Starting phenix.real_space_refine on Wed Oct 28 23:13:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11hc_75685/10_2026/11hc_75685.cif Found real_map, /net/cci-nas-00/data/ceres_data/11hc_75685/10_2026/11hc_75685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11hc_75685/10_2026/11hc_75685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11hc_75685/10_2026/11hc_75685.map" model { file = "/net/cci-nas-00/data/ceres_data/11hc_75685/10_2026/11hc_75685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11hc_75685/10_2026/11hc_75685.cif" } resolution = 3.37 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 76 5.49 5 Mg 2 5.21 5 S 75 5.16 5 C 18751 2.51 5 N 4901 2.21 5 O 5670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29476 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4099 Classifications: {'peptide': 504} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 481} Chain breaks: 3 Chain: "B" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2356 Classifications: {'peptide': 285} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 269} Chain breaks: 1 Chain: "C" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2288 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 14, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2304 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 14, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2358 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 14, 'TRANS': 288} Chain: "F" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2358 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 14, 'TRANS': 288} Chain: "G" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2358 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 14, 'TRANS': 288} Chain: "H" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2358 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 14, 'TRANS': 288} Chain: "I" Number of atoms: 2289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2289 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 14, 'TRANS': 278} Chain breaks: 1 Chain: "K" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 864 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "L" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 864 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "M" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 864 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "N" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 873 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain: "O" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 837 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 1, 'TRANS': 103} Chain breaks: 1 Chain: "P" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 785 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain breaks: 1 Chain: "R" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 1002 Classifications: {'RNA': 47} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 12, 'rna3p_pur': 15, 'rna3p_pyr': 8} Link IDs: {'rna2p': 24, 'rna3p': 22} Chain: "S" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 616 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2727 SG CYS A 382 50.436 71.941 41.009 1.00312.43 S ATOM 2751 SG CYS A 385 48.849 68.618 41.281 1.00319.61 S ATOM 2804 SG CYS A 420 48.596 70.509 37.939 1.00320.88 S ATOM 2822 SG CYS A 423 46.784 71.964 40.901 1.00335.25 S Time building chain proxies: 6.32, per 1000 atoms: 0.21 Number of scatterers: 29476 At special positions: 0 Unit cell: (115.56, 121.98, 250.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 75 16.00 P 76 15.00 Mg 2 11.99 O 5670 8.00 N 4901 7.00 C 18751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 156 " distance=2.03 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: 2.63 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 382 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 423 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 420 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 385 " Number of angles added : 6 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6540 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 55 sheets defined 50.2% alpha, 15.2% beta 12 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 67 through 81 removed outlier: 3.704A pdb=" N PHE A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 121 through 128 Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.503A pdb=" N VAL A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.653A pdb=" N SER A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 222 Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 364 through 374 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 468 through 487 Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.566A pdb=" N GLN A 492 " --> pdb=" O LYS A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 507 removed outlier: 3.734A pdb=" N TYR A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 569 Processing helix chain 'A' and resid 572 through 582 removed outlier: 3.633A pdb=" N SER A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 47 Processing helix chain 'B' and resid 50 through 61 removed outlier: 3.556A pdb=" N ALA B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 144 removed outlier: 4.164A pdb=" N ILE B 138 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 248 through 258 Processing helix chain 'C' and resid 45 through 73 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 116 through 123 Processing helix chain 'C' and resid 147 through 153 removed outlier: 3.718A pdb=" N LEU C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 168 removed outlier: 3.519A pdb=" N ILE C 168 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 186 Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 232 through 245 removed outlier: 3.661A pdb=" N HIS C 245 " --> pdb=" O LYS C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 268 through 286 Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 298 through 303 removed outlier: 4.391A pdb=" N PHE C 302 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 73 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 116 through 123 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.555A pdb=" N ILE D 168 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 186 Processing helix chain 'D' and resid 232 through 245 removed outlier: 3.785A pdb=" N HIS D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 268 through 286 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 297 through 303 removed outlier: 4.313A pdb=" N PHE D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE D 302 " --> pdb=" O PRO D 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 73 Processing helix chain 'E' and resid 80 through 89 Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 116 through 123 Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 164 through 167 Processing helix chain 'E' and resid 179 through 186 Processing helix chain 'E' and resid 195 through 200 removed outlier: 3.718A pdb=" N VAL E 199 " --> pdb=" O LYS E 195 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS E 200 " --> pdb=" O VAL E 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 195 through 200' Processing helix chain 'E' and resid 232 through 244 Processing helix chain 'E' and resid 252 through 256 Processing helix chain 'E' and resid 268 through 286 Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 297 through 301 removed outlier: 3.950A pdb=" N PHE E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 73 Processing helix chain 'F' and resid 80 through 89 Processing helix chain 'F' and resid 104 through 112 Processing helix chain 'F' and resid 116 through 123 Processing helix chain 'F' and resid 147 through 155 Processing helix chain 'F' and resid 164 through 167 Processing helix chain 'F' and resid 179 through 186 Processing helix chain 'F' and resid 232 through 244 Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 268 through 286 Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 297 through 303 Processing helix chain 'G' and resid 45 through 72 Processing helix chain 'G' and resid 81 through 89 Processing helix chain 'G' and resid 104 through 112 Processing helix chain 'G' and resid 116 through 123 Processing helix chain 'G' and resid 144 through 146 No H-bonds generated for 'chain 'G' and resid 144 through 146' Processing helix chain 'G' and resid 147 through 155 Processing helix chain 'G' and resid 164 through 168 removed outlier: 3.641A pdb=" N ILE G 168 " --> pdb=" O LEU G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 186 Processing helix chain 'G' and resid 232 through 245 removed outlier: 3.645A pdb=" N HIS G 245 " --> pdb=" O LYS G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 256 Processing helix chain 'G' and resid 268 through 286 Processing helix chain 'G' and resid 286 through 296 Processing helix chain 'G' and resid 297 through 303 removed outlier: 4.382A pdb=" N PHE G 301 " --> pdb=" O SER G 297 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE G 302 " --> pdb=" O PRO G 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 73 Processing helix chain 'H' and resid 81 through 89 Processing helix chain 'H' and resid 104 through 112 Processing helix chain 'H' and resid 116 through 123 Processing helix chain 'H' and resid 147 through 155 removed outlier: 3.538A pdb=" N GLY H 155 " --> pdb=" O LEU H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 168 Processing helix chain 'H' and resid 179 through 186 Processing helix chain 'H' and resid 196 through 200 removed outlier: 3.502A pdb=" N VAL H 199 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 246 removed outlier: 3.579A pdb=" N HIS H 245 " --> pdb=" O LYS H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 286 Processing helix chain 'H' and resid 286 through 296 Processing helix chain 'H' and resid 298 through 303 removed outlier: 