Starting phenix.real_space_refine on Mon Jan 20 16:19:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9brs_44842/01_2025/9brs_44842.cif Found real_map, /net/cci-nas-00/data/ceres_data/9brs_44842/01_2025/9brs_44842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9brs_44842/01_2025/9brs_44842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9brs_44842/01_2025/9brs_44842.map" model { file = "/net/cci-nas-00/data/ceres_data/9brs_44842/01_2025/9brs_44842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9brs_44842/01_2025/9brs_44842.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 387 5.16 5 C 41941 2.51 5 N 11101 2.21 5 O 12119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 222 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 65548 Number of models: 1 Model: "" Number of chains: 32 Chain: "8" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "9" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "Q" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "R" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "T" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "V" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "6" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2931 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 9, 'TRANS': 351} Chain breaks: 1 Chain: "U" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3501 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 8, 'TRANS': 417} Chain breaks: 1 Chain: "a" Number of atoms: 6117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6117 Classifications: {'peptide': 752} Link IDs: {'PTRANS': 31, 'TRANS': 720} Chain breaks: 2 Chain: "e" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 623 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain: "f" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 658 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "X" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "d" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2842 Classifications: {'peptide': 351} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 337} Chain: "c" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1642 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain: "p" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "b" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1484 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 194} Chain: "g" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "1" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "2" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4671 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 571} Chain: "0" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "4" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3610 Classifications: {'peptide': 461} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 433} Chain breaks: 1 Chain: "5" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3667 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "3" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3667 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "7" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1676 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 3, 'TRANS': 204} Time building chain proxies: 27.04, per 1000 atoms: 0.41 Number of scatterers: 65548 At special positions: 0 Unit cell: (157.109, 181.45, 296.515, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 387 16.00 O 12119 8.00 N 11101 7.00 C 41941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.21 Conformation dependent library (CDL) restraints added in 6.5 seconds 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15510 Finding SS restraints... Secondary structure from input PDB file: 308 helices and 47 sheets defined 61.2% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.81 Creating SS restraints... Processing helix chain '8' and resid 2 through 106 removed outlier: 4.006A pdb=" N LYS 8 52 " --> pdb=" O THR 8 48 " (cutoff:3.500A) Processing helix chain '8' and resid 108 through 128 removed outlier: 4.022A pdb=" N VAL 8 114 " --> pdb=" O THR 8 110 " (cutoff:3.500A) Processing helix chain '8' and resid 137 through 139 No H-bonds generated for 'chain '8' and resid 137 through 139' Processing helix chain '8' and resid 140 through 160 Proline residue: 8 153 - end of helix Processing helix chain '8' and resid 196 through 217 Proline residue: 8 209 - end of helix Processing helix chain '9' and resid 4 through 107 removed outlier: 4.026A pdb=" N LYS 9 107 " --> pdb=" O SER 9 103 " (cutoff:3.500A) Processing helix chain '9' and resid 108 through 128 removed outlier: 3.874A pdb=" N VAL 9 114 " --> pdb=" O THR 9 110 " (cutoff:3.500A) Processing helix chain '9' and resid 137 through 139 No H-bonds generated for 'chain '9' and resid 137 through 139' Processing helix chain '9' and resid 140 through 160 Proline residue: 9 153 - end of helix Processing helix chain '9' and resid 196 through 207 Processing helix chain '9' and resid 207 through 216 Processing helix chain 'Q' and resid 3 through 20 removed outlier: 4.397A pdb=" N PHE Q 18 " --> pdb=" O HIS Q 14 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU Q 20 " --> pdb=" O MET Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 42 Processing helix chain 'Q' and resid 44 through 106 Processing helix chain 'Q' and resid 108 through 128 removed outlier: 3.670A pdb=" N GLN Q 113 " --> pdb=" O THR Q 109 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL Q 114 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU Q 128 " --> pdb=" O LEU Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 140 through 159 Proline residue: Q 153 - end of helix Processing helix chain 'Q' and resid 195 through 207 Processing helix chain 'Q' and resid 207 through 217 Processing helix chain 'R' and resid 4 through 103 removed outlier: 4.060A pdb=" N ILE R 8 " --> pdb=" O GLN R 4 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLU R 93 " --> pdb=" O GLN R 89 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ARG R 94 " --> pdb=" O ARG R 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 89 Processing helix chain 'T' and resid 92 through 105 Processing helix chain 'V' and resid 5 through 89 removed outlier: 3.860A pdb=" N GLN V 9 " --> pdb=" O THR V 5 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN V 89 " --> pdb=" O GLN V 85 " (cutoff:3.500A) Processing helix chain 'V' and resid 91 through 105 Processing helix chain '6' and resid 15 through 22 removed outlier: 4.050A pdb=" N TRP 6 19 " --> pdb=" O CYS 6 15 " (cutoff:3.500A) Processing helix chain '6' and resid 23 through 27 Processing helix chain '6' and resid 50 through 78 Processing helix chain '6' and resid 98 through 104 Processing helix chain '6' and resid 117 through 158 Processing helix chain '6' and resid 171 through 175 Processing helix chain '6' and resid 190 through 192 No H-bonds generated for 'chain '6' and resid 190 through 192' Processing helix chain '6' and resid 193 through 201 Processing helix chain '6' and resid 232 through 242 removed outlier: 4.170A pdb=" N ASP 6 236 " --> pdb=" O LYS 6 232 " (cutoff:3.500A) Processing helix chain '6' and resid 243 through 245 No H-bonds generated for 'chain '6' and resid 243 through 245' Processing helix chain '6' and resid 254 through 311 removed outlier: 3.794A pdb=" N MET 6 258 " --> pdb=" O ASN 6 254 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASP 6 261 " --> pdb=" O GLU 6 257 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS 6 262 " --> pdb=" O MET 6 258 " (cutoff:3.500A) Proline residue: 6 278 - end of helix removed outlier: 3.511A pdb=" N GLY 6 311 " --> pdb=" O VAL 6 307 " (cutoff:3.500A) Processing helix chain '6' and resid 327 through 344 removed outlier: 4.569A pdb=" N HIS 6 341 " --> pdb=" O GLU 6 337 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU 6 342 " --> pdb=" O LEU 6 338 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP 6 343 " --> pdb=" O TYR 6 339 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 28 Processing helix chain 'U' and resid 47 through 52 Processing helix chain 'U' and resid 58 through 68 removed outlier: 3.539A pdb=" N LYS U 62 " --> pdb=" O SER U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 84 Processing helix chain 'U' and resid 86 through 104 removed outlier: 4.745A pdb=" N TYR U 92 " --> pdb=" O GLN U 88 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL U 97 " --> pdb=" O ILE U 93 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N MET U 100 " --> pdb=" O MET U 96 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN U 104 " --> pdb=" O MET U 100 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 146 removed outlier: 3.580A pdb=" N MET U 140 " --> pdb=" O PHE U 136 " (cutoff:3.500A) Processing helix chain 'U' and resid 158 through 163 removed outlier: 3.858A pdb=" N TYR U 163 " --> pdb=" O SER U 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 172 removed outlier: 3.983A pdb=" N LEU U 172 " --> pdb=" O LYS U 169 " (cutoff:3.500A) Processing helix chain 'U' and resid 196 through 209 Processing helix chain 'U' and resid 211 through 221 removed outlier: 3.929A pdb=" N ALA U 217 " --> pdb=" O GLU U 213 " (cutoff:3.500A) Processing helix chain 'U' and resid 222 through 233 Processing helix chain 'U' and resid 236 through 252 Processing helix chain 'U' and resid 253 through 261 Processing helix chain 'U' and resid 264 through 276 removed outlier: 3.539A pdb=" N VAL U 268 " --> pdb=" O ASN U 264 " (cutoff:3.500A) Processing helix chain 'U' and resid 279 through 296 removed outlier: 4.114A pdb=" N SER U 296 " --> pdb=" O PHE U 292 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 302 Processing helix chain 'U' and resid 303 through 312 removed outlier: 4.746A pdb=" N MET U 309 " --> pdb=" O TYR U 305 " (cutoff:3.500A) Processing helix chain 'U' and resid 314 through 324 Processing helix chain 'U' and resid 328 through 350 Processing helix chain 'U' and resid 352 through 361 Processing helix chain 'U' and resid 367 through 371 Processing helix chain 'U' and resid 372 through 378 Processing helix chain 'U' and resid 380 through 384 Processing helix chain 'U' and resid 388 through 401 Processing helix chain 'U' and resid 403 through 421 removed outlier: 4.283A pdb=" N HIS U 420 " --> pdb=" O GLU U 416 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR U 421 " --> pdb=" O TYR U 417 " (cutoff:3.500A) Processing helix chain 'U' and resid 421 through 432 removed outlier: 3.619A pdb=" N GLY U 432 " --> pdb=" O ILE U 428 " (cutoff:3.500A) Processing helix chain 'U' and resid 432 through 441 Processing helix chain 'U' and resid 445 through 460 Processing helix chain 'a' and resid 19 through 33 removed outlier: 3.748A pdb=" N TYR a 23 " --> pdb=" O SER a 19 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N CYS a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER a 27 " --> pdb=" O TYR a 23 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 76 Processing helix chain 'a' and resid 93 through 132 Processing helix chain 'a' and resid 186 through 198 Processing helix chain 'a' and resid 233 through 248 Processing helix chain 'a' and resid 259 through 295 Processing helix chain 'a' and resid 296 through 316 Processing helix chain 'a' and resid 336 through 351 Processing helix chain 'a' and resid 378 through 387 Processing helix chain 'a' and resid 398 through 414 Proline residue: a 407 - end of helix Processing helix chain 'a' and resid 416 through 433 Processing helix chain 'a' and resid 433 through 440 Processing helix chain 'a' and resid 444 through 453 removed outlier: 3.809A pdb=" N GLY a 453 " --> pdb=" O MET a 449 " (cutoff:3.500A) Processing helix chain 'a' and resid 453 through 472 Processing helix chain 'a' and resid 527 through 533 Processing helix chain 'a' and resid 535 through 571 removed outlier: 4.054A pdb=" N MET a 545 " --> pdb=" O ASN a 541 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS a 546 " --> pdb=" O SER a 542 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER a 563 " --> pdb=" O GLY a 559 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU a 564 " --> pdb=" O VAL a 560 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE a 565 " --> pdb=" O SER a 561 " (cutoff:3.500A) Processing helix chain 'a' and resid 573 through 578 removed outlier: 3.574A pdb=" N PHE a 578 " --> pdb=" O LEU a 574 " (cutoff:3.500A) Processing helix chain 'a' and resid 579 through 604 removed outlier: 5.075A pdb=" N TYR a 593 " --> pdb=" O SER a 589 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU a 594 " --> pdb=" O LEU a 590 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR a 603 " --> pdb=" O PHE a 599 " (cutoff:3.500A) Processing helix chain 'a' and resid 606 through 610 removed outlier: 3.650A pdb=" N SER a 610 " --> pdb=" O ALA a 607 " (cutoff:3.500A) Processing helix chain 'a' and resid 617 through 624 removed outlier: 4.022A pdb=" N ILE a 621 " --> pdb=" O LEU a 617 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE a 624 " --> pdb=" O PHE a 620 " (cutoff:3.500A) Processing helix chain 'a' and resid 639 through 652 Processing helix chain 'a' and resid 653 through 655 No H-bonds generated for 'chain 'a' and resid 653 through 655' Processing helix chain 'a' and resid 661 through 673 Processing helix chain 'a' and resid 716 through 740 removed outlier: 3.871A pdb=" N ILE a 734 " --> pdb=" O CYS a 730 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR a 740 " --> pdb=" O ASN a 736 " (cutoff:3.500A) Processing helix chain 'a' and resid 740 through 765 removed outlier: 4.008A pdb=" N TRP a 744 " --> pdb=" O TYR a 740 " (cutoff:3.500A) Processing helix chain 'a' and resid 769 through 791 removed outlier: 3.839A pdb=" N LEU a 775 " --> pdb=" O LEU a 771 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY a 776 " --> pdb=" O ALA a 772 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE a 779 " --> pdb=" O LEU a 775 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA a 782 " --> pdb=" O PHE a 778 " (cutoff:3.500A) Processing helix chain 'a' and resid 794 through 816 removed outlier: 3.817A pdb=" N GLN a 813 " --> pdb=" O TRP a 809 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN a 814 " --> pdb=" O VAL a 810 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE a 816 " --> pdb=" O PHE a 812 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 23 Processing helix chain 'e' and resid 23 through 28 Processing helix chain 'e' and resid 33 through 59 removed outlier: 3.707A pdb=" N GLN e 59 " --> pdb=" O ALA e 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 80 Processing helix chain 'f' and resid 8 through 36 Processing helix chain 'f' and resid 40 through 44 removed outlier: 3.517A pdb=" N VAL f 44 " --> pdb=" O ILE f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 58 through 90 removed outlier: 3.982A pdb=" N TYR f 62 " --> pdb=" O ILE f 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 23 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 67 through 74 removed outlier: 3.514A pdb=" N VAL X 74 " --> pdb=" O ILE X 70 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 80 Processing helix chain 'X' and resid 103 through 109 Processing helix chain 'd' and resid 8 through 12 removed outlier: 3.640A pdb=" N VAL d 11 " --> pdb=" O TYR d 8 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP d 12 " --> pdb=" O PHE d 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 8 through 12' Processing helix chain 'd' and resid 13 through 26 Processing helix chain 'd' and resid 29 through 37 removed outlier: 3.748A pdb=" N ASN d 35 " --> pdb=" O ALA d 31 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 50 Processing helix chain 'd' and resid 67 through 88 Processing helix chain 'd' and resid 90 through 113 removed outlier: 4.148A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 119 Processing helix chain 'd' and resid 121 through 125 Processing helix chain 'd' and resid 130 through 134 removed outlier: 3.622A pdb=" N SER d 134 " --> pdb=" O PRO d 131 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 158 Processing helix chain 'd' and resid 160 through 165 Processing helix chain 'd' and resid 169 through 176 removed outlier: 3.940A pdb=" N GLU d 175 " --> pdb=" O GLN d 171 " (cutoff:3.500A) Processing helix chain 'd' and resid 177 through 200 removed outlier: 3.692A pdb=" N ASN d 183 " --> pdb=" O GLU d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 202 through 227 Proline residue: d 210 - end of helix removed outlier: 3.769A pdb=" N THR d 224 " --> pdb=" O ALA d 220 " (cutoff:3.500A) Processing helix chain 'd' and resid 233 through 241 removed outlier: 3.543A pdb=" N ARG d 237 " --> pdb=" O SER d 233 " (cutoff:3.500A) Processing helix chain 'd' and resid 251 through 258 Processing helix chain 'd' and resid 260 through 269 Processing helix chain 'd' and resid 271 through 280 Processing helix chain 'd' and resid 289 through 308 removed outlier: 3.884A pdb=" N ASN d 308 " --> pdb=" O LEU d 304 " (cutoff:3.500A) Processing helix chain 'd' and resid 311 through 315 removed outlier: 3.730A pdb=" N VAL d 314 " --> pdb=" O HIS d 311 " (cutoff:3.500A) Processing helix chain 'd' and resid 316 through 339 Processing helix chain 'd' and resid 340 through 344 Processing helix chain 'c' and resid 280 through 283 Processing helix chain 'c' and resid 416 through 441 removed outlier: 3.575A pdb=" N TRP c 420 " --> pdb=" O SER c 416 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY c 422 " --> pdb=" O GLY c 418 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N MET c 439 " --> pdb=" O TYR c 435 " (cutoff:3.500A) Processing helix chain 'p' and resid 302 through 330 Processing helix chain 'b' and resid 7 through 29 removed outlier: 3.870A pdb=" N ILE b 11 " --> pdb=" O LEU b 7 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE b 29 " --> pdb=" O CYS b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 35 Processing helix chain 'b' and resid 36 through 43 removed outlier: 3.818A pdb=" N