc_final: 0.7544 (mmm) outliers start: 7 outliers final: 1 residues processed: 255 average time/residue: 0.2159 time to fit residues: 95.2937 Evaluate side-chains 231 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 432 optimal weight: 0.6980 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 0.5980 chunk 424 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 GLN A 725 GLN A 729 ASN ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN G 4 GLN H 264 GLN H 451 GLN H 464 GLN H 804 GLN H 927 ASN I 4 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN I 54 ASN ** J 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 ASN M 68 GLN N 50 GLN N 136 GLN X1497 ASN ** X1539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1543 GLN Y1559 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.038897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.027224 restraints weight = 716424.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.028003 restraints weight = 432607.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.028549 restraints weight = 314280.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.028911 restraints weight = 253750.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.029124 restraints weight = 219996.832| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38087 Z= 0.126 Angle : 0.496 8.788 51191 Z= 0.268 Chirality : 0.037 0.152 5607 Planarity : 0.003 0.049 6720 Dihedral : 4.518 89.063 5045 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.12 % Allowed : 3.57 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.12), residues: 4594 helix: 2.21 (0.09), residues: 3045 sheet: -0.63 (0.34), residues: 210 loop : 0.36 (0.18), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 248 TYR 0.020 0.001 TYR H 918 PHE 0.020 0.001 PHE N 90 TRP 0.012 0.002 TRP A 414 HIS 0.006 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00252 (38087) covalent geometry : angle 0.49555 (51191) hydrogen bonds : bond 0.03950 ( 2427) hydrogen bonds : angle 4.35900 ( 7194) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 249 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9243 (mt) cc_final: 0.8682 (pp) REVERT: A 239 MET cc_start: 0.8552 (mmp) cc_final: 0.8229 (mmm) REVERT: A 647 MET cc_start: 0.9699 (mmm) cc_final: 0.9174 (mmm) REVERT: A 714 MET cc_start: 0.8547 (tpt) cc_final: 0.7904 (tpp) REVERT: A 925 MET cc_start: 0.7745 (ptp) cc_final: 0.7347 (ptp) REVERT: D 72 MET cc_start: 0.7103 (ppp) cc_final: 0.6775 (ppp) REVERT: D 105 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8102 (pm20) REVERT: E 110 MET cc_start: 0.9231 (mmp) cc_final: 0.8970 (mmp) REVERT: F 72 MET cc_start: 0.7773 (ptp) cc_final: 0.7442 (ptt) REVERT: G 145 MET cc_start: 0.6506 (pmm) cc_final: 0.6176 (pmm) REVERT: H 647 MET cc_start: 0.9110 (mmp) cc_final: 0.8837 (mmm) REVERT: H 930 MET cc_start: 0.8746 (mpp) cc_final: 0.8052 (mpp) REVERT: H 1056 MET cc_start: 0.8761 (mmm) cc_final: 0.8355 (mmm) REVERT: I 110 MET cc_start: 0.8652 (mmp) cc_final: 0.8424 (mmm) REVERT: K 110 MET cc_start: 0.7926 (tpt) cc_final: 0.7449 (tpp) REVERT: L 54 ASN cc_start: 0.8724 (m-40) cc_final: 0.8244 (p0) REVERT: L 73 MET cc_start: 0.2238 (mmp) cc_final: 0.1851 (mmm) REVERT: M 61 ASN cc_start: 0.8732 (m110) cc_final: 0.8179 (t0) REVERT: X 1488 MET cc_start: 0.7947 (tpt) cc_final: 0.7684 (tpp) REVERT: X 1597 MET cc_start: 0.7867 (tpt) cc_final: 0.7405 (tpt) REVERT: X 1665 MET cc_start: 0.9066 (ptp) cc_final: 0.8799 (ptp) REVERT: X 1779 MET cc_start: 0.9203 (tmm) cc_final: 0.8905 (tmm) REVERT: Y 1648 MET cc_start: 0.9616 (ttt) cc_final: 0.9162 (ttt) REVERT: Y 1653 MET cc_start: 0.9030 (mmp) cc_final: 0.7381 (mmm) REVERT: Y 1679 LEU cc_start: 0.9155 (tp) cc_final: 0.8808 (tp) outliers start: 5 outliers final: 1 residues processed: 254 average time/residue: 0.2072 time to fit residues: 91.6520 Evaluate side-chains 232 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 230 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 338 optimal weight: 10.0000 chunk 263 optimal weight: 7.9990 chunk 431 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 406 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 236 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 ASN ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 GLN ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN ** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN C 50 GLN F 54 ASN ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 497 ASN H 742 GLN ** H 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 940 ASN H1001 GLN H1048 GLN H1079 GLN I 4 GLN ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN I 54 ASN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN L 42 GLN L 112 ASN M 136 GLN ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1497 ASN ** X1554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1558 GLN X1561 HIS ** X1573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1592 ASN X1789 GLN ** Y1476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1691 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.035786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.026642 restraints weight = 674330.