4.333A pdb=" N PHE H 302 " --> pdb=" O PRO H 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 73 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 104 through 112 Processing helix chain 'I' and resid 116 through 123 removed outlier: 3.524A pdb=" N SER I 120 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 155 Processing helix chain 'I' and resid 164 through 169 removed outlier: 4.193A pdb=" N ILE I 169 " --> pdb=" O SER I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 186 removed outlier: 3.546A pdb=" N LEU I 186 " --> pdb=" O LYS I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 245 Processing helix chain 'I' and resid 268 through 286 Processing helix chain 'I' and resid 286 through 296 Processing helix chain 'I' and resid 297 through 302 Processing helix chain 'K' and resid 17 through 29 Processing helix chain 'K' and resid 38 through 59 removed outlier: 5.802A pdb=" N TYR K 45 " --> pdb=" O HIS K 41 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N SER K 46 " --> pdb=" O ARG K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 73 Processing helix chain 'K' and resid 81 through 98 removed outlier: 3.538A pdb=" N HIS K 98 " --> pdb=" O LYS K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 109 Processing helix chain 'K' and resid 109 through 124 Processing helix chain 'L' and resid 17 through 30 Processing helix chain 'L' and resid 38 through 58 removed outlier: 6.544A pdb=" N TYR L 45 " --> pdb=" O HIS L 41 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N SER L 46 " --> pdb=" O ARG L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 73 Processing helix chain 'L' and resid 81 through 98 removed outlier: 3.697A pdb=" N HIS L 98 " --> pdb=" O LYS L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 109 Processing helix chain 'L' and resid 109 through 124 Processing helix chain 'M' and resid 17 through 31 Processing helix chain 'M' and resid 37 through 59 removed outlier: 6.704A pdb=" N TYR M 45 " --> pdb=" O HIS M 41 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER M 46 " --> pdb=" O ARG M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 73 Processing helix chain 'M' and resid 84 through 98 removed outlier: 3.519A pdb=" N HIS M 98 " --> pdb=" O LYS M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 109 Processing helix chain 'M' and resid 109 through 124 Processing helix chain 'N' and resid 16 through 31 Processing helix chain 'N' and resid 38 through 59 removed outlier: 6.547A pdb=" N TYR N 45 " --> pdb=" O HIS N 41 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER N 46 " --> pdb=" O ARG N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 73 Processing helix chain 'N' and resid 81 through 98 Processing helix chain 'N' and resid 98 through 109 Processing helix chain 'N' and resid 109 through 124 Processing helix chain 'O' and resid 16 through 30 removed outlier: 3.644A pdb=" N ILE O 30 " --> pdb=" O ALA O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 59 Processing helix chain 'O' and resid 61 through 73 Processing helix chain 'O' and resid 81 through 98 removed outlier: 3.538A pdb=" N HIS O 98 " --> pdb=" O LYS O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 109 Processing helix chain 'O' and resid 109 through 124 Processing helix chain 'P' and resid 18 through 30 Processing helix chain 'P' and resid 45 through 59 Processing helix chain 'P' and resid 61 through 73 Processing helix chain 'P' and resid 81 through 98 Processing helix chain 'P' and resid 98 through 109 Processing helix chain 'P' and resid 109 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 66 removed outlier: 6.041A pdb=" N HIS A 63 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR A 55 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASP A 65 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 188 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 231 Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 282 removed outlier: 5.902A pdb=" N TYR A 280 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE A 300 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASP A 294 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 290 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 381 removed outlier: 3.734A pdb=" N ALA A 380 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 443 removed outlier: 3.522A pdb=" N LEU A 524 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 547 through 548 removed outlier: 3.541A pdb=" N PHE A 547 " --> pdb=" O MET A 554 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 2 through 8 removed outlier: 4.355A pdb=" N MET B 177 " --> pdb=" O CYS B 78 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN B 98 " --> pdb=" O TYR B 107 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR B 107 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 15 through 19 removed outlier: 3.575A pdb=" N SER B 18 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG B 170 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLN B 25 " --> pdb=" O ARG B 170 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 127 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE B 123 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 5.926A pdb=" N ARG B 146 " --> pdb=" O ALA C 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 231 through 233 removed outlier: 6.004A pdb=" N LEU B 294 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU B 267 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLN B 296 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU B 265 " --> pdb=" O GLN B 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 272 through 275 Processing sheet with id=AB4, first strand: chain 'C' and resid 135 through 137 removed outlier: 3.539A pdb=" N TYR C 141 " --> pdb=" O TYR C 222 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 135 through 137 Processing sheet with id=AB6, first strand: chain 'C' and resid 19 through 20 removed outlier: 7.121A pdb=" N THR C 24 " --> pdb=" O GLN C 213 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 28 through 32 Processing sheet with id=AB8, first strand: chain 'C' and resid 124 through 126 Processing sheet with id=AB9, first strand: chain 'C' and resid 191 through 193 removed outlier: 3.798A pdb=" N ALA D 79 " --> pdb=" O ASN C 191 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 135 through 137 Processing sheet with id=AC2, first strand: chain 'D' and resid 135 through 137 Processing sheet with id=AC3, first strand: chain 'D' and resid 19 through 20 removed outlier: 7.031A pdb=" N THR D 24 " --> pdb=" O GLN D 213 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 28 through 32 Processing sheet with id=AC5, first strand: chain 'D' and resid 124 through 126 Processing sheet with id=AC6, first strand: chain 'D' and resid 191 through 192 removed outlier: 6.230A pdb=" N ASN D 191 " --> pdb=" O ALA E 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 135 through 137 Processing sheet with id=AC8, first strand: chain 'E' and resid 135 through 137 Processing sheet with id=AC9, first strand: chain 'E' and resid 19 through 20 removed outlier: 6.720A pdb=" N THR E 24 " --> pdb=" O GLN E 213 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N VAL E 215 " --> pdb=" O THR E 24 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 28 through 32 Processing sheet with id=AD2, first strand: chain 'E' and resid 124 through 126 Processing sheet with id=AD3, first strand: chain 'E' and resid 191 through 192 removed outlier: 6.454A pdb=" N ASN E 191 " --> pdb=" O ALA F 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 135 through 137 Processing sheet with id=AD5, first strand: chain 'F' and resid 135 through 137 Processing sheet with id=AD6, first strand: chain 'F' and resid 19 through 20 removed outlier: 7.011A pdb=" N THR F 24 " --> pdb=" O GLN F 213 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N VAL F 215 " --> pdb=" O THR F 24 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 28 through 32 Processing sheet with id=AD8, first strand: chain 'F' and resid 124 through 126 Processing sheet with id=AD9, first strand: chain 'F' and resid 191 through 193 Processing sheet with id=AE1, first strand: chain 'G' and resid 135 through 137 Processing sheet with id=AE2, first strand: chain 'G' and resid 135 through 137 Processing sheet with id=AE3, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AE4, first strand: chain 'G' and resid 28 through 32 Processing sheet with id=AE5, first strand: chain 'G' and resid 124 through 126 Processing sheet with id=AE6, first strand: chain 'G' and resid 170 through 176 Processing sheet with id=AE7, first strand: chain 'G' and resid 191 through 193 removed outlier: 3.645A pdb=" N ALA H 79 " --> pdb=" O ASN G 191 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 135 through 137 Processing sheet with id=AE9, first strand: chain 'H' and resid 135 through 137 Processing sheet with id=AF1, first strand: chain 'H' and resid 19 through 20 Processing sheet with id=AF2, first strand: chain 'H' and resid 28 through 32 Processing sheet with id=AF3, first strand: chain 'H' and resid 125 through 126 Processing sheet with id=AF4, first strand: chain 'H' and resid 170 through 176 Processing sheet with id=AF5, first strand: chain 'H' and resid 191 through 193 removed outlier: 3.765A pdb=" N ALA I 79 " --> pdb=" O ASN H 191 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 135 through 137 Processing sheet with id=AF7, first strand: chain 'I' and resid 135 through 137 Processing sheet with id=AF8, first strand: chain 'I' and resid 19 through 20 removed outlier: 7.035A pdb=" N THR I 24 " --> pdb=" O GLN I 213 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 28 through 32 Processing sheet with id=AG1, first strand: chain 'I' and resid 125 through 126 1477 hydrogen bonds defined for protein. 