GLU b 43 " --> pdb=" O TRP b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 83 removed outlier: 3.999A pdb=" N TRP b 49 " --> pdb=" O SER b 45 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY b 78 " --> pdb=" O SER b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 86 through 91 removed outlier: 3.814A pdb=" N ASN b 90 " --> pdb=" O ILE b 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 114 removed outlier: 3.884A pdb=" N ILE b 95 " --> pdb=" O LEU b 91 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 169 removed outlier: 3.500A pdb=" N GLY b 134 " --> pdb=" O ASN b 130 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN b 168 " --> pdb=" O LEU b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 176 removed outlier: 4.249A pdb=" N VAL b 174 " --> pdb=" O SER b 171 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE b 176 " --> pdb=" O PHE b 173 " (cutoff:3.500A) Processing helix chain 'b' and resid 177 through 200 removed outlier: 4.539A pdb=" N ARG b 200 " --> pdb=" O LEU b 196 " (cutoff:3.500A) Processing helix chain 'g' and resid 12 through 45 removed outlier: 3.540A pdb=" N ALA g 35 " --> pdb=" O ALA g 31 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER g 37 " --> pdb=" O GLY g 33 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY g 38 " --> pdb=" O THR g 34 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR g 39 " --> pdb=" O ALA g 35 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY g 40 " --> pdb=" O LYS g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 47 No H-bonds generated for 'chain 'g' and resid 46 through 47' Processing helix chain 'g' and resid 48 through 55 removed outlier: 5.540A pdb=" N MET g 53 " --> pdb=" O GLU g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 80 removed outlier: 3.817A pdb=" N VAL g 60 " --> pdb=" O ILE g 56 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET g 61 " --> pdb=" O ILE g 57 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE g 65 " --> pdb=" O MET g 61 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA g 66 " --> pdb=" O ALA g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 88 through 124 removed outlier: 3.619A pdb=" N ALA g 122 " --> pdb=" O VAL g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 127 through 138 removed outlier: 4.126A pdb=" N ILE g 134 " --> pdb=" O GLY g 130 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU g 135 " --> pdb=" O MET g 131 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE g 137 " --> pdb=" O LEU g 133 " (cutoff:3.500A) Processing helix chain 'g' and resid 139 through 155 removed outlier: 3.863A pdb=" N SER g 153 " --> pdb=" O ALA g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 12 through 48 removed outlier: 3.661A pdb=" N SER h 26 " --> pdb=" O ALA h 22 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA h 43 " --> pdb=" O THR h 39 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL h 46 " --> pdb=" O ALA h 42 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET h 47 " --> pdb=" O ALA h 43 " (cutoff:3.500A) Processing helix chain 'h' and resid 51 through 62 Proline residue: h 58 - end of helix Processing helix chain 'h' and resid 62 through 80 removed outlier: 4.359A pdb=" N ALA h 66 " --> pdb=" O ALA h 62 " (cutoff:3.500A) Processing helix chain 'h' and resid 88 through 124 removed outlier: 3.537A pdb=" N GLN h 92 " --> pdb=" O ARG h 88 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN h 123 " --> pdb=" O ARG h 119 " (cutoff:3.500A) Processing helix chain 'h' and resid 127 through 154 removed outlier: 3.793A pdb=" N GLY h 145 " --> pdb=" O LEU h 141 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU h 152 " --> pdb=" O VAL h 148 " (cutoff:3.500A) Processing helix chain 'i' and resid 10 through 45 removed outlier: 3.722A pdb=" N PHE i 14 " --> pdb=" O TYR i 10 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL i 16 " --> pdb=" O SER i 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 50 No H-bonds generated for 'chain 'i' and resid 48 through 50' Processing helix chain 'i' and resid 51 through 56 Processing helix chain 'i' and resid 56 through 63 removed outlier: 3.757A pdb=" N GLY i 63 " --> pdb=" O VAL i 59 " (cutoff:3.500A) Processing helix chain 'i' and resid 63 through 80 Processing helix chain 'i' and resid 88 through 121 Processing helix chain 'i' and resid 122 through 123 No H-bonds generated for 'chain 'i' and resid 122 through 123' Processing helix chain 'i' and resid 124 through 126 No H-bonds generated for 'chain 'i' and resid 124 through 126' Processing helix chain 'i' and resid 127 through 155 removed outlier: 3.980A pdb=" N GLY i 145 " --> pdb=" O LEU i 141 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS i 155 " --> pdb=" O ILE i 151 " (cutoff:3.500A) Processing helix chain 'j' and resid 11 through 48 removed outlier: 4.449A pdb=" N GLY j 15 " --> pdb=" O SER j 11 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA j 19 " --> pdb=" O GLY j 15 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER j 20 " --> pdb=" O VAL j 16 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS j 36 " --> pdb=" O TYR j 32 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR j 39 " --> pdb=" O ALA j 35 " (cutoff:3.500A) Processing helix chain 'j' and resid 52 through 55 removed outlier: 3.567A pdb=" N SER j 55 " --> pdb=" O ILE j 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 52 through 55' Processing helix chain 'j' and resid 56 through 79 removed outlier: 3.736A pdb=" N GLY j 63 " --> pdb=" O VAL j 59 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE j 64 " --> pdb=" O VAL j 60 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE j 65 " --> pdb=" O MET j 61 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA j 66 " --> pdb=" O ALA j 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 87 through 122 removed outlier: 3.573A pdb=" N ALA j 122 " --> pdb=" O VAL j 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 124 through 126 No H-bonds generated for 'chain 'j' and resid 124 through 126' Processing helix chain 'j' and resid 127 through 155 removed outlier: 3.788A pdb=" N LEU j 133 " --> pdb=" O VAL j 129 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU j 141 " --> pdb=" O PHE j 137 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY j 142 " --> pdb=" O ALA j 138 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU j 143 " --> pdb=" O GLU j 139 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR j 144 " --> pdb=" O VAL j 140 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY j 145 " --> pdb=" O LEU j 141 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR j 154 " --> pdb=" O LEU j 150 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 43 removed outlier: 3.829A pdb=" N SER k 26 " --> pdb=" O ALA k 22 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR k 39 " --> pdb=" O ALA k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 48 through 50 No H-bonds generated for 'chain 'k' and resid 48 through 50' Processing helix chain 'k' and resid 51 through 56 Processing helix chain 'k' and resid 56 through 79 removed outlier: 4.211A pdb=" N VAL k 60 " --> pdb=" O ILE k 56 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N MET k 61 " --> pdb=" O ILE k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 87 through 122 removed outlier: 3.896A pdb=" N LEU k 91 " --> pdb=" O TYR k 87 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL k 113 " --> pdb=" O ALA k 109 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA k 116 " --> pdb=" O ILE k 112 " (cutoff:3.500A) Processing helix chain 'k' and resid 124 through 126 No H-bonds generated for 'chain 'k' and resid 124 through 126' Processing helix chain 'k' and resid 127 through 140 Processing helix chain 'k' and resid 140 through 155 removed outlier: 3.617A pdb=" N GLY k 145 " --> pdb=" O LEU k 141 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU k 146 " --> pdb=" O GLY k 142 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL k 148 " --> pdb=" O TYR k 144 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR k 154 " --> pdb=" O LEU k 150 " (cutoff:3.500A) Processing helix chain 'l' and resid 12 through 44 removed outlier: 4.146A pdb=" N VAL l 16 " --> pdb=" O SER l 12 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET l 17 " --> pdb=" O PHE l 13 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR l 39 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing helix chain 'l' and resid 48 through 52 removed outlier: 3.963A pdb=" N ILE l 52 " --> pdb=" O PRO l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 79 removed outlier: 4.846A pdb=" N GLY l 63 " --> pdb=" O VAL l 59 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE l 65 " --> pdb=" O MET l 61 " (cutoff:3.500A) Processing helix chain 'l' and resid 88 through 120 Processing helix chain 'l' and resid 124 through 126 No H-bonds generated for 'chain 'l' and resid 124 through 126' Processing helix chain 'l' and resid 127 through 152 removed