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.026654 restraints weight = 485415.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.026789 restraints weight = 393830.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.026796 restraints weight = 364662.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.026904 restraints weight = 324155.994| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 38087 Z= 0.411 Angle : 0.900 13.064 51191 Z= 0.488 Chirality : 0.046 0.437 5607 Planarity : 0.006 0.075 6720 Dihedral : 5.754 86.182 5045 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 34.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 0.22 % Allowed : 5.86 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.12), residues: 4594 helix: 0.55 (0.09), residues: 2995 sheet: -0.61 (0.38), residues: 159 loop : -0.29 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 897 TYR 0.037 0.004 TYR A 882 PHE 0.031 0.003 PHE A 706 TRP 0.041 0.004 TRP Y1702 HIS 0.014 0.003 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00814 (38087) covalent geometry : angle 0.89963 (51191) hydrogen bonds : bond 0.05644 ( 2427) hydrogen bonds : angle 5.53875 ( 7194) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 226 time to evaluate : 1.524 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 239 MET cc_start: 0.9148 (mmp) cc_final: 0.8893 (mmm) REVERT: A 714 MET cc_start: 0.8573 (tpt) cc_final: 0.7915 (tpp) REVERT: A 886 MET cc_start: 0.8894 (mpp) cc_final: 0.8483 (mpp) REVERT: A 899 MET cc_start: 0.6876 (mmp) cc_final: 0.6436 (mmp) REVERT: A 1056 MET cc_start: 0.9549 (mtt) cc_final: 0.9232 (mtp) REVERT: C 73 MET cc_start: 0.4965 (mmm) cc_final: 0.4612 (mmm) REVERT: D 146 MET cc_start: 0.8168 (mmm) cc_final: 0.7608 (mmm) REVERT: E 110 MET cc_start: 0.9273 (mmp) cc_final: 0.9001 (mmp) REVERT: F 72 MET cc_start: 0.7884 (ptp) cc_final: 0.7597 (ptt) REVERT: F 119 ASP cc_start: 0.9558 (m-30) cc_final: 0.9302 (p0) REVERT: G 73 MET cc_start: 0.8660 (ppp) cc_final: 0.8358 (ppp) REVERT: H 305 MET cc_start: 0.5022 (mmp) cc_final: 0.4461 (mmm) REVERT: H 517 LYS cc_start: 0.7896 (ptpt) cc_final: 0.7654 (tppt) REVERT: H 647 MET cc_start: 0.9414 (mmp) cc_final: 0.9033 (mmm) REVERT: H 900 MET cc_start: 0.6423 (ptp) cc_final: 0.6093 (ptm) REVERT: H 930 MET cc_start: 0.8694 (mpp) cc_final: 0.8381 (mpp) REVERT: H 1056 MET cc_start: 0.8944 (mmm) cc_final: 0.8417 (mmt) REVERT: I 145 MET cc_start: 0.9241 (ppp) cc_final: 0.9029 (ppp) REVERT: J 125 MET cc_start: 0.9076 (mpp) cc_final: 0.8702 (mpp) REVERT: J 146 MET cc_start: 0.8405 (mmp) cc_final: 0.7975 (mmm) REVERT: K 73 MET cc_start: 0.7130 (mmp) cc_final: 0.6892 (mmm) REVERT: M 72 MET cc_start: 0.5287 (ppp) cc_final: 0.5086 (ppp) REVERT: N 52 MET cc_start: 0.7689 (mmt) cc_final: 0.7160 (mmt) REVERT: N 72 MET cc_start: 0.9218 (ppp) cc_final: 0.8990 (ppp) REVERT: X 1488 MET cc_start: 0.8144 (tpt) cc_final: 0.7883 (tpp) REVERT: X 1551 MET cc_start: 0.8669 (mpp) cc_final: 0.8410 (mpp) REVERT: X 1597 MET cc_start: 0.8432 (tpt) cc_final: 0.7941 (tpt) REVERT: X 1602 MET cc_start: 0.9061 (tpp) cc_final: 0.8826 (tpp) REVERT: Y 1653 MET cc_start: 0.9258 (mmp) cc_final: 0.9046 (mmm) REVERT: Y 1690 MET cc_start: 0.8872 (mpp) cc_final: 0.8574 (mpp) outliers start: 9 outliers final: 6 residues processed: 235 average time/residue: 0.2107 time to fit residues: 86.3254 Evaluate side-chains 218 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 212 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 143 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 317 optimal weight: 9.9990 chunk 368 optimal weight: 6.9990 chunk 342 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 422 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 HIS ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 HIS ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN H 149 GLN ** H 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 398 ASN H 455 ASN ** H 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 568 ASN H 704 GLN ** H 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 927 ASN I 50 GLN I 54 ASN ** I 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN J 68 GLN ** J 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1676 ASN ** Y1476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1605 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.036641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.027492 restraints weight = 667026.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.027535 restraints weight = 449063.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.027900 restraints weight = 374614.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.027888 restraints weight = 306981.