4167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 6.00 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8686 1.34 - 1.46: 4517 1.46 - 1.57: 16645 1.57 - 1.69: 151 1.69 - 1.81: 143 Bond restraints: 30142 Sorted by residual: bond pdb=" C3' DT S 7 " pdb=" C2' DT S 7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.53e+00 bond pdb=" C3' DA S 19 " pdb=" C2' DA S 19 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.30e+00 bond pdb=" C3' DA S 13 " pdb=" C2' DA S 13 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.66e+00 bond pdb=" C3' DA S 27 " pdb=" C2' DA S 27 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.49e+00 bond pdb=" C3' DG S 25 " pdb=" C2' DG S 25 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.05e+00 ... (remaining 30137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 39657 1.15 - 2.30: 1000 2.30 - 3.45: 293 3.45 - 4.60: 34 4.60 - 5.75: 18 Bond angle restraints: 41002 Sorted by residual: angle pdb=" O5' G R 4 " pdb=" C5' G R 4 " pdb=" C4' G R 4 " ideal model delta sigma weight residual 109.40 113.34 -3.94 8.00e-01 1.56e+00 2.43e+01 angle pdb=" N3 DT S 17 " pdb=" C4 DT S 17 " pdb=" O4 DT S 17 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.19e+01 angle pdb=" N3 DT S 11 " pdb=" C4 DT S 11 " pdb=" O4 DT S 11 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" O4' A R 37 " pdb=" C1' A R 37 " pdb=" N9 A R 37 " ideal model delta sigma weight residual 108.20 111.78 -3.58 8.00e-01 1.56e+00 2.01e+01 angle pdb=" N3 DT S 23 " pdb=" C4 DT S 23 " pdb=" O4 DT S 23 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 ... (remaining 40997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 17957 35.72 - 71.43: 427 71.43 - 107.15: 33 107.15 - 142.86: 3 142.86 - 178.58: 9 Dihedral angle restraints: 18429 sinusoidal: 8242 harmonic: 10187 Sorted by residual: dihedral pdb=" CB CYS A 152 " pdb=" SG CYS A 152 " pdb=" SG CYS A 156 " pdb=" CB CYS A 156 " ideal model delta sinusoidal sigma weight residual 93.00 17.84 75.16 1 1.00e+01 1.00e-02 7.14e+01 dihedral pdb=" O4' U R 2 " pdb=" C1' U R 2 " pdb=" N1 U R 2 " pdb=" C2 U R 2 " ideal model delta sinusoidal sigma weight residual 232.00 53.42 178.58 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U R 20 " pdb=" C1' U R 20 " pdb=" N1 U R 20 " pdb=" C2 U R 20 " ideal model delta sinusoidal sigma weight residual -128.00 47.76 -175.76 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 18426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3459 0.038 - 0.077: 887 0.077 - 0.115: 335 0.115 - 0.153: 97 0.153 - 0.192: 6 Chirality restraints: 4784 Sorted by residual: chirality pdb=" C3' DT S 30 " pdb=" C4' DT S 30 " pdb=" O3' DT S 30 " pdb=" C2' DT S 30 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" C1' C R 24 " pdb=" O4' C R 24 " pdb=" C2' C R 24 " pdb=" N1 C R 24 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" C3' A R 5 " pdb=" C4' A R 5 " pdb=" O3' A R 5 " pdb=" C2' A R 5 " both_signs ideal model delta sigma weight residual False -2.74 -2.58 -0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 4781 not shown) Planarity restraints: 4838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A R 37 " 0.031 2.00e-02 2.50e+03 1.51e-02 6.28e+00 pdb=" N9 A R 37 " -0.038 2.00e-02 2.50e+03 pdb=" C8 A R 37 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A R 37 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A R 37 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A R 37 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A R 37 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A R 37 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A R 37 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A R 37 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A R 37 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C R 24 " -0.028 2.00e-02 2.50e+03 1.44e-02 4.69e+00 pdb=" N1 C R 24 " 0.031 2.00e-02 2.50e+03 pdb=" C2 C R 24 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C R 24 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C R 24 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C R 24 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C R 24 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C R 24 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C R 24 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U R 18 " -0.026 2.00e-02 2.50e+03 1.40e-02 4.44e+00 pdb=" N1 U R 18 " 0.032 2.00e-02 2.50e+03 pdb=" C2 U R 18 " 0.004 2.00e-02 2.50e+03 pdb=" O2 U R 18 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U R 18 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U R 18 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U R 18 " -0.007 2.00e-02 2.50e+03 pdb=" C5 U R 18 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U R 18 " 0.002 2.00e-02 2.50e+03 ... (remaining 4835 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 32 2.62 - 3.19: 25687 3.19 - 3.76: 45949 3.76 - 4.33: 62614 4.33 - 4.90: 104448 Nonbonded interactions: 238730 Sorted by model distance: nonbonded pdb=" OD2 ASP A 94 " pdb="MG MG A 701 " model vdw 2.050 2.170 nonbonded pdb=" NE2 HIS A 93 " pdb="MG MG A 701 " model vdw 2.067 2.250 nonbonded pdb=" OD1 ASP A 94 " pdb="MG MG A 702 " model vdw 2.109 2.170 nonbonded pdb=" NE2 HIS A 70 " pdb="MG MG A 701 " model vdw 2.120 2.250 nonbonded pdb=" NH2 ARG A 54 " pdb="MG MG A 701 " model vdw 2.275 2.250 ... (remaining 238725 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 'C' and (resid 1 through 196 or resid 207 through 303)) selection = (chain 'D' and (resid 1 through 91 or resid 94 through 196 or resid 207 through \ 303)) selection = (chain 'E' and (resid 1 through 91 or resid 101 through 196 or resid 207 through \ 303)) selection = (chain 'F' and (resid 1 through 91 or resid 101 through 196 or resid 207 through \ 303)) selection = (chain 'G' and (resid 1 through 91 or resid 101 through 196 or resid 207 through \ 303)) selection = (chain 'H' and (resid 1 through 91 or resid 101 through 196 or resid 207 through \ 303)) selection = (chain 'I' and (resid 1 through 91 or resid 101 through 303)) } ncs_group { reference = (chain 'K' and (resid 17 through 32 or resid 42 through 124)) selection = (chain 'L' and (resid 17 through 32 or resid 42 through 124)) selection = (chain 'M' and (resid 17 through 32 or resid 42 through 124)) selection = (chain 'N' and (resid 17 through 32 or resid 42 through 124)) selection = (chain 'O' and (resid 17 through 32 or resid 42 through 124)) selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 32.560 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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 0.034 30147 Z= 0.187 Angle : 0.488 6.638 41010 Z= 0.318 Chirality : 0.042 0.192 4784 Planarity : 0.003 0.038 4838 Dihedral : 15.935 178.575 11886 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 1.21 (0.15), residues: 3477 helix: 2.74 (0.13), residues: 1569 sheet: -0.47 (0.23), residues: 493 loop : -1.00 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 54 TYR 0.019 0.001 TYR L 117 PHE 0.014 0.001 PHE N 65 TRP 0.016 0.001 TRP B 244 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.19 (30142) covalent geometry : angle 0.48497 / 0.32 (41002) SS BOND : bond 0.00195 / 0.10 ( 1) SS BOND : angle 1.09098 / 0.62 ( 2) hydrogen bonds : bond 0.13555 / 9.06 ( 1488) hydrogen bonds : angle 5.51385 / 3.85 ( 4209) metal coordination : bond 0.00657 / 0.34 ( 4) metal coordination : angle 4.23196 / 2.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 602 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.8202 (tpp) cc_final: 0.7982 (tpp) REVERT: A 300 ILE cc_start: 0.8991 (mt) cc_final: 0.8752 (tt) REVERT: A 309 MET cc_start: 0.8912 (ttm) cc_final: 0.8162 (mmp) REVERT: B 91 MET cc_start: 0.8696 (mmt) cc_final: 0.8379 (mmt) REVERT: B 208 MET cc_start: 0.9166 (mmt) cc_final: 0.8466 (mmt) REVERT: B 215 ASP cc_start: 0.8427 (t0) cc_final: 0.7987 (m-30) REVERT: B 255 MET cc_start: 0.9157 (mtp) cc_final: 0.8856 (mtm) REVERT: B 269 ASP cc_start: 0.7832 (t0) cc_final: 0.7601 (m-30) REVERT: C 122 MET cc_start: 0.9274 (mmm) cc_final: 0.8919 (mmm) REVERT: C 158 PHE cc_start: 0.8548 (t80) cc_final: 0.8329 (t80) REVERT: E 180 MET cc_start: 0.9093 (tmm) cc_final: 0.8851 (tpp) REVERT: E 184 MET cc_start: 0.9347 (mmm) cc_final: 0.9055 (mmm) REVERT: E 193 GLN cc_start: 0.8122 (mt0) cc_final: 0.7899 (mt0) REVERT: F 28 SER cc_start: 0.9282 (m) cc_final: 0.9059 (p) REVERT: F 63 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8809 (tm-30) REVERT: F 184 MET cc_start: 0.9128 (mmm) cc_final: 0.8912 (mmt) REVERT: F 247 ASP cc_start: 0.8850 (p0) cc_final: 0.8592 (p0) REVERT: F 299 ASN cc_start: 0.9200 (m-40) cc_final: 0.8905 (t0) REVERT: G 1 MET cc_start: 0.8549 (ttt) cc_final: 0.8200 (ttm) REVERT: G 100 GLN cc_start: 0.7818 (mm110) cc_final: 0.7249 (mp10) REVERT: G 291 GLN cc_start: 0.9157 (tt0) cc_final: 0.8672 (tp-100) REVERT: H 20 ILE cc_start: 0.9185 (mt) cc_final: 0.8969 (pt) REVERT: H 129 ILE cc_start: 0.9080 (mt) cc_final: 0.8862 (pt) REVERT: H 184 MET cc_start: 0.9039 (tpt) cc_final: 0.8577 (tmm) REVERT: H 271 ARG cc_start: 0.9226 (ttt180) cc_final: 0.8961 (mmm-85) REVERT: I 35 ASP cc_start: 0.9022 (m-30) cc_final: 0.8811 (p0) REVERT: I 92 ILE cc_start: 0.9070 (pt) cc_final: 0.8705 (mt) REVERT: I 211 TYR cc_start: 0.8742 (m-80) cc_final: 0.8531 (m-80) REVERT: K 39 LYS cc_start: 0.8097 (pttm) cc_final: 0.7868 (ptmm) REVERT: K 44 LYS cc_start: 0.7120 (mttt) cc_final: 0.6821 (tttp) REVERT: K 48 LEU cc_start: 0.9125 (tp) cc_final: 0.8719 (tt) REVERT: K 52 ILE cc_start: 0.8833 (mt) cc_final: 0.8483 (mt) REVERT: K 63 ASP cc_start: 0.9145 (m-30) cc_final: 0.8755 (m-30) REVERT: K 67 GLU cc_start: 0.9241 (tp30) cc_final: 0.8986 (tp30) REVERT: K 78 LEU cc_start: 0.8509 (mt) cc_final: 0.8194 (tt) REVERT: K 92 TYR cc_start: 0.9274 (t80) cc_final: 0.8675 (t80) REVERT: K 94 LYS cc_start: 0.9245 (mttt) cc_final: 0.9005 (ptmt) REVERT: L 18 ASP cc_start: 0.8905 (m-30) cc_final: 0.8468 (p0) REVERT: L 36 MET cc_start: 0.7464 (mtt) cc_final: 0.7003 (mtp) REVERT: L 57 LYS cc_start: 0.9061 (mttt) cc_final: 0.8580 (tmmt) REVERT: L 67 GLU cc_start: 0.8734 (tp30) cc_final: 0.8437 (tp30) REVERT: L 97 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8751 (mt-10) REVERT: M 63 ASP cc_start: 0.9080 (m-30) cc_final: 0.8809 (m-30) REVERT: M 64 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8613 (tt0) REVERT: M 67 GLU cc_start: 0.8633 (tp30) cc_final: 0.8423 (tp30) REVERT: M 97 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8783 (mt-10) REVERT: M 101 GLU cc_start: 0.8832 (mp0) cc_final: 0.8621 (mp0) REVERT: M 111 TYR cc_start: 0.9142 (m-80) cc_final: 0.8707 (m-10) REVERT: N 36 MET cc_start: 0.6393 (mtt) cc_final: 0.5681 (mtp) REVERT: N 72 GLN cc_start: 0.8470 (mt0) cc_final: 0.8244 (mt0) REVERT: N 87 ASN cc_start: 0.9479 (t0) cc_final: 0.9003 (t0) REVERT: O 18 ASP cc_start: 0.8887 (m-30) cc_final: 0.8016 (m-30) REVERT: O 31 ILE cc_start: 0.9458 (mt) cc_final: 0.9253 (mt) REVERT: O 33 TRP cc_start: 0.7103 (m100) cc_final: 0.6455 (p-90) REVERT: O 57 LYS cc_start: 0.9218 (mttt) cc_final: 0.8978 (mtmm) REVERT: O 86 GLU cc_start: 0.9239 (tt0) cc_final: 0.8761 (tp30) REVERT: O 90 GLU cc_start: 0.9456 (tt0) cc_final: 0.9199 (pt0) REVERT: O 111 TYR cc_start: 0.8761 (m-80) cc_final: 0.8370 (m-10) REVERT: O 114 THR cc_start: 0.8969 (m) cc_final: 0.8713 (p) REVERT: P 27 ILE cc_start: 0.8691 (mt) cc_final: 0.8289 (mm) REVERT: P 57 LYS cc_start: 0.8780 (mttt) cc_final: 0.8426 (mmmt) REVERT: P 59 SER cc_start: 0.4787 (m) cc_final: 0.4249 (t) REVERT: P 68 LYS cc_start: 0.9117 (mttt) cc_final: 0.8899 (mttt) REVERT: P 87 ASN cc_start: 0.8654 (t0) cc_final: 0.8245 (t0) REVERT: P 88 PHE cc_start: 0.9168 (t80) cc_final: 0.8620 (t80) REVERT: P 89 LYS cc_start: 0.9330 (tptp) cc_final: 0.9119 (mttt) outliers start: 0 outliers final: 0 residues processed: 602 average time/residue: 0.2227 time to fit residues: 202.7383 Evaluate side-chains 310 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 74 GLN D 208 GLN D 281 ASN E 47 ASN E 100 GLN F 245 HIS F 277 HIS F 281 ASN K 60 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.080934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.053502 restraints weight = 92324.927| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.46 r_work: 0.2759 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 30147 Z= 0.248 Angle : 0.644 11.776 41010 Z= 0.332 Chirality : 0.045 0.368 4784 Planarity : 0.004 0.052 4838 Dihedral : 14.881 179.324 4848 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.19 % Allowed : 9.88 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.96 (0.14), residues: 3477 helix: 2.48 (0.13), residues: 1586 sheet: -0.51 (0.23), residues: 496 loop : -1.15 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 303 TYR 0.024 0.001 TYR P 92 PHE 0.017 0.002 PHE O 88 TRP 0.015 0.001 TRP B 244 HIS 0.017 0.001 HIS F 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.25 (30142) covalent geometry : angle 0.64030 / 0.33 (41002) SS BOND : bond 0.00273 / 0.14 ( 1) SS BOND : angle 1.32924 / 0.74 ( 2) hydrogen bonds : bond 0.04865 / 3.23 ( 1488) hydrogen bonds : angle 4.91462 / 3.44 ( 4209) metal coordination : bond 0.01037 / 0.54 ( 4) metal coordination : angle 5.34090 / 3.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 311 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.9356 (mtp) cc_final: 0.9007 (mmm) REVERT: A 205 MET cc_start: 0.8304 (tpp) cc_final: 0.8010 (tpp) REVERT: B 208 MET cc_start: 0.9202 (mmt) cc_final: 0.8389 (mmt) REVERT: B 215 ASP cc_start: 0.8377 (t0) cc_final: 0.7903 (m-30) REVERT: B 255 MET cc_start: 0.9162 (mtp) cc_final: 0.8927 (mtp) REVERT: B 269 ASP cc_start: 0.7867 (t0) cc_final: 0.7614 (m-30) REVERT: B 296 GLN cc_start: 0.7982 (mm110) cc_final: 0.7779 (mm110) REVERT: C 158 PHE cc_start: 0.8672 (t80) cc_final: 0.8466 (t80) REVERT: C 184 MET cc_start: 0.9292 (mmt) cc_final: 0.9082 (mmt) REVERT: D 37 THR cc_start: 0.9172 (m) cc_final: 0.8875 (p) REVERT: D 122 MET cc_start: 0.9368 (mmm) cc_final: 0.9107 (mtp) REVERT: E 18 GLU cc_start: 0.8975 (pt0) cc_final: 0.8773 (tp30) REVERT: E 180 MET cc_start: 0.8965 (tmm) cc_final: 0.8533 (tpp) REVERT: E 184 MET cc_start: 0.9237 (mmm) cc_final: 0.8939 (mmm) REVERT: E 193 GLN cc_start: 0.8112 (mt0) cc_final: 0.7816 (mt0) REVERT: F 184 MET cc_start: 0.9104 (mmm) cc_final: 0.8902 (mmt) REVERT: F 247 ASP cc_start: 0.8956 (p0) cc_final: 0.8726 (p0) REVERT: G 1 MET cc_start: 0.8454 (ttt) cc_final: 0.8009 (ttm) REVERT: G 100 GLN cc_start: 0.7886 (mm110) cc_final: 0.7330 (mp10) REVERT: G 291 GLN cc_start: 0.9119 (tt0) cc_final: 0.8565 (tp-100) REVERT: H 11 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8624 (mt-10) REVERT: H 20 ILE cc_start: 0.8496 (mt) cc_final: 0.8138 (pt) REVERT: H 184 MET cc_start: 0.9024 (tpt) cc_final: 0.8501 (tmm) REVERT: H 271 ARG cc_start: 0.9342 (ttt180) cc_final: 0.9061 (mmm-85) REVERT: I 35 ASP cc_start: 0.9040 (m-30) cc_final: 0.8726 (p0) REVERT: I 74 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8557 (tm-30) REVERT: I 92 ILE cc_start: 0.9087 (pt) cc_final: 0.8619 (mt) REVERT: I 122 MET cc_start: 0.9309 (mmt) cc_final: 0.8482 (mmt) REVERT: I 211 TYR cc_start: 0.8631 (m-80) cc_final: 0.8400 (m-80) REVERT: I 231 MET cc_start: 0.8741 (mtp) cc_final: 0.8445 (mtm) REVERT: K 48 LEU cc_start: 0.9109 (tp) cc_final: 0.8683 (tt) REVERT: K 52 ILE cc_start: 0.8788 (mt) cc_final: 0.8407 (mt) REVERT: L 18 ASP cc_start: 0.9117 (m-30) cc_final: 0.8400 (p0) REVERT: L 36 MET cc_start: 0.7632 (mtt) cc_final: 0.7294 (mtm) REVERT: L 57 LYS cc_start: 0.9005 (mttt) cc_final: 0.8537 (ttpt) REVERT: L 67 GLU cc_start: 0.8688 (tp30) cc_final: 0.8359 (tp30) REVERT: L 101 GLU cc_start: 0.8858 (mp0) cc_final: 0.8508 (pm20) REVERT: M 67 GLU cc_start: 0.8483 (tp30) cc_final: 0.8189 (tp30) REVERT: M 69 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8125 (mm) REVERT: M 93 ARG cc_start: 0.9269 (tpp80) cc_final: 0.9007 (tpp80) REVERT: M 101 GLU cc_start: 0.8804 (mp0) cc_final: 0.8589 (mp0) REVERT: M 111 TYR cc_start: 0.9076 (m-80) cc_final: 0.8734 (m-10) REVERT: N 36 MET cc_start: 0.6033 (mtt) cc_final: 0.5311 (mtp) REVERT: N 86 GLU cc_start: 0.9119 (pp20) cc_final: 0.8639 (pp20) REVERT: O 31 ILE cc_start: 0.9503 (mt) cc_final: 0.9192 (mt) REVERT: O 33 TRP cc_start: 0.7183 (m100) cc_final: 0.6388 (p-90) REVERT: O 57 LYS cc_start: 0.9304 (mttt) cc_final: 0.9089 (mtpp) REVERT: O 86 GLU cc_start: 0.9276 (tt0) cc_final: 0.8680 (tp30) REVERT: O 90 GLU cc_start: 0.9542 (tt0) cc_final: 0.9175 (pt0) REVERT: O 111 TYR cc_start: 0.8752 (m-80) cc_final: 0.8407 (m-10) REVERT: P 65 PHE cc_start: 0.8619 (t80) cc_final: 0.8379 (t80) REVERT: P 88 PHE cc_start: 0.9252 (t80) cc_final: 0.8714 (t80) REVERT: P 93 ARG cc_start: 0.8921 (mmm160) cc_final: 0.8537 (mmm160) outliers start: 37 outliers final: 19 residues processed: 336 average time/residue: 0.1852 time to fit residues: 99.3604 Evaluate side-chains 291 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 271 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 24 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: [173, 40, 81, 22, 209, 294, 334, 244, 88, 289, 117] chunk 173 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 334 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 289 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN E 47 ASN I 47 ASN K 60 ASN O 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.079732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.052299 restraints weight = 92913.952| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.42 r_work: 0.2724 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 30147 Z= 0.292 Angle : 0.658 9.908 41010 Z= 0.340 Chirality : 0.046 0.373 4784 Planarity : 0.004 0.051 4838 Dihedral : 14.964 179.657 4848 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.55 % Allowed : 12.20 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.73 (0.14), residues: 3477 helix: 2.30 (0.13), residues: 1587 sheet: -0.65 (0.22), residues: 532 loop : -1.28 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 93 TYR 0.046 0.002 TYR G 17 PHE 0.020 0.002 PHE K 65 TRP 0.019 0.002 TRP B 244 HIS 0.005 0.001 HIS L 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.29 (30142) covalent geometry : angle 0.65525 / 0.34 (41002) SS BOND : bond 0.00301 / 0.16 ( 1) SS BOND : angle 1.34045 / 0.75 ( 2) hydrogen bonds : bond 0.04688 / 3.12 ( 1488) hydrogen bonds : angle 4.90809 / 3.44 ( 4209) metal coordination : bond 0.00903 / 0.47 ( 4) metal coordination : angle 4.96259 / 2.