outlier: 3.859A pdb=" N ILE l 134 " --> pdb=" O GLY l 130 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE l 137 " --> pdb=" O LEU l 133 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY l 145 " --> pdb=" O LEU l 141 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU l 146 " --> pdb=" O GLY l 142 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU l 152 " --> pdb=" O VAL l 148 " (cutoff:3.500A) Processing helix chain 'm' and resid 12 through 48 removed outlier: 4.422A pdb=" N VAL m 46 " --> pdb=" O ALA m 42 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET m 47 " --> pdb=" O ALA m 43 " (cutoff:3.500A) Processing helix chain 'm' and resid 51 through 56 Processing helix chain 'm' and resid 57 through 79 removed outlier: 3.637A pdb=" N ILE m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE m 65 " --> pdb=" O MET m 61 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA m 66 " --> pdb=" O ALA m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 88 through 120 Processing helix chain 'm' and resid 127 through 155 removed outlier: 4.690A pdb=" N ILE m 134 " --> pdb=" O GLY m 130 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU m 135 " --> pdb=" O MET m 131 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS m 155 " --> pdb=" O ILE m 151 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 48 removed outlier: 3.637A pdb=" N PHE n 25 " --> pdb=" O SER n 21 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER n 26 " --> pdb=" O ALA n 22 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY n 38 " --> pdb=" O THR n 34 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR n 39 " --> pdb=" O ALA n 35 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY n 40 " --> pdb=" O LYS n 36 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 52 Processing helix chain 'n' and resid 56 through 79 removed outlier: 4.339A pdb=" N ALA n 62 " --> pdb=" O PRO n 58 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLY n 63 " --> pdb=" O VAL n 59 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE n 65 " --> pdb=" O MET n 61 " (cutoff:3.500A) Processing helix chain 'n' and resid 87 through 121 Processing helix chain 'n' and resid 122 through 123 No H-bonds generated for 'chain 'n' and resid 122 through 123' Processing helix chain 'n' and resid 124 through 125 No H-bonds generated for 'chain 'n' and resid 124 through 125' Processing helix chain 'n' and resid 126 through 154 removed outlier: 4.682A pdb=" N GLY n 130 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY n 145 " --> pdb=" O LEU n 141 " (cutoff:3.500A) Processing helix chain 'o' and resid 15 through 40 Processing helix chain 'o' and resid 40 through 48 removed outlier: 4.269A pdb=" N MET o 44 " --> pdb=" O GLY o 40 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL o 46 " --> pdb=" O ALA o 42 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET o 47 " --> pdb=" O ALA o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 53 through 55 No H-bonds generated for 'chain 'o' and resid 53 through 55' Processing helix chain 'o' and resid 56 through 80 Processing helix chain 'o' and resid 88 through 121 removed outlier: 3.680A pdb=" N ILE o 112 " --> pdb=" O PHE o 108 " (cutoff:3.500A) Processing helix chain 'o' and resid 122 through 123 No H-bonds generated for 'chain 'o' and resid 122 through 123' Processing helix chain 'o' and resid 124 through 126 No H-bonds generated for 'chain 'o' and resid 124 through 126' Processing helix chain 'o' and resid 127 through 155 removed outlier: 4.272A pdb=" N ILE o 132 " --> pdb=" O PHE o 128 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU o 133 " --> pdb=" O VAL o 129 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ILE o 134 " --> pdb=" O GLY o 130 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU o 135 " --> pdb=" O MET o 131 " (cutoff:3.500A) Processing helix chain '1' and resid 105 through 114 Processing helix chain '1' and resid 255 through 266 removed outlier: 4.011A pdb=" N ILE 1 259 " --> pdb=" O GLY 1 255 " (cutoff:3.500A) Processing helix chain '1' and resid 280 through 291 removed outlier: 3.598A pdb=" N MET 1 284 " --> pdb=" O ARG 1 280 " (cutoff:3.500A) Processing helix chain '1' and resid 321 through 339 removed outlier: 3.725A pdb=" N ALA 1 325 " --> pdb=" O ALA 1 321 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE 1 327 " --> pdb=" O ARG 1 323 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR 1 328 " --> pdb=" O GLU 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 350 through 365 removed outlier: 3.796A pdb=" N TRP 1 354 " --> pdb=" O SER 1 350 " (cutoff:3.500A) Processing helix chain '1' and resid 377 through 388 removed outlier: 3.883A pdb=" N ARG 1 388 " --> pdb=" O SER 1 384 " (cutoff:3.500A) Processing helix chain '1' and resid 419 through 427 removed outlier: 3.716A pdb=" N GLY 1 427 " --> pdb=" O SER 1 423 " (cutoff:3.500A) Processing helix chain '1' and resid 436 through 442 Processing helix chain '1' and resid 457 through 469 removed outlier: 4.443A pdb=" N GLU 1 463 " --> pdb=" O ARG 1 459 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR 1 464 " --> pdb=" O ALA 1 460 " (cutoff:3.500A) Processing helix chain '1' and resid 472 through 497 removed outlier: 4.227A pdb=" N GLU 1 491 " --> pdb=" O GLU 1 487 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE 1 492 " --> pdb=" O ASP 1 488 " (cutoff:3.500A) Processing helix chain '1' and resid 502 through 519 Processing helix chain '1' and resid 526 through 530 removed outlier: 3.848A pdb=" N ARG 1 530 " --> pdb=" O PRO 1 527 " (cutoff:3.500A) Processing helix chain '1' and resid 533 through 561 removed outlier: 3.645A pdb=" N THR 1 537 " --> pdb=" O PRO 1 533 " (cutoff:3.500A) Processing helix chain '1' and resid 566 through 584 removed outlier: 3.505A pdb=" N ILE 1 570 " --> pdb=" O THR 1 566 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU 1 576 " --> pdb=" O GLU 1 572 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE 1 577 " --> pdb=" O HIS 1 573 " (cutoff:3.500A) Processing helix chain '1' and resid 593 through 616 Processing helix chain '2' and resid 105 through 114 Processing helix chain '2' and resid 255 through 266 Processing helix chain '2' and resid 280 through 294 Proline residue: 2 292 - end of helix Processing helix chain '2' and resid 319 through 340 removed outlier: 4.295A pdb=" N ILE 2 327 " --> pdb=" O ARG 2 323 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR 2 328 " --> pdb=" O GLU 2 324 " (cutoff:3.500A) Processing helix chain '2' and resid 350 through 365 removed outlier: 3.631A pdb=" N TRP 2 354 " --> pdb=" O SER 2 350 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU 2 365 " --> pdb=" O ILE 2 361 " (cutoff:3.500A) Processing helix chain '2' and resid 377 through 387 Processing helix chain '2' and resid 419 through 427 Processing helix chain '2' and resid 436 through 443 Processing helix chain '2' and resid 457 through 469 removed outlier: 3.919A pdb=" N GLU 2 463 " --> pdb=" O ARG 2 459 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR 2 464 " --> pdb=" O ALA 2 460 " (cutoff:3.500A) Processing helix chain '2' and resid 471 through 494 removed outlier: 3.843A pdb=" N LEU 2 475 " --> pdb=" O GLU 2 471 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN 2 494 " --> pdb=" O ALA 2 490 " (cutoff:3.500A) Processing helix chain '2' and resid 502 through 520 Processing helix chain '2' and resid 533 through 562 Processing helix chain '2' and resid 566 through 574 Processing helix chain '2' and resid 574 through 584 Processing helix chain '2' and resid 585 through 587 No H-bonds generated for 'chain '2' and resid 585 through 587' Processing helix chain '2' and resid 593 through 616 removed outlier: 3.562A pdb=" N ILE 2 597 " --> pdb=" O GLY 2 593 " (cutoff:3.500A) Processing helix chain '0' and resid 105 through 114 Processing helix chain '0' and resid 256 through 266 removed outlier: 3.739A pdb=" N SER 0 260 " --> pdb=" O LYS 0 256 " (cutoff:3.500A) Processing helix chain '0' and resid 280 through 294 removed outlier: 4.211A pdb=" N MET 0 284 " --> pdb=" O ARG 0 280 " (cutoff:3.500A) Proline residue: 0 292 - end of helix Processing helix chain '0' and resid 304 through 308 Processing helix chain '0' and resid 319 through 340 removed outlier: 4.372A pdb=" N ILE 0 327 " --> pdb=" O ARG 0 323 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR 0 328 " --> pdb=" O GLU 0 324 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET 0 340 " --> pdb=" O TYR 0 336 " (cutoff:3.500A) Processing helix chain '0' and resid 350 through 364 removed outlier: 3.732A pdb=" N ARG 0 364 " --> pdb=" O GLU 0 360 " (cutoff:3.500A) Processing helix chain '0' and resid 377 through 388 removed outlier: 3.890A pdb=" N ARG 0 388 " --> pdb=" O SER 0 384 " (cutoff:3.500A) Processing helix chain '0' and resid 419 through 427 Processing helix chain '0' and resid 436 through 442 removed outlier: 3.548A pdb=" N ALA 0 440 " --> pdb=" O ASP 0 436 " (cutoff:3.500A) Processing helix chain '0' and resid 457 through 469 removed outlier: 4.695A pdb=" N GLU 0 463 " --> pdb=" O ARG 0 459 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR 0 464 " --> pdb=" O ALA 0 460 " (cutoff:3.500A) Processing helix chain '0' and resid 471 through 497 removed outlier: 4.594A pdb=" N GLU 0 491 " --> pdb=" O GLU 0 487 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE 0 492 " --> pdb=" O ASP 0 488 " (cutoff:3.500A) Processing helix chain '0' and resid 502 through 519 Processing helix chain '0' and resid 533 through 561 removed outlier: 3.545A pdb=" N SER 0 561 " --> pdb=" O THR 0 557 " (cutoff:3.500A) Processing helix chain '0' and resid 566 through 583 removed outlier: 5.933A pdb=" N GLU 0 576 " --> pdb=" O GLU 0 572 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE 0 577 " --> pdb=" O HIS 0 573 " (cutoff:3.500A) Processing helix chain '0' and resid 593 through 616 Processing helix chain '4' and resid 124 through 128 Processing helix chain '4' and resid 159 through 161 No H-bonds generated for 'chain '4' and resid 159 through 161' Processing helix chain '4' and resid 198 through 209 Processing helix chain '4' and resid 237 through 251 removed outlier: 3.741A pdb=" N ASN 4 251 " --> pdb=" O ASP 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 252 through 255 removed outlier: 4.082A pdb=" N ASP 4 255 " --> pdb=" O GLY 4 252 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 252 through 255' Processing helix chain '4' and resid 269 through 288 removed outlier: 4.109A pdb=" N ILE 4 273 " --> pdb=" O ILE 4 269 " (cutoff:3.500A) Proline residue: 4 275 - end of helix Processing helix chain '4' and resid 299 through 315 removed outlier: 3.657A pdb=" N TYR 4 303 " --> pdb=" O ASP 4 299 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA 4 313 " --> pdb=" O GLU 4 309 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG 4 314 " --> pdb=" O VAL 4 310 " (cutoff:3.500A) Processing helix chain '4' and resid 319 through 323 Processing helix chain '4' and resid 324 through 325 No H-bonds generated for 'chain '4' and resid 324 through 325' Processing helix chain '4' and resid 326 through 336 Processing helix chain '4' and resid 357 through 360 Processing helix chain '4' and resid 363 through 373 Processing helix chain '4' and resid 381 through 386 Processing helix chain '4' and resid 401 through 406 Processing helix chain '4' and resid 414 through 440 removed outlier: 4.305A pdb=" N VAL 4 438 " --> pdb=" O ALA 4 434 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY 4 440 " --> pdb=" O LYS 4 436 " (cutoff:3.500A) Processing helix chain '4' and resid 441 through 444 Processing helix chain '4' and resid 445 through 462 Processing helix chain '4' and resid 472 through 485 Processing helix chain '4' and resid 496 through 504 Processing helix chain '5' and resid 124 through 128 removed outlier: 3.509A pdb=" N LEU 5 128 " --> pdb=" O GLU 5 125 " (cutoff:3.500A) Processing helix chain '5' and resid 159 through 161 No H-bonds generated for 'chain '5' and resid 159 through 161' Processing helix chain '5' and resid 198 through 209 removed outlier: 3.503A pdb=" N GLN 5 209 " --> pdb=" O GLN 5 205 " (cutoff:3.500A) Processing helix chain '5' and resid 218 through 224 removed outlier: 3.784A pdb=" N GLU 5 224 " --> pdb=" O VAL 5 220 " (cutoff:3.500A) Processing helix chain '5' and resid 237 through 252 Processing helix chain '5' and resid 253 through 255 No H-bonds generated for 'chain '5' and resid 253 through 255' Processing helix chain '5' and resid 268 through 272 Processing helix chain '5' and resid 273 through 288 Processing helix chain '5' and resid 299 through 315 removed outlier: 3.620A pdb=" N TYR 5 303 " --> pdb=" O ASP 5 299 " (cutoff:3.500A) Processing helix chain '5' and resid 319 through 323 Processing helix chain '5' and resid 324 through 325 No H-bonds generated for 'chain '5' and resid 324 through 325' Processing helix chain '5' and resid 326 through 336 Processing helix chain '5' and resid 357 through 360 Processing helix chain '5' and resid 363 through 373 Processing helix chain '5' and resid 380 through 386 removed outlier: 3.555A pdb=" N HIS 5 384 " --> pdb=" O ASP 5 380 " (cutoff:3.500A) Processing helix chain '5' and resid 401 through 406 removed outlier: 3.690A pdb=" N ILE 5 406 " --> pdb=" O MET 5 402 " (cutoff:3.500A) Processing helix chain '5' and resid 415 through 439 Processing helix chain '5' and resid 445 through 462 removed outlier: 3.636A pdb=" N LEU 5 449 " --> pdb=" O THR 5 445 " (cutoff:3.500A) Processing helix chain '5' and resid 472 through 485 Processing helix chain '5' and resid 496 through 504 removed outlier: 3.732A pdb=" N LEU 5 500 " --> pdb=" O PRO 5 496 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU 5 502 " --> pdb=" O SER 5 498 " (cutoff:3.500A) Processing helix chain '3' and resid 124 through 128 removed outlier: 3.524A pdb=" N LEU 3 128 " --> pdb=" O GLU 3 125 " (cutoff:3.500A) Processing helix chain '3' and resid 159 through 163 Processing helix chain '3' and resid 174 through 181 removed outlier: 3.655A pdb=" N MET 3 180 " --> pdb=" O ALA 3 176 " (cutoff:3.500A) Processing helix chain '3' and resid 198 through 210 Processing helix chain '3' and resid 213 through 217 removed outlier: 3.534A pdb=" N SER 3 216 " --> pdb=" O VAL 3 213 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS 3 217 " --> pdb=" O LYS 3 214 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 213 through 217' Processing helix chain '3' and resid 237 through 251 Processing helix chain '3' and resid 253 through 255 No H-bonds generated for 'chain '3' and resid 253 through 255' Processing helix chain '3' and resid 267 through 272 removed outlier: 3.653A pdb=" N ARG 3 271 " --> pdb=" O PRO 3 267 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE 3 272 " --> pdb=" O THR 3 268 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 267 through 272' Processing helix chain '3' and resid 273 through 290 Processing helix chain '3' and resid 299 through 314 removed outlier: 3.544A pdb=" N TYR 3 303 " --> pdb=" O ASP 3 299 " (cutoff:3.500A) Processing helix chain '3' and resid 319 through 323 Processing helix chain '3' and resid 324 through 325 No H-bonds generated for 'chain '3' and resid 324 through 325' Processing helix chain '3' and resid 326 through 336 Processing helix chain '3' and resid 357 through 360 Processing helix chain '3' and resid 363 through 373 Processing helix chain '3' and resid 380 through 386 Processing helix chain '3' and resid 401 through 406 removed outlier: 3.550A pdb=" N ILE 3 406 " --> pdb=" O MET 3 402 " (cutoff:3.500A) Processing helix chain '3' and resid 415 through 440 removed outlier: 4.168A pdb=" N VAL 3 438 " --> pdb=" O ALA 3 434 " (cutoff:3.500A) Processing helix chain '3' and resid 445 through 461 Processing helix chain '3' and resid 472 through 485 Processing helix chain '3' and resid 496 through 504 removed outlier: 3.901A pdb=" N GLU 3 502 " --> pdb=" O SER 3 498 " (cutoff:3.500A) Processing helix chain '7' and resid 12 through 50 removed outlier: 4.597A pdb=" N LYS 7 50 " --> pdb=" O GLN 7 46 " (cutoff:3.500A) Processing helix chain '7' and resid 50 through 76 removed outlier: 4.021A pdb=" N PHE 7 74 " --> pdb=" O ALA 7 70 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR 7 75 " --> pdb=" O GLU 7 71 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA 7 76 " --> pdb=" O ALA 7 72 " (cutoff:3.500A) Processing helix chain '7' and resid 78 through 86 removed outlier: 4.322A pdb=" N THR 7 82 " --> pdb=" O ASP 7 78 " (cutoff:3.500A) Processing helix chain '7' and resid 127 through 175 removed outlier: 3.651A pdb=" N LEU 7 131 " --> pdb=" O GLY 7 127 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU 7 160 " --> pdb=" O VAL 7 156 " (cutoff:3.500A) Processing helix chain '7' and resid 175 through 211 removed outlier: 3.630A pdb=" N ARG 7 179 " --> pdb=" O VAL 7 175 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU 7 198 " --> pdb=" O ARG 7 194 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS 7 210 " --> pdb=" O GLN 7 206 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE 7 211 " --> pdb=" O GLU 7 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '8' and resid 164 through 167 removed outlier: 3.579A pdb=" N ILE 8 183 " --> pdb=" O VAL 8 192 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE 8 190 " --> pdb=" O ASN 8 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '9' and resid 164 through 167 removed outlier: 3.538A pdb=" N GLN 9 166 " --> pdb=" O MET 9 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 133 through 136 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 166 through 167 current: chain 'Q' and resid 190 through 193 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 190 through 193 current: chain '1' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 28 through 32 current: chain '1' and resid 50 through 58 removed outlier: 6.819A pdb=" N THR 1 63 " --> pdb=" O ILE 1 55 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU 1 57 " --> pdb=" O MET 1 61 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N MET 1 61 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 61 through 66 current: chain '2' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 28 through 32 current: chain '2' and resid 50 through 58 removed outlier: 6.792A pdb=" N THR 2 63 " --> pdb=" O ILE 2 55 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU 2 57 " --> pdb=" O MET 2 61 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N MET 2 61 " --> pdb=" O LEU 2 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '2' and resid 61 through 66 current: chain '0' and resid 50 through 58 removed outlier: 6.555A pdb=" N THR 0 63 " --> pdb=" O ILE 0 55 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU 0 57 " --> pdb=" O MET 0 61 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N MET 0 61 " --> pdb=" O LEU 0 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '0' and resid 61 through 66 current: chain '4' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 57 through 60 current: chain '4' and resid 81 through 90 removed outlier: 5.787A pdb=" N VAL 4 86 " --> pdb=" O GLN 4 97 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLN 4 97 " --> pdb=" O VAL 4 86 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU 4 88 " --> pdb=" O VAL 4 95 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '4' and resid 93 through 98 current: chain '5' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 57 through 60 current: chain '5' and resid 81 through 90 removed outlier: 7.057A pdb=" N VAL 5 95 " --> pdb=" O LEU 5 87 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL 5 89 " --> pdb=" O LYS 5 93 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LYS 5 93 " --> pdb=" O VAL 5 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '5' and resid 93 through 98 current: chain '3' and resid 57 through 61 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 57 through 61 current: chain '3' and resid 81 through 90 removed outlier: 5.706A pdb=" N VAL 3 86 " --> pdb=" O GLN 3 97 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN 3 97 " --> pdb=" O VAL 3 86 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU 3 88 " --> pdb=" O VAL 3 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '6' and resid 34 through 37 Processing sheet with id=AA5, first strand: chain '6' and resid 92 through 93 Processing sheet with id=AA6, first strand: chain '6' and resid 182 through 185 Processing sheet with id=AA7, first strand: chain '6' and resid 187 through 188 Processing sheet with id=AA8, first strand: chain 'a' and resid 325 through 333 removed outlier: 3.525A pdb=" N MET a 362 " --> pdb=" O LEU a 12 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 204 through 209 Processing sheet with id=AB1, first strand: chain 'a' and resid 508 through 509 Processing sheet with id=AB2, first strand: chain 'X' and resid 36 through 39 Processing sheet with id=AB3, first strand: chain 'c' and resid 277 through 278 removed outlier: 3.767A pdb=" N ASN c 267 " --> pdb=" O HIS c 391 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU c 390 " --> pdb=" O VAL c 368 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 316 through 320 removed outlier: 3.641A pdb=" N ILE c 320 " --> pdb=" O ARG c 338 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG c 338 " --> pdb=" O ILE c 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 323 through 326 Processing sheet with id=AB6, first strand: chain '1' and resid 87 through 90 Processing sheet with id=AB7, first strand: chain '1' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 98 through 99 current: chain '1' and resid 309 through 312 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 309 through 312 current: chain '1' and resid 401 through 409 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 401 through 409 current: chain '1' and resid 454 through 455 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain '1' and resid 133 through 135 Processing sheet with id=AB9, first strand: chain '1' and resid 146 through 147 removed outlier: 3.562A pdb=" N GLY 1 174 " --> pdb=" O ILE 1 147 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU 1 193 " --> pdb=" O THR 1 177 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '1' and resid 152 through 157 removed outlier: 6.468A pdb=" N ILE 1 166 " --> pdb=" O TYR 1 153 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE 1 155 " --> pdb=" O HIS 1 164 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N HIS 1 164 " --> pdb=" O ILE 1 155 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '1' and resid 226 through 227 removed outlier: 4.771A pdb=" N CYS 1 240 " --> pdb=" O LEU 1 227 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '1' and resid 295 through 297 Processing sheet with id=AC4, first strand: chain '2' and resid 87 through 90 Processing sheet with id=AC5, first strand: chain '2' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 98 through 99 current: chain '2' and resid 309 through 312 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 309 through 312 current: chain '2' and resid 401 through 409 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 401 through 409 current: chain '2' and resid 454 through 455 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain '2' and resid 164 through 167 removed outlier: 3.825A pdb=" N GLY 2 154 " --> pdb=" O ILE 2 166 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '2' and resid 146 through 147 removed outlier: 6.872A pdb=" N GLU 2 193 " --> pdb=" O THR 2 177 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU 2 192 " --> pdb=" O PHE 2 203 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '2' and resid 295 through 297 Processing sheet with id=AC9, first strand: chain '0' and resid 87 through 90 Processing sheet with id=AD1, first strand: chain '0' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 98 through 99 current: chain '0' and resid 310 through 312 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 310 through 312 current: chain '0' and resid 401 through 410 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 401 through 410 current: chain '0' and resid 454 through 455 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain '0' and resid 163 through 167 removed outlier: 3.612A pdb=" N GLY 0 154 " --> pdb=" O ILE 0 166 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN 0 157 " --> pdb=" O GLU 0 134 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLU 0 134 " --> pdb=" O ASN 0 157 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '0' and resid 146 through 147 removed outlier: 6.524A pdb=" N GLU 0 193 " --> pdb=" O THR 0 177 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ILE 0 179 " --> pdb=" O VAL 0 191 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N VAL 0 191 " --> pdb=" O ILE 0 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '0' and resid 296 through 297 removed outlier: 3.582A pdb=" N MET 0 296 " --> pdb=" O GLU 0 303 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '4' and resid 120 through 123 removed outlier: 3.514A pdb=" N ASP 4 149 " --> pdb=" O VAL 4 123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '4' and resid 131 through 132 Processing sheet with id=AD7, first strand: chain '4' and resid 163 through 164 removed outlier: 4.327A pdb=" N ARG 4 340 " --> pdb=" O ILE 4 164 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '4' and resid 170 through 171 Processing sheet with id=AD9, first strand: chain '4' and resid 191 through 193 removed outlier: 6.165A pdb=" N ILE 4 191 " --> pdb=" O LEU 4 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain '4' and resid 375 through 376 Processing sheet with id=AE2, first strand: chain '5' and resid 120 through 123 Processing sheet with id=AE3, first strand: chain '5' and resid 130 through 132 removed outlier: 6.807A pdb=" N ARG 5 130 " --> pdb=" O LEU 5 259 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA 5 228 " --> pdb=" O LEU 5 294 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ILE 5 296 " --> pdb=" O ALA 5 228 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL 5 230 " --> pdb=" O ILE 5 296 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N THR 5 298 " --> pdb=" O VAL 5 230 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA 5 232 " --> pdb=" O THR 5 298 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '5' and resid 163 through 164 removed outlier: 4.422A pdb=" N ARG 5 340 " --> pdb=" O ILE 5 164 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '5' and resid 170 through 171 Processing sheet with id=AE6, first strand: chain '5' and resid 191 through 193 Processing sheet with id=AE7, first strand: chain '5' and resid 375 through 376 Processing sheet with id=AE8, first strand: chain '3' and resid 120 through 123 Processing sheet with id=AE9, first strand: chain '3' and resid 131 through 132 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 131 through 132 current: chain '3' and resid 257 through 263 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 257 through 263 current: chain '3' and resid 347 through 355 No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain '7' and resid 92 through 94 Processing sheet with id=AF2, first strand: chain '7' and resid 97 through 99 3906 hydrogen bonds defined for protein. 