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.027901 restraints weight = 290656.695| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 38087 Z= 0.214 Angle : 0.637 9.686 51191 Z= 0.344 Chirality : 0.040 0.246 5607 Planarity : 0.004 0.066 6720 Dihedral : 5.385 79.001 5045 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.07 % Allowed : 3.35 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.12), residues: 4594 helix: 0.93 (0.09), residues: 3020 sheet: -0.77 (0.38), residues: 163 loop : -0.23 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 38 TYR 0.031 0.002 TYR A 882 PHE 0.030 0.002 PHE N 90 TRP 0.024 0.002 TRP A 414 HIS 0.009 0.002 HIS I 108 Details of bonding type rmsd covalent geometry : bond 0.00433 (38087) covalent geometry : angle 0.63676 (51191) hydrogen bonds : bond 0.04498 ( 2427) hydrogen bonds : angle 5.02026 ( 7194) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 238 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.9422 (mt) cc_final: 0.8865 (pp) REVERT: A 239 MET cc_start: 0.8932 (mmp) cc_final: 0.8618 (mmm) REVERT: A 714 MET cc_start: 0.8549 (tpt) cc_final: 0.7894 (tpp) REVERT: A 886 MET cc_start: 0.8900 (mpp) cc_final: 0.8277 (mpp) REVERT: A 1056 MET cc_start: 0.9580 (mtt) cc_final: 0.9124 (mtp) REVERT: B 146 MET cc_start: 0.8599 (ttt) cc_final: 0.7932 (tpt) REVERT: C 73 MET cc_start: 0.4921 (mmm) cc_final: 0.4718 (mmm) REVERT: D 146 MET cc_start: 0.8257 (mmm) cc_final: 0.7662 (mmm) REVERT: E 73 MET cc_start: 0.2837 (mmp) cc_final: 0.2536 (mmp) REVERT: E 110 MET cc_start: 0.9346 (mmp) cc_final: 0.9099 (mmp) REVERT: F 72 MET cc_start: 0.8078 (ptp) cc_final: 0.7708 (ptt) REVERT: G 52 MET cc_start: 0.8361 (tpp) cc_final: 0.7854 (tpp) REVERT: H 132 MET cc_start: 0.9006 (tmm) cc_final: 0.8764 (tmm) REVERT: H 305 MET cc_start: 0.5609 (mmp) cc_final: 0.5099 (mmm) REVERT: H 647 MET cc_start: 0.9393 (mmp) cc_final: 0.8830 (mmt) REVERT: H 930 MET cc_start: 0.8786 (mpp) cc_final: 0.8379 (mpp) REVERT: H 1052 MET cc_start: 0.9006 (ttt) cc_final: 0.8429 (ttt) REVERT: H 1056 MET cc_start: 0.9025 (mmm) cc_final: 0.8439 (mmt) REVERT: I 145 MET cc_start: 0.9283 (ppp) cc_final: 0.9068 (ppp) REVERT: J 52 MET cc_start: 0.6802 (mpp) cc_final: 0.6545 (mpp) REVERT: J 146 MET cc_start: 0.8410 (mmp) cc_final: 0.8124 (mmm) REVERT: L 110 MET cc_start: 0.6494 (mtt) cc_final: 0.6071 (mtt) REVERT: N 72 MET cc_start: 0.9234 (ppp) cc_final: 0.8984 (ppp) REVERT: X 1597 MET cc_start: 0.8429 (tpt) cc_final: 0.8063 (tpt) REVERT: X 1665 MET cc_start: 0.8958 (ptp) cc_final: 0.8565 (ptp) REVERT: X 1675 ASN cc_start: 0.9383 (m-40) cc_final: 0.9161 (m110) REVERT: X 1779 MET cc_start: 0.8825 (tmm) cc_final: 0.8517 (tmm) REVERT: Y 1449 MET cc_start: 0.8489 (mmp) cc_final: 0.7549 (mmp) REVERT: Y 1690 MET cc_start: 0.8790 (mpp) cc_final: 0.8447 (mpp) outliers start: 3 outliers final: 1 residues processed: 241 average time/residue: 0.2119 time to fit residues: 88.6694 Evaluate side-chains 217 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 10 optimal weight: 6.9990 chunk 295 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 345 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 228 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 GLN ** H 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 742 GLN ** H 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 927 ASN H1048 GLN I 4 GLN ** I 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1463 ASN ** X1554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1476 ASN ** 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 = 0.3382 r_free = 0.3382 target = 0.036763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.026766 restraints weight = 676331.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.027372 restraints weight = 455952.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.027859 restraints weight = 305202.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.027853 restraints weight = 256169.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.027869 restraints weight = 242420.563| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 38087 Z= 0.193 Angle : 0.621 11.446 51191 Z= 0.334 Chirality : 0.039 0.172 5607 Planarity : 0.004 0.061 6720 Dihedral : 5.230 77.680 5045 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.12), residues: 4594 helix: 1.06 (0.09), residues: 3015 sheet: -0.73 (0.39), residues: 159 loop : -0.20 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 219 TYR 0.031 0.002 TYR H1016 PHE 0.024 0.002 PHE G 13 TRP 0.024 0.002 TRP A 414 HIS 0.010 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00397 (38087) covalent geometry : angle 0.62098 (51191) hydrogen bonds : bond 0.04343 ( 2427) hydrogen bonds : angle 4.92458 ( 7194) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8962 (mmp) cc_final: 0.8622 (mmm) REVERT: A 714 MET cc_start: 0.8559 (tpt) cc_final: 0.7964 (tpp) REVERT: A 886 MET cc_start: 0.8801 (mpp) cc_final: 0.8215 (mpp) REVERT: A 925 MET cc_start: 0.8165 (ptp) cc_final: 0.7456 (ptp) REVERT: A 1052 MET cc_start: 0.9445 (mpp) cc_final: 0.9182 (mmt) REVERT: A 1056 MET cc_start: 0.9634 (mtt) cc_final: 0.9054 (mtp) REVERT: C 73 MET cc_start: 0.5083 (mmm) cc_final: 0.4802 (mmm) REVERT: D 77 MET cc_start: 0.6255 (ptt) cc_final: 0.5749 (ppp) REVERT: E 73 MET cc_start: 0.3124 (mmp) cc_final: 0.2897 (mmp) REVERT: E 110 MET cc_start: 0.9379 (mmp) cc_final: 0.9128 (mmp) REVERT: F 72 MET cc_start: 0.8026 (ptp) cc_final: 0.7679 (ptp) REVERT: F 119 ASP cc_start: 0.9618 (m-30) cc_final: 