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 290 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.9392 (mtp) cc_final: 0.9033 (mmm) REVERT: A 205 MET cc_start: 0.8102 (tpp) cc_final: 0.7777 (tpp) REVERT: B 208 MET cc_start: 0.9284 (mmt) cc_final: 0.8510 (mmt) REVERT: B 215 ASP cc_start: 0.8394 (t0) cc_final: 0.7923 (m-30) REVERT: B 269 ASP cc_start: 0.7792 (t0) cc_final: 0.7543 (m-30) REVERT: C 158 PHE cc_start: 0.8729 (t80) cc_final: 0.8337 (t80) REVERT: D 74 GLN cc_start: 0.9540 (mm110) cc_final: 0.9139 (mp10) REVERT: D 122 MET cc_start: 0.9374 (mmm) cc_final: 0.9027 (mtp) REVERT: E 18 GLU cc_start: 0.8983 (pt0) cc_final: 0.8772 (tp30) REVERT: E 180 MET cc_start: 0.8992 (tmm) cc_final: 0.8487 (tpp) REVERT: E 184 MET cc_start: 0.9232 (mmm) cc_final: 0.8983 (mmm) REVERT: F 184 MET cc_start: 0.9172 (mmm) cc_final: 0.8963 (mmt) REVERT: G 1 MET cc_start: 0.8519 (ttt) cc_final: 0.7878 (ttt) REVERT: G 100 GLN cc_start: 0.7792 (mm110) cc_final: 0.7231 (mp10) REVERT: G 122 MET cc_start: 0.9339 (mmm) cc_final: 0.9089 (mtt) REVERT: G 180 MET cc_start: 0.9023 (tpp) cc_final: 0.8483 (tpt) REVERT: G 291 GLN cc_start: 0.9138 (tt0) cc_final: 0.8573 (tp-100) REVERT: H 11 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8624 (mt-10) REVERT: H 184 MET cc_start: 0.9031 (tpt) cc_final: 0.8490 (tmm) REVERT: I 35 ASP cc_start: 0.9070 (m-30) cc_final: 0.8747 (p0) REVERT: I 74 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8567 (tm-30) REVERT: I 92 ILE cc_start: 0.9094 (pt) cc_final: 0.8719 (mt) REVERT: I 129 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8824 (tt) REVERT: I 211 TYR cc_start: 0.8629 (m-80) cc_final: 0.8371 (m-80) REVERT: I 231 MET cc_start: 0.8770 (mtp) cc_final: 0.8475 (mtm) REVERT: K 17 GLU cc_start: 0.8507 (pm20) cc_final: 0.8266 (pm20) REVERT: K 36 MET cc_start: 0.7659 (mtp) cc_final: 0.7304 (mpp) REVERT: K 48 LEU cc_start: 0.9097 (tp) cc_final: 0.8698 (tt) REVERT: K 52 ILE cc_start: 0.8807 (mt) cc_final: 0.8451 (mt) REVERT: K 90 GLU cc_start: 0.9432 (tp30) cc_final: 0.9194 (tp30) REVERT: K 93 ARG cc_start: 0.9437 (tpp-160) cc_final: 0.9191 (ttm110) REVERT: L 18 ASP cc_start: 0.9118 (m-30) cc_final: 0.8391 (p0) REVERT: L 36 MET cc_start: 0.7656 (mtt) cc_final: 0.7327 (mtm) REVERT: L 57 LYS cc_start: 0.9006 (mttt) cc_final: 0.8501 (ttpt) REVERT: L 101 GLU cc_start: 0.8987 (mp0) cc_final: 0.8760 (pm20) REVERT: M 67 GLU cc_start: 0.8510 (tp30) cc_final: 0.8166 (tp30) REVERT: N 36 MET cc_start: 0.6052 (mtt) cc_final: 0.5318 (mtp) REVERT: N 67 GLU cc_start: 0.8231 (tp30) cc_final: 0.7926 (tp30) REVERT: O 33 TRP cc_start: 0.7297 (m100) cc_final: 0.6389 (p-90) REVERT: O 76 ASP cc_start: 0.9281 (p0) cc_final: 0.8981 (t70) REVERT: O 86 GLU cc_start: 0.9277 (tt0) cc_final: 0.8673 (tp30) REVERT: O 90 GLU cc_start: 0.9546 (tt0) cc_final: 0.9214 (pt0) REVERT: P 72 GLN cc_start: 0.7239 (mt0) cc_final: 0.6961 (mt0) REVERT: P 88 PHE cc_start: 0.9111 (t80) cc_final: 0.8583 (t80) REVERT: P 93 ARG cc_start: 0.8962 (mmm160) cc_final: 0.8602 (mmm160) outliers start: 48 outliers final: 33 residues processed: 326 average time/residue: 0.1930 time to fit residues: 100.4484 Evaluate side-chains 299 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 265 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 59 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: [344, 199, 223, 232, 348, 225, 190, 282, 184, 18, 34] chunk 344 optimal weight: 0.8980 chunk 199 optimal weight: 0.1980 chunk 223 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 348 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 190 optimal weight: 0.5980 chunk 282 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 ASN E 47 ASN K 60 ASN N 87 ASN O 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.082341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.055487 restraints weight = 91187.199| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.24 r_work: 0.2815 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30147 Z= 0.133 Angle : 0.551 10.598 41010 Z= 0.290 Chirality : 0.043 0.363 4784 Planarity : 0.004 0.061 4838 Dihedral : 14.930 179.051 4848 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.42 % Allowed : 13.33 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.84 (0.14), residues: 3477 helix: 2.40 (0.13), residues: 1585 sheet: -0.61 (0.23), residues: 492 loop : -1.21 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 93 TYR 0.025 0.001 TYR P 117 PHE 0.021 0.001 PHE B 124 TRP 0.010 0.001 TRP B 244 HIS 0.004 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (30142) covalent geometry : angle 0.54811 / 0.29 (41002) SS BOND : bond 0.00384 / 0.20 ( 1) SS BOND : angle 1.42271 / 0.80 ( 2) hydrogen bonds : bond 0.04142 / 2.76 ( 1488) hydrogen bonds : angle 4.67972 / 3.27 ( 4209) metal coordination : bond 0.00666 / 0.35 ( 4) metal coordination : angle 4.77186 / 2.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 302 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.8199 (tpp) cc_final: 0.7905 (tpp) REVERT: A 381 MET cc_start: 0.8207 (mmm) cc_final: 0.8007 (mmm) REVERT: A 519 MET cc_start: 0.9457 (ttt) cc_final: 0.8844 (tmm) REVERT: B 1 MET cc_start: 0.8780 (tmm) cc_final: 0.8579 (tmm) REVERT: B 208 MET cc_start: 0.9152 (mmt) cc_final: 0.8564 (mmt) REVERT: B 215 ASP cc_start: 0.8411 (t0) cc_final: 0.8045 (m-30) REVERT: B 269 ASP cc_start: 0.7796 (t0) cc_final: 0.7557 (m-30) REVERT: C 158 PHE cc_start: 0.8386 (t80) cc_final: 0.8028 (t80) REVERT: C 184 MET cc_start: 0.9339 (mmt) cc_final: 0.9138 (mmt) REVERT: D 74 GLN cc_start: 0.9473 (mm110) cc_final: 0.8911 (mp10) REVERT: D 122 MET cc_start: 0.9141 (mmm) cc_final: 0.8923 (mtp) REVERT: E 109 MET cc_start: 0.9332 (tpp) cc_final: 0.8803 (mmm) REVERT: E 180 MET cc_start: 0.9157 (tmm) cc_final: 0.8826 (tpp) REVERT: E 184 MET cc_start: 0.9370 (mmm) cc_final: 0.9109 (mmm) REVERT: E 193 GLN cc_start: 0.8054 (mt0) cc_final: 0.7824 (mm-40) REVERT: F 184 MET cc_start: 0.9178 (mmm) cc_final: 0.8977 (mmt) REVERT: G 1 MET cc_start: 0.8697 (ttt) cc_final: 0.8269 (ttt) REVERT: G 100 GLN cc_start: 0.7693 (mm110) cc_final: 0.7158 (mp10) REVERT: G 180 MET cc_start: 0.9053 (tpp) cc_final: 0.8684 (tpt) REVERT: G 291 GLN cc_start: 0.9158 (tt0) cc_final: 0.8723 (tp-100) REVERT: H 184 MET cc_start: 0.9056 (tpt) cc_final: 0.8554 (tmm) REVERT: H 271 ARG cc_start: 0.9239 (ttt180) cc_final: 0.8971 (mmm-85) REVERT: I 74 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8822 (tm-30) REVERT: I 92 ILE cc_start: 0.9034 (pt) cc_final: 0.8732 (mt) REVERT: I 211 TYR cc_start: 0.8814 (m-80) cc_final: 0.8587 (m-80) REVERT: I 231 MET cc_start: 0.8822 (mtp) cc_final: 0.8597 (mtm) REVERT: K 18 ASP cc_start: 0.9518 (m-30) cc_final: 0.9089 (p0) REVERT: K 48 LEU cc_start: 0.9172 (tp) cc_final: 0.8704 (tt) REVERT: K 52 ILE cc_start: 0.8940 (mt) cc_final: 0.8542 (mt) REVERT: K 72 GLN cc_start: 0.8801 (mt0) cc_final: 0.8557 (mt0) REVERT: K 90 GLU cc_start: 0.9367 (tp30) cc_final: 0.9149 (tp30) REVERT: L 18 ASP cc_start: 0.8993 (m-30) cc_final: 0.8272 (p0) REVERT: L 36 MET cc_start: 0.7623 (mtt) cc_final: 0.7389 (mtp) REVERT: L 57 LYS cc_start: 0.9039 (mttt) cc_final: 0.8620 (ttpt) REVERT: M 64 GLU cc_start: 0.8565 (tp30) cc_final: 0.7755 (tp30) REVERT: M 67 GLU cc_start: 0.8609 (tp30) cc_final: 0.8344 (tp30) REVERT: M 97 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8756 (mt-10) REVERT: M 111 TYR cc_start: 0.9000 (m-10) cc_final: 0.8763 (m-10) REVERT: N 36 MET cc_start: 0.6486 (mtt) cc_final: 0.5708 (mtp) REVERT: N 67 GLU cc_start: 0.8333 (tp30) cc_final: 0.8021 (tp30) REVERT: O 33 TRP cc_start: 0.7225 (m100) cc_final: 0.6371 (p-90) REVERT: O 76 ASP cc_start: 0.9169 (p0) cc_final: 0.8909 (t70) REVERT: O 86 GLU cc_start: 0.9196 (tt0) cc_final: 0.8710 (tp30) REVERT: O 90 GLU cc_start: 0.9467 (tt0) cc_final: 0.9185 (pt0) REVERT: P 64 GLU cc_start: 0.9159 (tp30) cc_final: 0.8594 (tm-30) REVERT: P 72 GLN cc_start: 0.7185 (mt0) cc_final: 0.6726 (mt0) REVERT: P 88 PHE cc_start: 0.9050 (t80) cc_final: 0.8642 (t80) REVERT: P 93 ARG cc_start: 0.9010 (mmm160) cc_final: 0.8525 (mmm160) outliers start: 44 outliers final: 31 residues processed: 334 average time/residue: 0.1882 time to fit residues: 101.0756 Evaluate side-chains 307 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 276 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 59 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: [200, 281, 149, 348, 67, 3, 257, 279, 128, 169, 193] chunk 200 optimal weight: 0.0980 chunk 281 optimal weight: 0.0040 chunk 149 optimal weight: 0.8980 chunk 348 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 257 optimal weight: 4.9990 chunk 279 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 169 optimal weight: 0.2980 chunk 193 optimal weight: 2.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 ASN K 60 ASN O 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.082938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.056200 restraints weight = 91932.957| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.25 r_work: 0.2832 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 30147 Z= 0.116 Angle : 0.539 10.581 41010 Z= 0.285 Chirality : 0.043 0.359 4784 Planarity : 0.004 0.049 4838 Dihedral : 14.900 179.009 4848 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.42 % Allowed : 14.17 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.85 (0.14), residues: 3477 helix: 2.37 (0.13), residues: 1586 sheet: -0.47 (0.23), residues: 492 loop : -1.21 (0.15), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 51 TYR 0.030 0.001 TYR P 117 PHE 0.020 0.001 PHE K 65 TRP 0.009 0.001 TRP B 118 HIS 0.005 0.001 HIS L 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (30142) covalent geometry : angle 0.53629 / 0.28 (41002) SS BOND : bond 0.00389 / 0.20 ( 1) SS BOND : angle 1.43913 / 0.81 ( 2) hydrogen bonds : bond 0.03904 / 2.60 ( 1488) hydrogen bonds : angle 4.55340 / 3.18 ( 4209) metal coordination : bond 0.00534 / 0.28 ( 4) metal coordination : angle 4.37240 / 2.