11427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.72 Time building geometry restraints manager: 15.49 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: 20737 1.34 - 1.46: 11242 1.46 - 1.58: 34106 1.58 - 1.70: 3 1.70 - 1.82: 685 Bond restraints: 66773 Sorted by residual: bond pdb=" C ASN 4 265 " pdb=" N ASP 4 266 " ideal model delta sigma weight residual 1.331 1.242 0.089 2.83e-02 1.25e+03 9.91e+00 bond pdb=" CE1 TYR j 10 " pdb=" CZ TYR j 10 " ideal model delta sigma weight residual 1.378 1.307 0.071 2.40e-02 1.74e+03 8.83e+00 bond pdb=" N VAL 4 144 " pdb=" CA VAL 4 144 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.21e+00 bond pdb=" CG GLU 4 336 " pdb=" CD GLU 4 336 " ideal model delta sigma weight residual 1.516 1.451 0.065 2.50e-02 1.60e+03 6.76e+00 bond pdb=" C ARG a 489 " pdb=" N PRO a 490 " ideal model delta sigma weight residual 1.331 1.351 -0.020 7.90e-03 1.60e+04 6.23e+00 ... (remaining 66768 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 89416 3.27 - 6.55: 774 6.55 - 9.82: 46 9.82 - 13.09: 6 13.09 - 16.36: 2 Bond angle restraints: 90244 Sorted by residual: angle pdb=" N GLY o 40 " pdb=" CA GLY o 40 " pdb=" C GLY o 40 " ideal model delta sigma weight residual 114.67 107.22 7.45 1.10e+00 8.26e-01 4.58e+01 angle pdb=" N TYR 2 20 " pdb=" CA TYR 2 20 " pdb=" CB TYR 2 20 " ideal model delta sigma weight residual 111.69 100.04 11.65 1.74e+00 3.30e-01 4.48e+01 angle pdb=" N LEU 4 146 " pdb=" CA LEU 4 146 " pdb=" C LEU 4 146 " ideal model delta sigma weight residual 109.96 101.43 8.53 1.49e+00 4.50e-01 3.27e+01 angle pdb=" CB ARG T 32 " pdb=" CG ARG T 32 " pdb=" CD ARG T 32 " ideal model delta sigma weight residual 111.30 124.32 -13.02 2.30e+00 1.89e-01 3.21e+01 angle pdb=" N PRO 4 143 " pdb=" CA PRO 4 143 " pdb=" CB PRO 4 143 " ideal model delta sigma weight residual 103.25 97.36 5.89 1.05e+00 9.07e-01 3.15e+01 ... (remaining 90239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 37189 17.99 - 35.97: 2613 35.97 - 53.96: 424 53.96 - 71.94: 77 71.94 - 89.93: 46 Dihedral angle restraints: 40349 sinusoidal: 16177 harmonic: 24172 Sorted by residual: dihedral pdb=" CA VAL g 46 " pdb=" C VAL g 46 " pdb=" N MET g 47 " pdb=" CA MET g 47 " ideal model delta harmonic sigma weight residual 180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA GLY 0 23 " pdb=" C GLY 0 23 " pdb=" N VAL 0 24 " pdb=" CA VAL 0 24 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA TYR d 90 " pdb=" C TYR d 90 " pdb=" N GLU d 91 " pdb=" CA GLU d 91 " ideal model delta harmonic sigma weight residual 180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 40346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 7714 0.048 - 0.095: 1965 0.095 - 0.143: 499 0.143 - 0.190: 45 0.190 - 0.238: 7 Chirality restraints: 10230 Sorted by residual: chirality pdb=" CB THR b 143 " pdb=" CA THR b 143 " pdb=" OG1 THR b 143 " pdb=" CG2 THR b 143 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CG LEU l 70 " pdb=" CB LEU l 70 " pdb=" CD1 LEU l 70 " pdb=" CD2 LEU l 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CG LEU k 86 " pdb=" CB LEU k 86 " pdb=" CD1 LEU k 86 " pdb=" CD2 LEU k 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 10227 not shown) Planarity restraints: 11573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE b 150 " 0.047 2.00e-02 2.50e+03 4.39e-02 3.37e+01 pdb=" CG PHE b 150 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 PHE b 150 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE b 150 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE b 150 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE b 150 " 0.030 2.00e-02 2.50e+03 pdb=" CZ PHE b 150 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 4 141 " -0.515 9.50e-02 1.11e+02 2.31e-01 3.27e+01 pdb=" NE ARG 4 141 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG 4 141 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG 4 141 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG 4 141 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG k 48 " 0.451 9.50e-02 1.11e+02 2.03e-01 2.73e+01 pdb=" NE ARG k 48 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG k 48 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG k 48 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG k 48 " 0.007 2.00e-02 2.50e+03 ... (remaining 11570 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 15469 2.79 - 3.32: 69314 3.32 - 3.85: 107423 3.85 - 4.37: 125749 4.37 - 4.90: 206440 Nonbonded interactions: 524395 Sorted by model distance: nonbonded pdb=" O THR 7 122 " pdb=" NH1 ARG 7 126 " model vdw 2.264 3.120 nonbonded pdb=" O ASN 3 54 " pdb=" ND2 ASN 3 54 " model vdw 2.266 3.120 nonbonded pdb=" OG SER o 45 " pdb=" N VAL o 46 " model vdw 2.318 3.120 nonbonded pdb=" CG1 ILE 9 91 " pdb=" NH2 ARG 9 212 " model vdw 2.333 3.520 nonbonded pdb=" O ALA o 42 " pdb=" OG SER o 45 " model vdw 2.337 3.040 ... (remaining 524390 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 '0' selection = chain '1' selection = (chain '2' and resid 17 through 616) } ncs_group { reference = (chain '3' and (resid 39 through 216 or resid 224 through 506)) selection = chain '4' selection = (chain '5' and (resid 39 through 216 or resid 224 through 506)) } ncs_group { reference = chain '8' selection = chain '9' selection = chain 'Q' } ncs_group { reference = chain 'R' selection = chain 'T' selection = chain 'V' } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.520 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: 0.070 Extract box with map and model: 2.100 Check model and map are aligned: 0.380 Set scattering table: 0.490 Process input model: 109.540 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.370 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: 0.020 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5692 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 : 0.005 0.089 66773 Z= 0.352 Angle : 0.814 16.365 90244 Z= 0.455 Chirality : 0.045 0.238 10230 Planarity : 0.008 0.231 11573 Dihedral : 12.950 89.931 24839 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.88 % Favored : 94.03 % Rotamer: Outliers : 0.09 % Allowed : 0.34 % Favored : 99.57 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.09), residues: 8314 helix: 0.54 (0.07), residues: 4655 sheet: -2.11 (0.18), residues: 666 loop : -1.68 (0.11), residues: 2993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 0 567 HIS 0.014 0.002 HIS 4 363 PHE 0.098 0.003 PHE b 150 TYR 0.077 0.003 TYR j 10 ARG 0.026 0.001 ARG k 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1920 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1914 time to evaluate : 5.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 78 GLN cc_start: 0.8899 (mt0) cc_final: 0.8334 (mp10) REVERT: 8 120 VAL cc_start: 0.9459 (t) cc_final: 0.9214 (p) REVERT: 8 122 GLN cc_start: 0.7978 (tt0) cc_final: 0.7482 (tp-100) REVERT: 8 127 LEU cc_start: 0.8353 (tp) cc_final: 0.6944 (tp) REVERT: 8 132 MET cc_start: 0.8677 (mtp) cc_final: 0.8361 (mtt) REVERT: 8 173 LEU cc_start: 0.7552 (mt) cc_final: 0.6622 (mp) REVERT: 8 194 ASN cc_start: 0.8332 (t0) cc_final: 0.7516 (t0) REVERT: 8 203 ILE cc_start: 0.9159 (mm) cc_final: 0.8933 (tp) REVERT: 9 16 MET cc_start: 0.8164 (ttp) cc_final: 0.7887 (mtt) REVERT: 9 132 MET cc_start: 0.7966 (mtt) cc_final: 0.7675 (mtt) REVERT: 9 182 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7344 (mt-10) REVERT: 9 197 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7558 (tt0) REVERT: 9 210 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8611 (mt-10) REVERT: Q 51 LEU cc_start: 0.6525 (mt) cc_final: 0.6299 (tp) REVERT: Q 58 GLU cc_start: 0.7654 (tt0) cc_final: 0.7430 (mm-30) REVERT: Q 127 LEU cc_start: 0.9224 (tp) cc_final: 0.8571 (tp) REVERT: Q 184 TYR cc_start: 0.8795 (m-80) cc_final: 0.8567 (m-80) REVERT: R 27 LYS cc_start: 0.6496 (pttp) cc_final: 0.5904 (mptt) REVERT: R 47 TYR cc_start: 0.7132 (m-10) cc_final: 0.6660 (m-80) REVERT: R 51 ARG cc_start: 0.3060 (mmt-90) cc_final: 0.1250 (mpt-90) REVERT: V 28 ARG cc_start: 0.6183 (mtt180) cc_final: 0.5665 (mmp-170) REVERT: V 52 GLU cc_start: 0.4757 (mm-30) cc_final: 0.4162 (pt0) REVERT: 6 19 TRP cc_start: 0.3313 (m-10) cc_final: 0.2981 (m-10) REVERT: 6 42 ASP cc_start: 0.3674 (t0) cc_final: 0.3433 (t0) REVERT: 6 157 ASN cc_start: 0.4387 (m-40) cc_final: 0.3957 (m110) REVERT: 6 332 ARG cc_start: 0.6001 (ttp80) cc_final: 0.5320 (mmm160) REVERT: 6 373 LYS cc_start: 0.6654 (tttp) cc_final: 0.6352 (tttm) REVERT: U 222 ASP cc_start: 0.6737 (m-30) cc_final: 0.6529 (m-30) REVERT: U 393 ILE cc_start: 0.5672 (mt) cc_final: 0.5427 (mt) REVERT: U 458 LYS cc_start: 0.6923 (tppt) cc_final: 0.5871 (mmmt) REVERT: a 74 LYS cc_start: 0.6828 (mttt) cc_final: 