0.9366 (p0) REVERT: H 132 MET cc_start: 0.9075 (tmm) cc_final: 0.8824 (tmm) REVERT: H 305 MET cc_start: 0.6169 (mmm) cc_final: 0.5710 (mmm) REVERT: H 515 MET cc_start: 0.7383 (mmp) cc_final: 0.6752 (ptm) REVERT: H 587 MET cc_start: 0.4137 (tpp) cc_final: 0.3837 (tpp) REVERT: H 647 MET cc_start: 0.9406 (mmp) cc_final: 0.9060 (mmm) REVERT: H 900 MET cc_start: 0.6428 (ptp) cc_final: 0.6220 (ptm) REVERT: H 930 MET cc_start: 0.8785 (mpp) cc_final: 0.8163 (mpp) REVERT: I 145 MET cc_start: 0.9310 (ppp) cc_final: 0.9087 (ppp) REVERT: J 52 MET cc_start: 0.6773 (mpp) cc_final: 0.6507 (mpp) REVERT: J 146 MET cc_start: 0.8452 (mmp) cc_final: 0.8152 (mmm) REVERT: K 73 MET cc_start: 0.7132 (mmp) cc_final: 0.6924 (mmm) REVERT: L 110 MET cc_start: 0.6511 (mtt) cc_final: 0.6202 (mtt) REVERT: N 37 MET cc_start: 0.7941 (tpt) cc_final: 0.6842 (tpt) REVERT: N 52 MET cc_start: 0.7555 (mmt) cc_final: 0.7025 (mmt) REVERT: X 1488 MET cc_start: 0.8049 (tpt) cc_final: 0.7637 (tpp) REVERT: X 1597 MET cc_start: 0.8525 (tpt) cc_final: 0.8066 (tpt) REVERT: X 1665 MET cc_start: 0.9102 (ptp) cc_final: 0.8744 (ptp) REVERT: X 1779 MET cc_start: 0.9002 (tmm) cc_final: 0.8669 (tmm) REVERT: Y 1449 MET cc_start: 0.8101 (mmp) cc_final: 0.7616 (mmp) REVERT: Y 1690 MET cc_start: 0.8833 (mpp) cc_final: 0.8473 (mpp) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2147 time to fit residues: 88.5467 Evaluate side-chains 219 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 172 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 354 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 427 optimal weight: 0.9980 chunk 405 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 309 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 381 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS ** H 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 927 ASN ** I 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN J 108 HIS ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 GLN X1463 ASN ** X1554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1558 GLN X1573 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.037370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.027613 restraints weight = 666870.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.028237 restraints weight = 446289.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.028193 restraints weight = 304392.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.028256 restraints weight = 323825.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.028315 restraints weight = 291441.085| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38087 Z= 0.141 Angle : 0.573 11.035 51191 Z= 0.304 Chirality : 0.039 0.177 5607 Planarity : 0.004 0.056 6720 Dihedral : 5.002 77.553 5045 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.02 % Allowed : 1.78 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.12), residues: 4594 helix: 1.39 (0.09), residues: 3033 sheet: -0.75 (0.40), residues: 160 loop : -0.10 (0.18), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 38 TYR 0.026 0.002 TYR A 882 PHE 0.041 0.002 PHE D 142 TRP 0.023 0.002 TRP A 825 HIS 0.008 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00296 (38087) covalent geometry : angle 0.57266 (51191) hydrogen bonds : bond 0.04031 ( 2427) hydrogen bonds : angle 4.66846 ( 7194) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8816 (mmp) cc_final: 0.8458 (mmm) REVERT: A 714 MET cc_start: 0.8448 (tpt) cc_final: 0.7904 (tpp) REVERT: A 886 MET cc_start: 0.8873 (mpp) cc_final: 0.8126 (mpp) REVERT: A 925 MET cc_start: 0.7925 (ptp) cc_final: 0.7279 (ptp) REVERT: A 1056 MET cc_start: 0.9494 (mtt) cc_final: 0.9198 (mmt) REVERT: B 146 MET cc_start: 0.8587 (ttt) cc_final: 0.7928 (tpt) REVERT: C 73 MET cc_start: 0.4997 (mmm) cc_final: 0.4709 (mmm) REVERT: D 146 MET cc_start: 0.7904 (mmm) cc_final: 0.7525 (mmm) REVERT: E 52 MET cc_start: 0.0454 (tpp) cc_final: 0.0109 (tpp) REVERT: E 72 MET cc_start: 0.7879 (mmp) cc_final: 0.7571 (mmm) REVERT: E 110 MET cc_start: 0.9306 (mmp) cc_final: 0.9042 (mmp) REVERT: F 72 MET cc_start: 0.8021 (ptp) cc_final: 0.7660 (ptp) REVERT: F 119 ASP cc_start: 0.9631 (m-30) cc_final: 0.9373 (p0) REVERT: G 52 MET cc_start: 0.7975 (tpp) cc_final: 0.7446 (tpp) REVERT: H 107 LEU cc_start: 0.9215 (tp) cc_final: 0.8963 (tp) REVERT: H 132 MET cc_start: 0.9002 (tmm) cc_final: 0.8760 (tmm) REVERT: H 177 MET cc_start: 0.8960 (ppp) cc_final: 0.8757 (ppp) REVERT: H 515 MET cc_start: 0.7494 (mmp) cc_final: 0.6829 (ptm) REVERT: H 587 MET cc_start: 0.4047 (tpp) cc_final: 0.3799 (tpp) REVERT: H 900 MET cc_start: 0.6643 (ptp) cc_final: 0.6408 (ptm) REVERT: H 930 MET cc_start: 0.8702 (mpp) cc_final: 0.7908 (mpp) REVERT: H 1052 MET cc_start: 0.9029 (ttt) cc_final: 0.8420 (ttt) REVERT: H 1056 MET cc_start: 0.8849 (mmt) cc_final: 0.7546 (mmt) REVERT: I 145 MET cc_start: 0.9250 (ppp) cc_final: 0.9048 (ppp) REVERT: J 37 MET cc_start: 0.7510 (tpp) cc_final: 0.7291 (tpp) REVERT: J 52 MET cc_start: 0.6787 (mpp) cc_final: 0.6484 (mpp) REVERT: J 146 MET cc_start: 0.8261 (mmp) cc_final: 0.8031 (mmm) REVERT: K 146 MET cc_start: 0.5730 (mmp) cc_final: 