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.8199 (tpp) cc_final: 0.7922 (tpp) REVERT: A 519 MET cc_start: 0.9438 (ttt) cc_final: 0.8798 (tmm) REVERT: B 1 MET cc_start: 0.8706 (tmm) cc_final: 0.8451 (tmm) REVERT: B 115 LEU cc_start: 0.9062 (mt) cc_final: 0.8703 (mt) REVERT: B 208 MET cc_start: 0.9140 (mmt) cc_final: 0.8565 (mmt) REVERT: B 215 ASP cc_start: 0.8373 (t0) cc_final: 0.7978 (m-30) REVERT: B 269 ASP cc_start: 0.7820 (t0) cc_final: 0.7562 (m-30) REVERT: D 122 MET cc_start: 0.9153 (mmm) cc_final: 0.8887 (mtp) REVERT: E 109 MET cc_start: 0.9318 (tpp) cc_final: 0.8803 (mmm) REVERT: E 180 MET cc_start: 0.9146 (tmm) cc_final: 0.8885 (tpp) REVERT: E 184 MET cc_start: 0.9365 (mmm) cc_final: 0.9091 (mmm) REVERT: E 193 GLN cc_start: 0.8022 (mt0) cc_final: 0.7802 (mm-40) REVERT: E 208 GLN cc_start: 0.8136 (tt0) cc_final: 0.7847 (tt0) REVERT: G 1 MET cc_start: 0.8721 (ttt) cc_final: 0.8320 (ttt) REVERT: G 100 GLN cc_start: 0.7723 (mm110) cc_final: 0.7183 (mp10) REVERT: G 291 GLN cc_start: 0.9141 (tt0) cc_final: 0.8714 (tp-100) REVERT: H 184 MET cc_start: 0.9066 (tpt) cc_final: 0.8527 (tmm) REVERT: H 271 ARG cc_start: 0.9206 (ttt180) cc_final: 0.8972 (mmm-85) REVERT: I 74 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8869 (tm-30) REVERT: I 92 ILE cc_start: 0.8989 (pt) cc_final: 0.8678 (mt) REVERT: I 211 TYR cc_start: 0.8840 (m-80) cc_final: 0.8625 (m-80) REVERT: K 48 LEU cc_start: 0.9157 (tp) cc_final: 0.8694 (tt) REVERT: K 52 ILE cc_start: 0.8939 (mt) cc_final: 0.8552 (mt) REVERT: K 72 GLN cc_start: 0.8817 (mt0) cc_final: 0.8550 (mt0) REVERT: K 90 GLU cc_start: 0.9398 (tp30) cc_final: 0.9138 (tp30) REVERT: L 18 ASP cc_start: 0.8988 (m-30) cc_final: 0.8297 (p0) REVERT: L 36 MET cc_start: 0.7655 (mtt) cc_final: 0.7450 (mtp) REVERT: L 57 LYS cc_start: 0.9019 (mttt) cc_final: 0.8607 (tmmt) REVERT: L 93 ARG cc_start: 0.9585 (mmm-85) cc_final: 0.9357 (mmm160) REVERT: M 64 GLU cc_start: 0.8627 (tp30) cc_final: 0.7810 (tp30) REVERT: M 67 GLU cc_start: 0.8634 (tp30) cc_final: 0.8363 (tp30) REVERT: M 82 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.5958 (tpm170) REVERT: N 36 MET cc_start: 0.6432 (mtt) cc_final: 0.5762 (mtp) REVERT: N 64 GLU cc_start: 0.8635 (mp0) cc_final: 0.8274 (mp0) REVERT: N 67 GLU cc_start: 0.8349 (tp30) cc_final: 0.8054 (tp30) REVERT: N 72 GLN cc_start: 0.8498 (mt0) cc_final: 0.8277 (mt0) REVERT: O 33 TRP cc_start: 0.7271 (m100) cc_final: 0.6378 (p-90) REVERT: O 76 ASP cc_start: 0.9177 (p0) cc_final: 0.8966 (t70) REVERT: O 86 GLU cc_start: 0.9221 (tt0) cc_final: 0.8712 (tp30) REVERT: O 90 GLU cc_start: 0.9483 (tt0) cc_final: 0.9169 (pt0) REVERT: P 64 GLU cc_start: 0.9219 (tp30) cc_final: 0.8664 (tm-30) REVERT: P 88 PHE cc_start: 0.8864 (t80) cc_final: 0.8429 (t80) REVERT: P 93 ARG cc_start: 0.9021 (mmm160) cc_final: 0.8492 (mmm160) outliers start: 44 outliers final: 25 residues processed: 318 average time/residue: 0.1773 time to fit residues: 90.0957 Evaluate side-chains 302 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 59 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: [283, 215, 208, 232, 109, 173, 25, 167, 12, 21, 14] chunk 283 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 chunk 208 optimal weight: 0.9980 chunk 232 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN K 60 ASN O 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.082578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.056193 restraints weight = 91267.501| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.47 r_work: 0.2778 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30147 Z= 0.142 Angle : 0.541 12.631 41010 Z= 0.284 Chirality : 0.043 0.350 4784 Planarity : 0.004 0.051 4838 Dihedral : 14.889 179.228 4848 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.39 % Allowed : 14.62 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.87 (0.14), residues: 3477 helix: 2.38 (0.13), residues: 1586 sheet: -0.45 (0.23), residues: 494 loop : -1.21 (0.15), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 93 TYR 0.030 0.001 TYR P 117 PHE 0.039 0.001 PHE N 88 TRP 0.009 0.001 TRP K 33 HIS 0.006 0.001 HIS L 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (30142) covalent geometry : angle 0.53851 / 0.28 (41002) SS BOND : bond 0.00366 / 0.19 ( 1) SS BOND : angle 1.34092 / 0.75 ( 2) hydrogen bonds : bond 0.03875 / 2.57 ( 1488) hydrogen bonds : angle 4.52697 / 3.16 ( 4209) metal coordination : bond 0.00552 / 0.29 ( 4) metal coordination : angle 4.31412 / 2.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 282 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.8246 (tpp) cc_final: 0.7956 (tpp) REVERT: A 439 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7611 (p0) REVERT: A 519 MET cc_start: 0.9445 (ttt) cc_final: 0.8790 (tmm) REVERT: B 1 MET cc_start: 0.8731 (tmm) cc_final: 0.8457 (tmm) REVERT: B 115 LEU cc_start: 0.9069 (mt) cc_final: 0.8720 (mt) REVERT: B 208 MET cc_start: 0.9166 (mmt) cc_final: 0.8595 (mmt) REVERT: B 215 ASP cc_start: 0.8410 (t0) cc_final: 0.8029 (m-30) REVERT: B 255 MET cc_start: 0.8992 (mtm) cc_final: 0.8588 (ptp) REVERT: B 269 ASP cc_start: 0.7764 (t0) cc_final: 0.7544 (m-30) REVERT: D 122 MET cc_start: 0.9201 (mmm) cc_final: 0.8901 (mtp) REVERT: E 109 MET cc_start: 0.9323 (tpp) cc_final: 0.8820 (mmm) REVERT: E 180 MET cc_start: 0.9157 (tmm) cc_final: 0.8853 (tpp) REVERT: E 184 MET cc_start: 0.9399 (mmm) cc_final: 0.9142 (mmm) REVERT: E 193 GLN cc_start: 0.8114 (mt0) cc_final: 0.7836 (mm-40) REVERT: E 208 GLN cc_start: 0.8244 (tt0) cc_final: 0.7989 (tt0) REVERT: G 1 MET cc_start: 0.8751 (ttt) cc_final: 0.8350 (ttt) REVERT: G 100 GLN cc_start: 0.7728 (mm110) cc_final: 0.7188 (mp10) REVERT: G 291 GLN cc_start: 0.9157 (tt0) cc_final: 0.8721 (tp-100) REVERT: H 184 MET cc_start: 0.9101 (tpt) cc_final: 0.8538 (tmm) REVERT: H 271 ARG cc_start: 0.9242 (ttt180) cc_final: 0.8992 (mmm-85) REVERT: I 74 GLN cc_start: 0.9170 (tm-30) cc_final: 0.8910 (tm-30) REVERT: I 92 ILE cc_start: 0.8961 (pt) cc_final: 0.8649 (mt) REVERT: I 211 TYR cc_start: 0.8840 (m-80) cc_final: 0.8619 (m-80) REVERT: I 213 GLN cc_start: 0.8841 (mt0) cc_final: 0.8532 (mt0) REVERT: K 17 GLU cc_start: 0.8481 (pm20) cc_final: 0.8209 (pm20) REVERT: K 48 LEU cc_start: 0.9153 (tp) cc_final: 0.8679 (tt) REVERT: K 52 ILE cc_start: 0.8942 (mt) cc_final: 0.8550 (mt) REVERT: K 72 GLN cc_start: 0.8871 (mt0) cc_final: 0.8616 (mt0) REVERT: K 90 GLU cc_start: 0.9485 (tp30) cc_final: 0.9255 (tp30) REVERT: K 93 ARG cc_start: 0.9414 (tpp-160) cc_final: 0.9200 (ttm110) REVERT: L 18 ASP cc_start: 0.9003 (m-30) cc_final: 0.8284 (p0) REVERT: L 36 MET cc_start: 0.7687 (mtt) cc_final: 0.7455 (mtp) REVERT: L 57 LYS cc_start: 0.9014 (mttt) cc_final: 0.8599 (tmmt) REVERT: L 93 ARG cc_start: 0.9583 (mmm-85) cc_final: 0.9351 (mmm160) REVERT: M 64 GLU cc_start: 0.8645 (tp30) cc_final: 0.7859 (tp30) REVERT: M 67 GLU cc_start: 0.8668 (tp30) cc_final: 0.8400 (tp30) REVERT: M 82 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.5989 (tpm170) REVERT: M 97 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8763 (mt-10) REVERT: N 36 MET cc_start: 0.6241 (mtt) cc_final: 0.5689 (mtp) REVERT: N 67 GLU cc_start: 0.8421 (tp30) cc_final: 0.8165 (tp30) REVERT: N 93 ARG cc_start: 0.8975 (ptp-170) cc_final: 0.8717 (ptp-170) REVERT: O 33 TRP cc_start: 0.7198 (m100) cc_final: 0.6361 (p-90) REVERT: O 76 ASP cc_start: 0.9176 (p0) cc_final: 0.8973 (t70) REVERT: O 86 GLU cc_start: 0.9211 (tt0) cc_final: 0.8688 (tp30) REVERT: O 90 GLU cc_start: 0.9480 (tt0) cc_final: 0.9178 (pt0) REVERT: P 64 GLU cc_start: 0.9270 (tp30) cc_final: 0.8713 (tm-30) REVERT: P 88 PHE cc_start: 0.8901 (t80) cc_final: 0.8477 (t80) REVERT: P 93 ARG cc_start: 0.9000 (mmm160) cc_final: 0.8467 (mmm160) outliers start: 43 outliers final: 30 residues processed: 309 average time/residue: 0.1923 time to fit residues: 95.2274 Evaluate side-chains 292 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 260 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 68 LYS Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 59 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: [289, 280, 268, 165, 303, 318, 294, 131, 67, 206, 97] chunk 289 optimal weight: 2.9990 chunk 280 optimal weight: 5.9990 chunk 268 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 303 optimal weight: 5.9990 chunk 318 optimal weight: 6.9990 chunk 294 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN C 80 HIS ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN L 98 HIS O 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.080751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.054754 restraints weight = 92473.993| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.32 r_work: 0.2772 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 30147 Z= 0.272 Angle : 0.626 12.094 41010 Z= 0.324 Chirality : 0.045 0.366 4784 Planarity : 0.004 0.054 4838 Dihedral : 14.928 179.163 4848 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.65 % Allowed : 15.17 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.76 (0.14), residues: 3477 helix: 2.31 (0.13), residues: 1588 sheet: -0.61 (0.22), residues: 532 loop : -1.26 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 51 TYR 0.024 0.002 TYR K 92 PHE 0.022 0.002 PHE O 88 TRP 0.017 0.001 TRP B 244 HIS 0.006 0.001 HIS L 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.27 (30142) covalent geometry : angle 0.62379 / 0.32 (41002) SS BOND : bond 0.00322 / 0.17 ( 1) SS BOND : angle 1.23654 / 0.69 ( 2) hydrogen bonds : bond 0.04230 / 2.80 ( 1488) hydrogen bonds : angle 4.69243 / 3.29 ( 4209) metal coordination : bond 0.00723 / 0.38 ( 4) metal coordination : angle 4.37221 / 2.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 261 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.8223 (tpp) cc_final: 0.7930 (tpp) REVERT: A 439 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7627 (p0) REVERT: A 445 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8094 (pm20) REVERT: A 519 MET cc_start: 0.9464 (ttt) cc_final: 0.8799 (tmm) REVERT: B 1 MET cc_start: 0.8791 (tmm) cc_final: 0.8393 (tmm) REVERT: B 115 LEU cc_start: 0.9086 (mt) cc_final: 0.8736 (mt) REVERT: B 208 MET cc_start: 0.9192 (mmt) cc_final: 0.8647 (mmt) REVERT: B 215 ASP cc_start: 0.8457 (t0) cc_final: 0.8094 (m-30) REVERT: B 269 ASP cc_start: 0.7803 (t0) cc_final: 0.7590 (m-30) REVERT: D 122 MET cc_start: 0.9203 (mmm) cc_final: 0.8881 (mtp) REVERT: E 180 MET cc_start: 0.9178 (tmm) cc_final: 0.8801 (tpp) REVERT: E 184 MET cc_start: 0.9383 (mmm) cc_final: 0.9154 (mmm) REVERT: E 193 GLN cc_start: 0.8166 (mt0) cc_final: 0.7867 (mm-40) REVERT: E 208 GLN cc_start: 0.8276 (tt0) cc_final: 0.8035 (tt0) REVERT: F 247 ASP cc_start: 0.8794 (p0) cc_final: 0.8587 (p0) REVERT: G 1 MET cc_start: 0.8817 (ttt) cc_final: 0.8406 (ttt) REVERT: G 100 GLN cc_start: 0.7670 (mm110) cc_final: 0.7111 (mp10) REVERT: G 291 GLN cc_start: 0.9176 (tt0) cc_final: 0.8723 (tp-100) REVERT: H 184 MET cc_start: 0.9141 (tpt) cc_final: 0.8518 (tmm) REVERT: H 206 VAL cc_start: 0.9060 (t) cc_final: 0.8829 (m) REVERT: I 74 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8865 (tm-30) REVERT: I 92 ILE cc_start: 0.8982 (pt) cc_final: 0.8700 (mt) REVERT: I 129 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9160 (tt) REVERT: I 211 TYR cc_start: 0.8844 (m-80) cc_final: 0.8624 (m-80) REVERT: I 213 GLN cc_start: 0.8887 (mt0) cc_final: 0.8583 (mt0) REVERT: K 48 LEU cc_start: 0.9194 (tp) cc_final: 0.8713 (tt) REVERT: K 52 ILE cc_start: 0.8966 (mt) cc_final: 0.8572 (mt) REVERT: K 72 GLN cc_start: 0.8882 (mt0) cc_final: 0.8642 (mt0) REVERT: L 18 ASP cc_start: 0.8998 (m-30) cc_final: 0.8266 (p0) REVERT: L 36 MET cc_start: 0.7641 (mtt) cc_final: 0.7395 (mtp) REVERT: L 57 LYS cc_start: 0.9058 (mttt) cc_final: 0.8593 (ttpt) REVERT: L 93 ARG cc_start: 0.9584 (mmm-85) cc_final: 0.9364 (mmm160) REVERT: M 67 GLU cc_start: 0.8668 (tp30) cc_final: 0.8362 (tp30) REVERT: N 36 MET cc_start: 0.6359 (mtt) cc_final: 0.5789 (mtp) REVERT: N 93 ARG cc_start: 0.9007 (ptp-170) cc_final: 0.8735 (ptp-170) REVERT: O 33 TRP cc_start: 0.7287 (m100) cc_final: 0.6354 (p-90) REVERT: O 86 GLU cc_start: 0.9219 (tt0) cc_final: 0.8695 (tp30) REVERT: O 90 GLU cc_start: 0.9492 (tt0) cc_final: 0.9197 (pt0) REVERT: P 64 GLU cc_start: 0.9324 (tp30) cc_final: 0.8837 (tm-30) REVERT: P 65 PHE cc_start: 0.8229 (t80) cc_final: 0.7899 (t80) REVERT: P 69 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8785 (mm) REVERT: P 93 ARG cc_start: 0.8997 (mmm160) cc_final: 0.8490 (mmm160) outliers start: 51 outliers final: 40 residues processed: 298 average time/residue: 0.1829 time to fit residues: 88.0393 Evaluate side-chains 292 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain B residue 296 GLN Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 18 ASP Chi-restraints excluded: chain P residue 59 SER Chi-restraints excluded: chain P residue 69 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: [110, 289, 218, 106, 215, 284, 186, 105, 217, 82, 161] chunk 110 optimal weight: 0.5980 chunk 289 optimal weight: 3.9990 chunk 218 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 284 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 217 optimal weight: 0.0670 chunk 82 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN D 74 GLN E 47 ASN K 60 ASN O 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.082285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.055407 restraints weight = 91369.605| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.25 r_work: 0.2782 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 30147 Z= 0.127 Angle : 0.546 13.283 41010 Z= 0.288 Chirality : 0.043 0.366 4784 Planarity : 0.003 0.051 4838 Dihedral : 14.888 178.798 4848 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.61 % Allowed : 15.46 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.81 (0.14), residues: 3477 helix: 2.31 (0.13), residues: 1588 sheet: -0.53 (0.22), residues: 526 loop : -1.21 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 51 TYR 0.025 0.001 TYR K 92 PHE 0.043 0.001 PHE P 88 TRP 0.010 0.001 TRP B 118 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (30142) covalent geometry : angle 0.54348 / 0.29 (41002) SS BOND : bond 0.00356 / 0.19 ( 1) SS BOND : angle 1.29754 / 0.73 ( 2) hydrogen bonds : bond 0.03961 / 2.63 ( 1488) hydrogen bonds : angle 4.56362 / 3.19 ( 4209) metal coordination : bond 0.00556 / 0.29 ( 4) metal coordination : angle 4.25579 / 2.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 275 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.8241 (tpp) cc_final: 0.7955 (tpp) REVERT: A 439 ASN cc_start: 0.8013 (OUTLIER) cc_final: 0.7661 (p0) REVERT: A 445 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8083 (pm20) REVERT: A 519 MET cc_start: 0.9422 (ttt) cc_final: 0.8689 (tmm) REVERT: B 1 MET cc_start: 0.8722 (tmm) cc_final: 0.8376 (tmm) REVERT: B 115 LEU cc_start: 0.9071 (mt) cc_final: 0.8721 (mt) REVERT: B 208 MET cc_start: 0.9155 (mmt) cc_final: 0.8591 (mmt) REVERT: B 215 ASP cc_start: 0.8402 (t0) cc_final: 0.8029 (m-30) REVERT: B 269 ASP cc_start: 0.7782 (t0) cc_final: 0.7559 (m-30) REVERT: D 104 ASN cc_start: 0.9055 (t0) cc_final: 0.8782 (p0) REVERT: D 122 MET cc_start: 0.9140 (mmm) cc_final: 0.8866 (mtp) REVERT: E 109 MET cc_start: 0.9298 (tpp) cc_final: 0.8871 (mmm) REVERT: E 180 MET cc_start: 0.9159 (tmm) cc_final: 0.8836 (tpp) REVERT: E 184 MET cc_start: 0.9390 (mmm) cc_final: 0.9127 (mmm) REVERT: E 193 GLN cc_start: 0.8081 (mt0) cc_final: 0.7826 (mm-40) REVERT: F 247 ASP cc_start: 0.8735 (p0) cc_final: 0.8531 (p0) REVERT: G 1 MET cc_start: 0.8728 (ttt) cc_final: 0.8364 (ttt) REVERT: G 100 GLN cc_start: 0.7724 (mm110) cc_final: 0.7182 (mp10) REVERT: G 180 MET cc_start: 0.9010 (tpp) cc_final: 0.8792 (tpt) REVERT: G 291 GLN cc_start: 0.9156 (tt0) cc_final: 0.8728 (tp-100) REVERT: H 184 MET cc_start: 0.9085 (tpt) cc_final: 0.8506 (tmm) REVERT: H 206 VAL cc_start: 0.9012 (t) cc_final: 0.8788 (m) REVERT: H 271 ARG cc_start: 0.9216 (ttt180) cc_final: 0.8960 (mmm-85) REVERT: I 74 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8852 (tm-30) REVERT: I 92 ILE cc_start: 0.8972 (pt) cc_final: 0.8698 (mt) REVERT: I 211 TYR cc_start: 0.8834 (m-80) cc_final: 0.8613 (m-80) REVERT: I 213 GLN cc_start: 0.8854 (mt0) cc_final: 0.8638 (mt0) REVERT: K 18 ASP cc_start: 0.9496 (m-30) cc_final: 0.9094 (p0) REVERT: K 48 LEU cc_start: 0.9160 (tp) cc_final: 0.8675 (tt) REVERT: K 52 ILE cc_start: 0.8948 (mt) cc_final: 0.8557 (mt) REVERT: K 72 GLN cc_start: 0.8861 (mt0) cc_final: 0.8600 (mt0) REVERT: K 90 GLU cc_start: 0.9443 (tp30) cc_final: 0.9162 (tp30) REVERT: L 18 ASP cc_start: 0.9003 (m-30) cc_final: 0.8259 (p0) REVERT: L 36 MET cc_start: 0.7616 (mtt) cc_final: 0.7385 (mtp) REVERT: L 57 LYS cc_start: 0.9015 (mttt) cc_final: 0.8602 (tmmt) REVERT: L 93 ARG cc_start: 0.9577 (mmm-85) cc_final: 0.9356 (mmm160) REVERT: M 67 GLU cc_start: 0.8629 (tp30) cc_final: 0.8327 (tp30) REVERT: M 82 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.6062 (tpm170) REVERT: N 36 MET cc_start: 0.6262 (mtt) cc_final: 0.5583 (mtp) REVERT: N 67 GLU cc_start: 0.8263 (tp30) cc_final: 0.7991 (tp30) REVERT: N 93 ARG cc_start: 0.9060 (ptp-170) cc_final: 0.8758 (ptp-170) REVERT: O 33 TRP cc_start: 0.7257 (m100) cc_final: 0.6354 (p-90) REVERT: O 76 ASP cc_start: 0.8915 (t70) cc_final: 0.8632 (p0) REVERT: O 86 GLU cc_start: 0.9215 (tt0) cc_final: 0.8682 (tp30) REVERT: O 90 GLU cc_start: 0.9486 (tt0) cc_final: 0.9146 (pt0) REVERT: O 109 TYR cc_start: 0.8970 (m-10) cc_final: 0.8756 (m-10) REVERT: P 61 SER cc_start: 0.7133 (t) cc_final: 0.6700 (p) REVERT: P 64 GLU cc_start: 0.9392 (tp30) cc_final: 0.8911 (tm-30) REVERT: P 65 PHE cc_start: 0.8202 (t80) cc_final: 0.7891 (t80) REVERT: P 69 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8769 (mm) REVERT: P 93 ARG cc_start: 0.9040 (mmm160) cc_final: 0.8623 (mmm160) outliers start: 50 outliers final: 36 residues processed: 307 average time/residue: 0.1802 time to fit residues: 90.2934 Evaluate side-chains 300 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain B residue 296 GLN Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 18 ASP Chi-restraints excluded: chain P residue 59 SER Chi-restraints excluded: chain P residue 69 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: [345, 318, 163, 60, 330, 344, 225, 326, 157, 19, 104] chunk 345 optimal weight: 9.9990 chunk 318 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 330 optimal weight: 0.0770 chunk 344 optimal weight: 0.5980 chunk 225 optimal weight: 2.9990 chunk 326 optimal weight: 1.9990 chunk 157 optimal weight: 0.4980 chunk 19 optimal weight: 30.0000 chunk 104 optimal weight: 4.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN D 208 GLN K 60 ASN O 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.081988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.055173 restraints weight = 92092.640| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.22 r_work: 0.2773 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 30147 Z= 0.177 Angle : 0.579 12.694 41010 Z= 0.303 Chirality : 0.044 0.363 4784 Planarity : 0.004 0.051 4838 Dihedral : 14.887 178.900 4848 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.65 % Allowed : 15.72 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.74 (0.14), residues: 3477 helix: 2.25 (0.13), residues: 1588 sheet: -0.56 (0.22), residues: 535 loop : -1.25 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG M 93 TYR 0.040 0.001 TYR O 120 PHE 0.030 0.001 PHE P 88 TRP 0.013 0.001 TRP B 244 HIS 0.008 0.001 HIS O 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (30142) covalent geometry : angle 0.57066 / 0.30 (41002) SS BOND : bond 0.00334 / 0.18 ( 1) SS BOND : angle 1.24753 / 0.70 ( 2) hydrogen bonds : bond 0.04015 / 2.66 ( 1488) hydrogen bonds : angle 4.62233 / 3.23 ( 4209) metal coordination : bond 0.01183 / 0.60 ( 4) metal coordination : angle 8.12865 / 4.