0.5138 (mmm) REVERT: L 73 MET cc_start: 0.3501 (mmp) cc_final: 0.3127 (mmm) REVERT: L 110 MET cc_start: 0.6748 (mtt) cc_final: 0.6432 (mtt) REVERT: N 37 MET cc_start: 0.7806 (tpt) cc_final: 0.6795 (tpt) REVERT: X 1488 MET cc_start: 0.7785 (tpt) cc_final: 0.7414 (tpp) REVERT: X 1665 MET cc_start: 0.9149 (ptp) cc_final: 0.8745 (ptp) REVERT: X 1779 MET cc_start: 0.8876 (tmm) cc_final: 0.8553 (tmm) REVERT: Y 1449 MET cc_start: 0.7791 (mmp) cc_final: 0.7483 (mmp) REVERT: Y 1653 MET cc_start: 0.9066 (mmm) cc_final: 0.8741 (mmm) REVERT: Y 1690 MET cc_start: 0.8678 (mpp) cc_final: 0.8384 (mpp) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.2090 time to fit residues: 85.6535 Evaluate side-chains 218 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 263 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 437 optimal weight: 2.9990 chunk 13 optimal weight: 0.0570 chunk 239 optimal weight: 1.9990 chunk 325 optimal weight: 9.9990 chunk 283 optimal weight: 9.9990 chunk 336 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 291 optimal weight: 9.9990 chunk 391 optimal weight: 0.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 ASN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 GLN ** H 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 290 GLN ** H 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 742 GLN ** H 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 927 ASN ** I 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN X1463 ASN ** X1554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1558 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.036881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.026751 restraints weight = 675261.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.027691 restraints weight = 424108.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.027965 restraints weight = 288848.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.028144 restraints weight = 242785.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.028123 restraints weight = 217052.615| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 38087 Z= 0.184 Angle : 0.617 11.858 51191 Z= 0.329 Chirality : 0.039 0.192 5607 Planarity : 0.004 0.054 6720 Dihedral : 5.056 78.209 5045 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.02 % Allowed : 1.42 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.12), residues: 4594 helix: 1.32 (0.09), residues: 3010 sheet: -1.00 (0.39), residues: 159 loop : -0.10 (0.18), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 38 TYR 0.026 0.002 TYR A 882 PHE 0.039 0.002 PHE D 142 TRP 0.025 0.002 TRP A 414 HIS 0.009 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00379 (38087) covalent geometry : angle 0.61704 (51191) hydrogen bonds : bond 0.04181 ( 2427) hydrogen bonds : angle 4.77451 ( 7194) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 1.579 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 239 MET cc_start: 0.8933 (mmp) cc_final: 0.8731 (mmm) REVERT: A 714 MET cc_start: 0.8510 (tpt) cc_final: 0.7911 (tpp) REVERT: A 886 MET cc_start: 0.8835 (mpp) cc_final: 0.8243 (mpp) REVERT: A 925 MET cc_start: 0.8006 (ptp) cc_final: 0.7578 (ptp) REVERT: A 1056 MET cc_start: 0.9415 (mtt) cc_final: 0.8973 (mmt) REVERT: C 73 MET cc_start: 0.4749 (mmm) cc_final: 0.4533 (mmm) REVERT: E 110 MET cc_start: 0.9360 (mmp) cc_final: 0.9073 (mmp) REVERT: F 72 MET cc_start: 0.8023 (ptp) cc_final: 0.7681 (ptp) REVERT: F 119 ASP cc_start: 0.9611 (m-30) cc_final: 0.9339 (p0) REVERT: H 305 MET cc_start: 0.4112 (mmp) cc_final: 0.3771 (mmm) REVERT: H 515 MET cc_start: 0.7623 (mmp) cc_final: 0.6973 (ptm) REVERT: H 587 MET cc_start: 0.3961 (tpp) cc_final: 0.3730 (tpp) REVERT: H 647 MET cc_start: 0.9246 (mmm) cc_final: 0.8699 (mmm) REVERT: H 930 MET cc_start: 0.8722 (mpp) cc_final: 0.8303 (mpp) REVERT: H 1056 MET cc_start: 0.8839 (mmt) cc_final: 0.7831 (mmt) REVERT: I 145 MET cc_start: 0.9287 (ppp) cc_final: 0.9084 (ppp) REVERT: J 37 MET cc_start: 0.7480 (tpp) cc_final: 0.7255 (tpp) REVERT: J 52 MET cc_start: 0.6719 (mpp) cc_final: 0.6392 (mpp) REVERT: J 146 MET cc_start: 0.8423 (mmp) cc_final: 0.8101 (mmm) REVERT: L 110 MET cc_start: 0.6696 (mtt) cc_final: 0.6409 (mtt) REVERT: N 37 MET cc_start: 0.7942 (tpt) cc_final: 0.6874 (tpt) REVERT: N 52 MET cc_start: 0.7528 (mmt) cc_final: 0.7070 (mmt) REVERT: X 1488 MET cc_start: 0.7890 (tpt) cc_final: 0.7643 (tpp) REVERT: X 1597 MET cc_start: 0.8448 (tpt) cc_final: 0.8233 (tpt) REVERT: X 1665 MET cc_start: 0.9143 (ptp) cc_final: 0.8822 (ptp) REVERT: X 1779 MET cc_start: 0.9036 (tmm) cc_final: 0.8691 (tmm) REVERT: Y 1449 MET cc_start: 0.7924 (mmp) cc_final: 0.7622 (mmp) REVERT: Y 1678 LEU cc_start: 0.9402 (mp) cc_final: 0.8940 (tp) REVERT: Y 1690 MET cc_start: 0.8896 (mpp) cc_final: 0.8565 (mpp) outliers start: 1 outliers final: 0 residues processed: 233 average time/residue: 0.2152 time to fit residues: 87.0566 Evaluate side-chains 218 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 308 optimal weight: 6.9990 chunk 324 optimal weight: 0.7980 chunk 325 optimal weight: 3.9990 chunk 451 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 348 optimal weight: 1.9990 chunk 419 optimal weight: 0.0870 chunk 224 optimal weight: 3.9990 chunk 263 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 322 GLN ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 GLN ** H 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 742 GLN ** H 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 927 ASN ** I 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1463 ASN ** X1554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1558 GLN Y1605 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.036972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.026871 restraints weight = 669775.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.027744 restraints weight = 420468.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.028174 restraints weight = 285804.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.028271 restraints weight = 237662.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.028276 restraints weight = 209431.403| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38087 Z= 0.172 Angle : 0.613 13.266 51191 Z= 0.325 Chirality : 0.039 0.193 5607 Planarity : 0.004 0.095 6720 Dihedral : 5.063 77.630 5045 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.12), residues: 4594 helix: 1.31 (0.09), residues: 3019 sheet: -0.98 (0.39), residues: 160 loop : -0.13 (0.18), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 248 TYR 0.025 0.002 TYR A 882 PHE 0.036 0.002 PHE G 13 TRP 0.024 0.002 TRP A 414 HIS 0.010 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00355 (38087) covalent geometry : angle 0.61345 (51191) hydrogen bonds : bond 0.04107 ( 2427) hydrogen bonds : angle 4.76345 ( 7194) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.564 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 239 MET cc_start: 0.8895 (mmp) cc_final: 0.8692 (mmm) REVERT: A 886 MET cc_start: 0.8799 (mpp) cc_final: 0.8207 (mpp) REVERT: A 925 MET cc_start: 0.7992 (ptp) cc_final: 0.7514 (ptp) REVERT: A 1052 MET cc_start: 0.9229 (mpp) cc_final: 0.9001 (mmt) REVERT: A 1056 MET cc_start: 0.9443 (mtt) cc_final: 0.8991 (mmt) REVERT: A 1099 MET cc_start: 0.4357 (tpt) cc_final: 0.2775 (mtt) REVERT: B 146 MET cc_start: 0.8524 (ttt) cc_final: 0.7850 (tpt) REVERT: E 110 MET cc_start: 0.9343 (mmp) cc_final: 0.9064 (mmp) REVERT: F 72 MET cc_start: 0.8072 (ptp) cc_final: 0.7751 (ptp) REVERT: F 119 ASP cc_start: 0.9623 (m-30) cc_final: 0.9370 (p0) REVERT: G 52 MET cc_start: 0.7994 (tpp) cc_final: 0.7371 (tpp) REVERT: G 145 MET cc_start: 0.6557 (pmm) cc_final: 0.6332 (pmm) REVERT: H 107 LEU cc_start: 0.9271 (tp) cc_final: 0.8987 (tp) REVERT: H 305 MET cc_start: 0.5084 (mmp) cc_final: 0.4665 (mmm) REVERT: H 515 MET cc_start: 0.7638 (mmp) cc_final: 0.6987 (ptm) REVERT: H 587 MET cc_start: 0.3728 (tpp) cc_final: 0.3513 (tpp) REVERT: H 647 MET cc_start: 0.9239 (mmm) cc_final: 0.8949 (mmm) REVERT: H 900 MET cc_start: 0.6510 (ptp) cc_final: 0.6234 (ptm) REVERT: H 930 MET cc_start: 0.8747 (mpp) cc_final: 0.8257 (mpp) REVERT: H 1056 MET cc_start: 0.8903 (mmt) cc_final: 0.8030 (mmt) REVERT: H 1102 MET cc_start: 0.7167 (mpp) cc_final: 0.6944 (mmt) REVERT: I 145 MET cc_start: 0.9289 (ppp) cc_final: 0.9085 (ppp) REVERT: J 52 MET cc_start: 0.6699 (mpp) cc_final: 0.6378 (mpp) REVERT: J 125 MET cc_start: 0.9014 (mpp) cc_final: 0.8749 (mpp) REVERT: J 146 MET cc_start: 0.8335 (mmp) cc_final: 0.8029 (mmm) REVERT: K 146 MET cc_start: 0.6144 (mmp) cc_final: 0.5663 (mmm) REVERT: L 73 MET cc_start: 0.3602 (mmp) cc_final: 0.3145 (mmm) REVERT: L 110 MET cc_start: 0.6693 (mtt) cc_final: 0.6384 (mmt) REVERT: N 37 MET cc_start: 0.8058 (tpt) cc_final: 0.6979 (tpt) REVERT: N 52 MET cc_start: 0.7490 (mmt) cc_final: 0.7090 (mmt) REVERT: X 1551 MET cc_start: 0.8472 (mpp) cc_final: 0.7999 (mpp) REVERT: X 1597 MET cc_start: 0.8418 (tpt) cc_final: 0.8151 (tpt) REVERT: X 1665 MET cc_start: 0.9145 (ptp) cc_final: 0.8822 (ptp) REVERT: X 1779 MET cc_start: 0.9034 (tmm) cc_final: 0.8672 (tmm) REVERT: Y 1449 MET cc_start: 0.7995 (mmp) cc_final: 0.7722 (mmp) REVERT: Y 1653 MET cc_start: 0.9128 (mmm) cc_final: 0.8800 (mmm) REVERT: Y 1690 MET cc_start: 0.8769 (mpp) cc_final: 0.8412 (mpp) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.2139 time to fit residues: 86.5796 Evaluate side-chains 219 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 65 optimal weight: 4.9990 chunk 348 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 359 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 57 optimal weight: 0.4980 chunk 290 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 282 optimal weight: 2.9990 chunk 127 optimal weight: 30.0000 chunk 368 optimal weight: 0.7980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 GLN ** H 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 742 GLN ** H 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 927 ASN ** I 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.036941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.026839 restraints weight = 676422.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.027922 restraints weight = 418486.