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 262 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.8249 (tpp) cc_final: 0.7962 (tpp) REVERT: A 439 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7768 (p0) REVERT: A 445 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8106 (pm20) REVERT: A 519 MET cc_start: 0.9425 (ttt) cc_final: 0.8728 (tmm) REVERT: B 115 LEU cc_start: 0.9063 (mt) cc_final: 0.8705 (mt) REVERT: B 208 MET cc_start: 0.9153 (mmt) cc_final: 0.8610 (mmt) REVERT: B 215 ASP cc_start: 0.8403 (t0) cc_final: 0.8052 (m-30) REVERT: B 269 ASP cc_start: 0.7754 (t0) cc_final: 0.7544 (m-30) REVERT: D 122 MET cc_start: 0.9128 (mmm) cc_final: 0.8851 (mtp) REVERT: E 109 MET cc_start: 0.9298 (tpp) cc_final: 0.9020 (tpp) REVERT: E 180 MET cc_start: 0.9166 (tmm) cc_final: 0.8831 (tpp) REVERT: E 184 MET cc_start: 0.9388 (mmm) cc_final: 0.9169 (mmm) REVERT: E 193 GLN cc_start: 0.8133 (mt0) cc_final: 0.7874 (mm-40) REVERT: G 1 MET cc_start: 0.8780 (ttt) cc_final: 0.8418 (ttt) REVERT: G 100 GLN cc_start: 0.7709 (mm110) cc_final: 0.7170 (mp10) REVERT: G 291 GLN cc_start: 0.9160 (tt0) cc_final: 0.8745 (tp-100) REVERT: H 184 MET cc_start: 0.9091 (tpt) cc_final: 0.8512 (tmm) REVERT: H 206 VAL cc_start: 0.9054 (t) cc_final: 0.8809 (m) REVERT: H 208 GLN cc_start: 0.7838 (tt0) cc_final: 0.7604 (tt0) REVERT: H 271 ARG cc_start: 0.9216 (ttt180) cc_final: 0.8967 (mmm-85) REVERT: I 74 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8849 (tm-30) REVERT: I 92 ILE cc_start: 0.8958 (pt) cc_final: 0.8684 (mt) REVERT: I 211 TYR cc_start: 0.8827 (m-80) cc_final: 0.8616 (m-80) REVERT: I 213 GLN cc_start: 0.8858 (mt0) cc_final: 0.8555 (mt0) REVERT: K 48 LEU cc_start: 0.9195 (tp) cc_final: 0.8698 (tt) REVERT: K 52 ILE cc_start: 0.8976 (mt) cc_final: 0.8583 (mt) REVERT: K 72 GLN cc_start: 0.8857 (mt0) cc_final: 0.8591 (mt0) REVERT: K 90 GLU cc_start: 0.9474 (tp30) cc_final: 0.9213 (tp30) REVERT: K 93 ARG cc_start: 0.9415 (tpp-160) cc_final: 0.9192 (ttm110) REVERT: L 18 ASP cc_start: 0.8984 (m-30) cc_final: 0.8250 (p0) REVERT: L 36 MET cc_start: 0.7605 (mtt) cc_final: 0.7381 (mtp) REVERT: L 57 LYS cc_start: 0.9031 (mttt) cc_final: 0.8625 (ttpt) REVERT: L 93 ARG cc_start: 0.9558 (mmm-85) cc_final: 0.9094 (mmm160) REVERT: L 99 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8500 (tm-30) REVERT: M 67 GLU cc_start: 0.8643 (tp30) cc_final: 0.8350 (tp30) REVERT: M 82 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.5924 (tpm170) REVERT: N 36 MET cc_start: 0.6466 (mtt) cc_final: 0.5791 (mtp) REVERT: N 67 GLU cc_start: 0.8212 (tp30) cc_final: 0.8009 (tp30) REVERT: N 93 ARG cc_start: 0.9027 (ptp-170) cc_final: 0.8732 (ptp-170) REVERT: O 33 TRP cc_start: 0.7261 (m100) cc_final: 0.6333 (p-90) REVERT: O 76 ASP cc_start: 0.8885 (t70) cc_final: 0.8588 (p0) REVERT: O 86 GLU cc_start: 0.9192 (tt0) cc_final: 0.8676 (tp30) REVERT: O 90 GLU cc_start: 0.9447 (tt0) cc_final: 0.9123 (pt0) REVERT: O 109 TYR cc_start: 0.9015 (m-10) cc_final: 0.8746 (m-10) REVERT: P 61 SER cc_start: 0.7243 (t) cc_final: 0.6772 (p) REVERT: P 64 GLU cc_start: 0.9440 (tp30) cc_final: 0.8959 (tm-30) REVERT: P 65 PHE cc_start: 0.8132 (t80) cc_final: 0.7821 (t80) REVERT: P 69 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8770 (mm) REVERT: P 93 ARG cc_start: 0.9053 (mmm160) cc_final: 0.8435 (mmm160) outliers start: 51 outliers final: 37 residues processed: 297 average time/residue: 0.1893 time to fit residues: 91.0917 Evaluate side-chains 299 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 259 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain B residue 296 GLN Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 59 SER Chi-restraints excluded: chain P residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: [175, 99, 351, 206, 91, 240, 314, 164, 75, 307, 95] chunk 175 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 351 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 240 optimal weight: 0.9990 chunk 314 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 307 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN D 208 GLN K 60 ASN O 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.082550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.055493 restraints weight = 91408.360| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.26 r_work: 0.2782 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30147 Z= 0.144 Angle : 0.570 11.188 41010 Z= 0.297 Chirality : 0.044 0.365 4784 Planarity : 0.003 0.051 4838 Dihedral : 14.874 178.807 4848 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.42 % Allowed : 16.01 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.74 (0.14), residues: 3477 helix: 2.25 (0.13), residues: 1589 sheet: -0.58 (0.22), residues: 533 loop : -1.24 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 51 TYR 0.035 0.001 TYR O 120 PHE 0.026 0.001 PHE O 88 TRP 0.012 0.001 TRP B 244 HIS 0.007 0.001 HIS O 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (30142) covalent geometry : angle 0.56241 / 0.30 (41002) SS BOND : bond 0.00331 / 0.17 ( 1) SS BOND : angle 1.24125 / 0.70 ( 2) hydrogen bonds : bond 0.03942 / 2.61 ( 1488) hydrogen bonds : angle 4.57458 / 3.19 ( 4209) metal coordination : bond 0.01171 / 0.60 ( 4) metal coordination : angle 7.60607 / 4.16 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6954 Ramachandran restraints generated. 3477 Oldfield, 0 Emsley, 3477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 1.008 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 205 MET cc_start: 0.8243 (tpp) cc_final: 0.7955 (tpp) REVERT: A 439 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7716 (p0) REVERT: A 445 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8109 (pm20) REVERT: A 519 MET cc_start: 0.9400 (ttt) cc_final: 0.8687 (tmm) REVERT: B 208 MET cc_start: 0.9168 (mmt) cc_final: 0.8606 (mmt) REVERT: B 215 ASP cc_start: 0.8400 (t0) cc_final: 0.8024 (m-30) REVERT: B 269 ASP cc_start: 0.7753 (t0) cc_final: 0.7540 (m-30) REVERT: D 104 ASN cc_start: 0.9051 (t0) cc_final: 0.8822 (p0) REVERT: D 122 MET cc_start: 0.9158 (mmm) cc_final: 0.8870 (mtp) REVERT: E 109 MET cc_start: 0.9327 (tpp) cc_final: 0.9061 (tpp) REVERT: E 180 MET cc_start: 0.9159 (tmm) cc_final: 0.8805 (tpp) REVERT: E 184 MET cc_start: 0.9391 (mmm) cc_final: 0.9122 (mmm) REVERT: E 193 GLN cc_start: 0.8114 (mt0) cc_final: 0.7841 (mm-40) REVERT: G 1 MET cc_start: 0.8770 (ttt) cc_final: 0.8391 (ttt) REVERT: G 100 GLN cc_start: 0.7716 (mm110) cc_final: 0.7179 (mp10) REVERT: G 180 MET cc_start: 0.9030 (tpp) cc_final: 0.8811 (tpt) REVERT: G 291 GLN cc_start: 0.9155 (tt0) cc_final: 0.8725 (tp-100) REVERT: H 156 VAL cc_start: 0.9528 (m) cc_final: 0.9301 (p) REVERT: H 184 MET cc_start: 0.9100 (tpt) cc_final: 0.8505 (tmm) REVERT: H 208 GLN cc_start: 0.7805 (tt0) cc_final: 0.7575 (tt0) REVERT: I 74 GLN cc_start: 0.9188 (tm-30) cc_final: 0.8833 (tm-30) REVERT: I 92 ILE cc_start: 0.8965 (pt) cc_final: 0.8670 (mt) REVERT: I 100 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7949 (mm-40) REVERT: I 211 TYR cc_start: 0.8826 (m-80) cc_final: 0.8613 (m-80) REVERT: I 213 GLN cc_start: 0.8841 (mt0) cc_final: 0.8530 (mt0) REVERT: K 17 GLU cc_start: 0.8361 (pm20) cc_final: 0.8030 (pm20) REVERT: K 48 LEU cc_start: 0.9191 (tp) cc_final: 0.8697 (tt) REVERT: K 52 ILE cc_start: 0.8960 (mt) cc_final: 0.8562 (mt) REVERT: K 72 GLN cc_start: 0.8875 (mt0) cc_final: 0.8601 (mt0) REVERT: K 90 GLU cc_start: 0.9454 (tp30) cc_final: 0.9174 (tp30) REVERT: L 18 ASP cc_start: 0.8996 (m-30) cc_final: 0.8253 (p0) REVERT: L 36 MET cc_start: 0.7601 (mtt) cc_final: 0.7367 (mtp) REVERT: L 57 LYS cc_start: 0.9016 (mttt) cc_final: 0.8605 (tmmt) REVERT: L 93 ARG cc_start: 0.9565 (mmm-85) cc_final: 0.9092 (mmm160) REVERT: L 99 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8522 (tm-30) REVERT: M 67 GLU cc_start: 0.8653 (tp30) cc_final: 0.8359 (tp30) REVERT: M 82 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.5973 (tpm170) REVERT: N 36 MET cc_start: 0.6447 (mtt) cc_final: 0.5846 (mtp) REVERT: N 93 ARG cc_start: 0.9055 (ptp-170) cc_final: 0.8757 (ptp-170) REVERT: O 33 TRP cc_start: 0.7300 (m100) cc_final: 0.6352 (p-90) REVERT: O 76 ASP cc_start: 0.8886 (t70) cc_final: 0.8593 (p0) REVERT: O 86 GLU cc_start: 0.9203 (tt0) cc_final: 0.8671 (tp30) REVERT: O 90 GLU cc_start: 0.9455 (tt0) cc_final: 0.9128 (pt0) REVERT: O 109 TYR cc_start: 0.9011 (m-10) cc_final: 0.8783 (m-10) REVERT: P 61 SER cc_start: 0.7275 (t) cc_final: 0.6842 (p) REVERT: P 64 GLU cc_start: 0.9434 (tp30) cc_final: 0.8967 (tm-30) REVERT: P 65 PHE cc_start: 0.8084 (t80) cc_final: 0.7802 (t80) REVERT: P 69 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8705 (mm) REVERT: P 93 ARG cc_start: 0.9027 (mmm160) cc_final: 0.8533 (mmm160) outliers start: 44 outliers final: 37 residues processed: 305 average time/residue: 0.1904 time to fit residues: 94.2176 Evaluate side-chains 300 residues out of total 3098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 260 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 282 TRP Chi-restraints excluded: chain B residue 296 GLN Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain I residue 87 LEU Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 109 TYR Chi-restraints excluded: chain M residue 121 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 77 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 77 SER Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 18 ASP Chi-restraints excluded: chain P residue 59 SER Chi-restraints excluded: chain P residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: [289, 268, 41, 38, 165, 207, 98, 179, 47, 339, 316] chunk 289 optimal weight: 0.9990 chunk 268 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 339 optimal weight: 9.9990 chunk 316 optimal weight: 0.0030 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 ASN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN K 60 ASN O 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.082171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.055453 restraints weight = 91754.998| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.42 r_work: 0.2778 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30147 Z= 0.155 Angle : 0.578 11.158 41010 Z= 0.302 Chirality : 0.044 0.357 4784 Planarity : 0.004 0.051 4838 Dihedral : 14.862 178.800 4848 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.39 % Allowed : 16.11 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.42 % 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: 0.74 (0.14), residues: 3477 helix: 2.25 (0.13), residues: 1588 sheet: -0.58 (0.22), residues: 533 loop : -1.24 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG M 42 TYR 0.032 0.001 TYR O 120 PHE 0.046 0.001 PHE P 88 TRP 0.012 0.001 TRP B 244 HIS 0.008 0.001 HIS O 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (30142) covalent geometry : angle 0.57115 / 0.30 (41002) SS BOND : bond 0.00316 / 0.17 ( 1) SS BOND : angle 1.21838 / 0.68 ( 2) hydrogen bonds : bond 0.03937 / 2.61 ( 1488) hydrogen bonds : angle 4.57413 / 3.19 ( 4209) metal coordination : bond 0.01077 / 0.55 ( 4) metal coordination : angle 7.17629 / 3.93 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6808.35 seconds wall clock time: 117 minutes 40.11 seconds (7060.11 seconds total)