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.027915 restraints weight = 275791.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.028124 restraints weight = 245175.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.028144 restraints weight = 226581.516| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38087 Z= 0.167 Angle : 0.617 12.485 51191 Z= 0.327 Chirality : 0.039 0.185 5607 Planarity : 0.004 0.093 6720 Dihedral : 5.065 77.996 5045 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.12), residues: 4594 helix: 1.31 (0.09), residues: 3020 sheet: -0.91 (0.40), residues: 150 loop : -0.12 (0.18), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 38 TYR 0.025 0.002 TYR A 882 PHE 0.046 0.002 PHE N 90 TRP 0.024 0.002 TRP A 414 HIS 0.010 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00347 (38087) covalent geometry : angle 0.61664 (51191) hydrogen bonds : bond 0.04086 ( 2427) hydrogen bonds : angle 4.76331 ( 7194) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8931 (mmp) cc_final: 0.8717 (mmm) REVERT: A 886 MET cc_start: 0.8827 (mpp) cc_final: 0.8247 (mpp) REVERT: A 925 MET cc_start: 0.7911 (ptp) cc_final: 0.7438 (ptp) REVERT: A 1052 MET cc_start: 0.9206 (mpp) cc_final: 0.8974 (mmt) REVERT: A 1056 MET cc_start: 0.9456 (mtt) cc_final: 0.9003 (mmt) REVERT: A 1099 MET cc_start: 0.4671 (tpt) cc_final: 0.3139 (mtt) REVERT: B 146 MET cc_start: 0.8521 (ttt) cc_final: 0.7834 (tpt) REVERT: D 146 MET cc_start: 0.7929 (mmm) cc_final: 0.7361 (mmm) REVERT: E 110 MET cc_start: 0.9349 (mmp) cc_final: 0.9068 (mmp) REVERT: F 72 MET cc_start: 0.8038 (ptp) cc_final: 0.7737 (ptp) REVERT: F 119 ASP cc_start: 0.9627 (m-30) cc_final: 0.9389 (p0) REVERT: G 145 MET cc_start: 0.6669 (pmm) cc_final: 0.6437 (pmm) REVERT: H 107 LEU cc_start: 0.9220 (tp) cc_final: 0.8961 (tp) REVERT: H 305 MET cc_start: 0.5528 (mmp) cc_final: 0.5049 (mmm) REVERT: H 515 MET cc_start: 0.7669 (mmp) cc_final: 0.7067 (ptm) REVERT: H 587 MET cc_start: 0.3700 (tpp) cc_final: 0.3476 (tpp) REVERT: H 647 MET cc_start: 0.9248 (mmm) cc_final: 0.8946 (mmm) REVERT: H 900 MET cc_start: 0.6553 (ptp) cc_final: 0.6259 (ptm) REVERT: H 925 MET cc_start: 0.6934 (ttt) cc_final: 0.5760 (mtp) REVERT: H 930 MET cc_start: 0.8740 (mpp) cc_final: 0.8250 (mpp) REVERT: H 1052 MET cc_start: 0.9006 (ttt) cc_final: 0.8295 (ttt) REVERT: H 1056 MET cc_start: 0.8907 (mmt) cc_final: 0.7972 (mmt) REVERT: H 1102 MET cc_start: 0.7229 (mpp) cc_final: 0.6954 (mmt) REVERT: J 52 MET cc_start: 0.6649 (mpp) cc_final: 0.6351 (mpp) REVERT: J 125 MET cc_start: 0.8986 (mpp) cc_final: 0.8719 (mpp) REVERT: J 146 MET cc_start: 0.8315 (mmp) cc_final: 0.8023 (mmm) REVERT: K 146 MET cc_start: 0.5822 (mmp) cc_final: 0.5319 (mmm) REVERT: L 110 MET cc_start: 0.6686 (mtt) cc_final: 0.6362 (mmt) REVERT: L 146 MET cc_start: 0.3532 (mtm) cc_final: 0.3330 (mtp) REVERT: N 37 MET cc_start: 0.8168 (tpt) cc_final: 0.7087 (tpt) REVERT: N 52 MET cc_start: 0.7427 (mmt) cc_final: 0.7072 (mmt) REVERT: X 1488 MET cc_start: 0.7923 (tpt) cc_final: 0.7586 (tpp) REVERT: X 1551 MET cc_start: 0.8511 (mpp) cc_final: 0.7959 (mpp) REVERT: X 1597 MET cc_start: 0.8434 (tpt) cc_final: 0.8088 (tpt) REVERT: X 1665 MET cc_start: 0.9134 (ptp) cc_final: 0.8803 (ptp) REVERT: X 1779 MET cc_start: 0.9059 (tmm) cc_final: 0.8701 (tmm) REVERT: Y 1449 MET cc_start: 0.8220 (mmp) cc_final: 0.7913 (mmp) REVERT: Y 1653 MET cc_start: 0.9084 (mmm) cc_final: 0.8782 (mmm) REVERT: Y 1690 MET cc_start: 0.8808 (mpp) cc_final: 0.8437 (mpp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2114 time to fit residues: 85.1677 Evaluate side-chains 219 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 343 optimal weight: 0.2980 chunk 182 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 311 optimal weight: 10.0000 chunk 273 optimal weight: 0.8980 chunk 195 optimal weight: 0.0670 chunk 184 optimal weight: 7.9990 chunk 346 optimal weight: 0.6980 overall best weight: 1.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 GLN G 136 GLN ** H 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 742 GLN ** H 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 927 ASN ** I 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 108 HIS ** X1554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.037430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.027295 restraints weight = 669043.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.028229 restraints weight = 421660.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.028650 restraints weight = 277525.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.028793 restraints weight = 237431.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.028737 restraints weight = 205668.949| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 38087 Z= 0.132 Angle : 0.590 12.962 51191 Z= 0.309 Chirality : 0.039 0.190 5607 Planarity : 0.004 0.087 6720 Dihedral : 4.926 77.806 5045 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.13), residues: 4594 helix: 1.50 (0.09), residues: 3026 sheet: -1.13 (0.38), residues: 176 loop : -0.07 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 38 TYR 0.029 0.002 TYR X1495 PHE 0.042 0.001 PHE G 13 TRP 0.020 0.002 TRP A 414 HIS 0.009 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00279 (38087) covalent geometry : angle 0.59036 (51191) hydrogen bonds : bond 0.03912 ( 2427) hydrogen bonds : angle 4.61105 ( 7194) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9188 Ramachandran restraints generated. 4594 Oldfield, 0 Emsley, 4594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8775 (mmp) cc_final: 0.8530 (mmm) REVERT: A 307 HIS cc_start: 0.8952 (m-70) cc_final: 0.8484 (m-70) REVERT: A 886 MET cc_start: 0.8784 (mpp) cc_final: 0.8230 (mpp) REVERT: A 925 MET cc_start: 0.7766 (ptp) cc_final: 0.7324 (ptp) REVERT: A 1052 MET cc_start: 0.9224 (mpp) cc_final: 0.8981 (mmt) REVERT: A 1056 MET cc_start: 0.9441 (mtt) cc_final: 0.8963 (mmt) REVERT: A 1099 MET cc_start: 0.4709 (tpt) cc_final: 0.3171 (mtt) REVERT: B 146 MET cc_start: 0.8359 (ttt) cc_final: 0.7740 (tpt) REVERT: C 73 MET cc_start: 0.4028 (mmm) cc_final: 0.3752 (mmm) REVERT: D 146 MET cc_start: 0.7756 (mmm) cc_final: 0.7455 (mmm) REVERT: E 110 MET cc_start: 0.9330 (mmp) cc_final: 0.9063 (mmp) REVERT: F 72 MET cc_start: 0.8022 (ptp) cc_final: 0.7715 (ptp) REVERT: G 52 MET cc_start: 0.7893 (tpp) cc_final: 0.7114 (tpp) REVERT: G 145 MET cc_start: 0.6493 (pmm) cc_final: 0.6279 (pmm) REVERT: H 107 LEU cc_start: 0.9198 (tp) cc_final: 0.8935 (tp) REVERT: H 305 MET cc_start: 0.5507 (mmp) cc_final: 0.5026 (mmm) REVERT: H 515 MET cc_start: 0.7729 (mmp) cc_final: 0.7143 (ptm) REVERT: H 587 MET cc_start: 0.3621 (tpp) cc_final: 0.3351 (tpp) REVERT: H 647 MET cc_start: 0.9237 (mmm) cc_final: 0.8974 (mmm) REVERT: H 900 MET cc_start: 0.6546 (ptp) cc_final: 0.6250 (ptm) REVERT: H 925 MET cc_start: 0.6859 (ttt) cc_final: 0.5669 (mtp) REVERT: H 930 MET cc_start: 0.8713 (mpp) cc_final: 0.8179 (mpp) REVERT: H 1052 MET cc_start: 0.9002 (ttt) cc_final: 0.8269 (ttt) REVERT: H 1056 MET cc_start: 0.8943 (mmt) cc_final: 0.7990 (mmt) REVERT: H 1102 MET cc_start: 0.7188 (mpp) cc_final: 0.6888 (mmt) REVERT: J 52 MET cc_start: 0.6708 (mpp) cc_final: 0.6371 (mpp) REVERT: J 125 MET cc_start: 0.8947 (mpp) cc_final: 0.8703 (mpp) REVERT: J 146 MET cc_start: 0.8261 (mmp) cc_final: 0.7912 (mmm) REVERT: L 110 MET cc_start: 0.6767 (mtt) cc_final: 0.6412 (mmt) REVERT: N 37 MET cc_start: 0.8008 (tpt) cc_final: 0.7013 (tpt) REVERT: N 52 MET cc_start: 0.7349 (mmt) cc_final: 0.6970 (mmt) REVERT: X 1488 MET cc_start: 0.7911 (tpt) cc_final: 0.7558 (tpp) REVERT: X 1551 MET cc_start: 0.8560 (mpp) cc_final: 0.8066 (mpp) REVERT: X 1597 MET cc_start: 0.8398 (tpt) cc_final: 0.8078 (tpt) REVERT: X 1665 MET cc_start: 0.9107 (ptp) cc_final: 0.8763 (ptp) REVERT: X 1683 MET cc_start: 0.8839 (mmt) cc_final: 0.8276 (tpt) REVERT: X 1779 MET cc_start: 0.9015 (tmm) cc_final: 0.8650 (tmm) REVERT: Y 1449 MET cc_start: 0.8051 (mmp) cc_final: 0.7794 (mmp) REVERT: Y 1653 MET cc_start: 0.9080 (mmm) cc_final: 0.8631 (mmm) REVERT: Y 1678 LEU cc_start: 0.9410 (mp) cc_final: 0.8991 (tp) REVERT: Y 1690 MET cc_start: 0.8790 (mpp) cc_final: 0.8461 (mpp) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.2115 time to fit residues: 86.7000 Evaluate side-chains 221 residues out of total 4093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 333 optimal weight: 10.0000 chunk 201 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 246 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 443 optimal weight: 0.9980 chunk 240 optimal weight: 0.1980 chunk 55 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS B 112 ASN D 42 GLN G 4 GLN ** H 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 398 ASN ** H 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 725 GLN ** H 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 927 ASN ** H 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN ** X1554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.037699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.026336 restraints weight = 726393.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.027110 restraints weight = 442011.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.027652 restraints weight = 320507.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.028009 restraints weight = 258318.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.028221 restraints weight = 223516.445| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38087 Z= 0.120 Angle : 0.569 12.732 51191 Z= 0.299 Chirality : 0.038 0.186 5607 Planarity : 0.004 0.078 6720 Dihedral : 4.785 79.844 5045 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.13), residues: 4594 helix: 1.66 (0.09), residues: 3025 sheet: -1.01 (0.38), residues: 181 loop : -0.07 (0.18), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 38 TYR 0.027 0.002 TYR X1495 PHE 0.029 0.001 PHE N 90 TRP 0.019 0.001 TRP A 414 HIS 0.008 0.001 HIS A 922 Details of bonding type rmsd covalent geometry : bond 0.00251 (38087) covalent geometry : angle 0.56899 (51191) hydrogen bonds : bond 0.03800 ( 2427) hydrogen bonds : angle 4.46866 ( 7194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7793.91 seconds wall clock time: 135 minutes 39.01 seconds (8139.01 seconds total)