0.6148 (tptt) REVERT: a 94 MET cc_start: 0.6149 (tpp) cc_final: 0.5914 (ttp) REVERT: a 111 ILE cc_start: 0.5732 (mt) cc_final: 0.5508 (mt) REVERT: a 112 ASN cc_start: 0.4085 (m-40) cc_final: 0.3758 (m-40) REVERT: a 124 GLU cc_start: 0.6726 (mm-30) cc_final: 0.6403 (tp30) REVERT: a 297 ILE cc_start: 0.6413 (tp) cc_final: 0.5583 (mt) REVERT: a 491 MET cc_start: 0.4309 (ptp) cc_final: 0.4031 (ptm) REVERT: a 570 PHE cc_start: 0.7957 (t80) cc_final: 0.7680 (t80) REVERT: a 571 LYS cc_start: 0.8686 (tmtt) cc_final: 0.8284 (tptp) REVERT: a 572 LYS cc_start: 0.6809 (mmpt) cc_final: 0.6604 (mmmt) REVERT: a 637 TYR cc_start: 0.4785 (p90) cc_final: 0.3051 (t80) REVERT: a 756 VAL cc_start: 0.6911 (t) cc_final: 0.6376 (t) REVERT: X 45 ILE cc_start: 0.4108 (mm) cc_final: 0.3573 (tt) REVERT: X 73 MET cc_start: 0.2243 (mtp) cc_final: 0.1774 (tmm) REVERT: d 77 LYS cc_start: 0.5070 (ttpt) cc_final: 0.4780 (pptt) REVERT: d 83 ARG cc_start: 0.4108 (mtp85) cc_final: 0.3312 (tpt-90) REVERT: d 120 ARG cc_start: 0.4068 (mmm-85) cc_final: 0.3575 (mtp-110) REVERT: d 262 GLU cc_start: 0.7281 (pp20) cc_final: 0.6352 (pp20) REVERT: d 326 CYS cc_start: 0.6007 (m) cc_final: 0.5670 (m) REVERT: d 328 ASN cc_start: 0.6027 (m110) cc_final: 0.5486 (m110) REVERT: d 339 ARG cc_start: 0.5256 (mtp85) cc_final: 0.4159 (mmp-170) REVERT: b 19 MET cc_start: 0.5772 (mtm) cc_final: 0.5521 (ttt) REVERT: b 91 LEU cc_start: 0.5897 (mt) cc_final: 0.4135 (pp) REVERT: b 203 MET cc_start: 0.3130 (tmm) cc_final: 0.2336 (ttt) REVERT: g 90 PHE cc_start: 0.5440 (m-80) cc_final: 0.5226 (m-80) REVERT: h 41 ILE cc_start: 0.6671 (mt) cc_final: 0.6384 (mt) REVERT: h 90 PHE cc_start: 0.5481 (t80) cc_final: 0.5135 (t80) REVERT: h 118 VAL cc_start: 0.8050 (t) cc_final: 0.7843 (p) REVERT: h 121 THR cc_start: 0.7720 (t) cc_final: 0.7443 (t) REVERT: k 68 TYR cc_start: 0.5943 (m-10) cc_final: 0.5157 (m-10) REVERT: k 135 LEU cc_start: 0.4796 (mt) cc_final: 0.4553 (mt) REVERT: k 139 GLU cc_start: 0.4786 (tp30) cc_final: 0.4414 (pt0) REVERT: l 72 VAL cc_start: 0.7012 (t) cc_final: 0.6742 (p) REVERT: l 80 LEU cc_start: 0.6086 (mt) cc_final: 0.5848 (mt) REVERT: l 146 LEU cc_start: 0.7390 (tp) cc_final: 0.7097 (tp) REVERT: l 150 LEU cc_start: 0.8849 (mt) cc_final: 0.8567 (mt) REVERT: m 44 MET cc_start: 0.6375 (tpp) cc_final: 0.4840 (ppp) REVERT: m 53 MET cc_start: 0.3270 (mmp) cc_final: 0.2817 (mmp) REVERT: m 68 TYR cc_start: 0.7259 (m-10) cc_final: 0.6723 (m-10) REVERT: m 131 MET cc_start: 0.4330 (mpp) cc_final: 0.3733 (mpp) REVERT: n 47 MET cc_start: 0.6645 (mtm) cc_final: 0.6220 (tmm) REVERT: n 70 LEU cc_start: 0.6679 (tp) cc_final: 0.6147 (tp) REVERT: n 121 THR cc_start: 0.6057 (p) cc_final: 0.5795 (p) REVERT: o 41 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.7086 (mp) REVERT: o 61 MET cc_start: 0.6784 (mtt) cc_final: 0.6552 (mtt) REVERT: o 133 LEU cc_start: 0.6485 (pp) cc_final: 0.6266 (pp) REVERT: o 136 ILE cc_start: 0.7696 (mt) cc_final: 0.7385 (mt) REVERT: 1 232 ARG cc_start: 0.7012 (mtm-85) cc_final: 0.6492 (ttp-110) REVERT: 1 240 CYS cc_start: 0.8603 (m) cc_final: 0.8375 (m) REVERT: 1 296 MET cc_start: 0.6593 (ttp) cc_final: 0.6061 (tmm) REVERT: 1 401 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7590 (tm-30) REVERT: 1 484 GLN cc_start: 0.8453 (tp40) cc_final: 0.8071 (tp40) REVERT: 1 519 PHE cc_start: 0.8190 (t80) cc_final: 0.7842 (t80) REVERT: 1 584 MET cc_start: 0.8665 (mtp) cc_final: 0.8233 (mtp) REVERT: 2 39 MET cc_start: 0.8728 (mmm) cc_final: 0.7993 (mmm) REVERT: 2 41 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7800 (mp0) REVERT: 2 127 LEU cc_start: 0.8573 (mt) cc_final: 0.8369 (mt) REVERT: 2 165 LYS cc_start: 0.7678 (mttp) cc_final: 0.7005 (mmtp) REVERT: 2 264 SER cc_start: 0.7365 (m) cc_final: 0.6987 (p) REVERT: 2 272 ILE cc_start: 0.8813 (mt) cc_final: 0.8500 (mm) REVERT: 2 284 MET cc_start: 0.7615 (ppp) cc_final: 0.7221 (ppp) REVERT: 2 323 ARG cc_start: 0.7960 (mtm180) cc_final: 0.7638 (ttm110) REVERT: 2 360 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8236 (tp30) REVERT: 2 368 MET cc_start: 0.8338 (tpp) cc_final: 0.7726 (ttt) REVERT: 2 462 ASP cc_start: 0.8722 (m-30) cc_final: 0.8469 (m-30) REVERT: 2 520 LEU cc_start: 0.8120 (mt) cc_final: 0.7341 (mt) REVERT: 2 540 MET cc_start: 0.1816 (mtm) cc_final: 0.1531 (mtm) REVERT: 2 550 MET cc_start: 0.3679 (mtt) cc_final: 0.3449 (mmt) REVERT: 2 613 ARG cc_start: 0.7583 (mtp180) cc_final: 0.6459 (mtp85) REVERT: 0 58 GLU cc_start: 0.7933 (tt0) cc_final: 0.7605 (tt0) REVERT: 0 104 ARG cc_start: 0.8366 (mmp-170) cc_final: 0.7632 (mtm-85) REVERT: 0 171 ARG cc_start: 0.8203 (mtt180) cc_final: 0.7957 (ptt-90) REVERT: 0 295 THR cc_start: 0.5636 (p) cc_final: 0.5125 (p) REVERT: 0 296 MET cc_start: 0.6297 (mpp) cc_final: 0.6082 (mpp) REVERT: 0 346 MET cc_start: 0.9008 (ttt) cc_final: 0.8544 (ttt) REVERT: 0 406 ILE cc_start: 0.8769 (mt) cc_final: 0.8365 (mt) REVERT: 0 463 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8150 (tp30) REVERT: 4 54 ASN cc_start: 0.8726 (t0) cc_final: 0.8408 (m110) REVERT: 4 87 LEU cc_start: 0.9121 (mt) cc_final: 0.8812 (mt) REVERT: 4 92 SER cc_start: 0.9173 (p) cc_final: 0.8372 (t) REVERT: 4 100 GLU cc_start: 0.8237 (mp0) cc_final: 0.7880 (mp0) REVERT: 4 156 GLN cc_start: 0.8000 (pt0) cc_final: 0.7715 (pp30) REVERT: 4 187 GLN cc_start: 0.8677 (tt0) cc_final: 0.7143 (tp40) REVERT: 4 189 ILE cc_start: 0.9264 (tt) cc_final: 0.9050 (tt) REVERT: 4 193 SER cc_start: 0.7635 (t) cc_final: 0.7319 (p) REVERT: 4 214 LYS cc_start: 0.6659 (mmmt) cc_final: 0.6408 (tppt) REVERT: 4 238 MET cc_start: 0.7670 (tpp) cc_final: 0.7412 (tpp) REVERT: 4 239 GLU cc_start: 0.6597 (tp30) cc_final: 0.6345 (tp30) REVERT: 4 289 CYS cc_start: 0.8879 (m) cc_final: 0.8248 (t) REVERT: 4 363 HIS cc_start: 0.8490 (t-90) cc_final: 0.8107 (t-90) REVERT: 4 380 ASP cc_start: 0.8691 (t0) cc_final: 0.8438 (t0) REVERT: 4 392 ILE cc_start: 0.8839 (mt) cc_final: 0.8566 (mp) REVERT: 4 414 ASP cc_start: 0.7325 (p0) cc_final: 0.6885 (p0) REVERT: 4 450 LEU cc_start: 0.6543 (mm) cc_final: 0.6255 (tp) REVERT: 5 156 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8553 (mp10) REVERT: 5 237 ASN cc_start: 0.8800 (p0) cc_final: 0.8569 (p0) REVERT: 5 250 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8785 (tm-30) REVERT: 5 290 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8044 (mm-30) REVERT: 5 328 TYR cc_start: 0.8530 (t80) cc_final: 0.8180 (t80) REVERT: 5 335 TYR cc_start: 0.9081 (m-10) cc_final: 0.8871 (m-80) REVERT: 5 401 LEU cc_start: 0.8575 (tp) cc_final: 0.8315 (tp) REVERT: 5 417 ASP cc_start: 0.8233 (m-30) cc_final: 0.7993 (m-30) REVERT: 3 61 ASP cc_start: 0.8776 (p0) cc_final: 0.8337 (p0) REVERT: 3 187 GLN cc_start: 0.8433 (tt0) cc_final: 0.7948 (tt0) REVERT: 3 315 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7300 (tm-30) REVERT: 3 354 LEU cc_start: 0.9425 (pt) cc_final: 0.9189 (pt) REVERT: 3 401 LEU cc_start: 0.8004 (mt) cc_final: 0.7137 (mt) REVERT: 3 482 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7701 (tt0) REVERT: 7 33 LEU cc_start: 0.8723 (mt) cc_final: 0.8098 (tp) REVERT: 7 119 TYR cc_start: 0.6254 (m-80) cc_final: 0.5975 (m-80) REVERT: 7 196 ARG cc_start: 0.7739 (ttm170) cc_final: 0.7045 (ttp-170) outliers start: 6 outliers final: 0 residues processed: 1918 average time/residue: 0.6656 time to fit residues: 2165.7980 Evaluate side-chains 1551 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1550 time to evaluate : 5.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 700 optimal weight: 0.9990 chunk 629 optimal weight: 0.9980 chunk 349 optimal weight: 30.0000 chunk 214 optimal weight: 20.0000 chunk 424 optimal weight: 2.9990 chunk 336 optimal weight: 6.9990 chunk 650 optimal weight: 3.9990 chunk 251 optimal weight: 9.9990 chunk 395 optimal weight: 6.9990 chunk 484 optimal weight: 4.9990 chunk 753 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 77 ASN ** 9 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 221 ASN ** Q 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 126 GLN V 13 GLN 6 336 HIS 6 341 HIS U 63 GLN U 91 GLN U 171 GLN U 387 ASN a 419 HIS ** a 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 535 ASN d 13 ASN ** d 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 349 HIS c 364 HIS ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 92 GLN k 123 GLN 1 207 GLN 1 543 ASN ** 0 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 314 ASN 4 288 GLN 4 358 ASN 4 465 GLN 5 73 HIS 5 181 ASN 5 205 GLN 5 251 ASN ** 5 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 97 GLN 3 161 GLN 3 376 GLN ** 7 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 206 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.200887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.168098 restraints weight = 141309.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.164965 restraints weight = 125678.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.166266 restraints weight = 97243.901| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 66773 Z= 0.265 Angle : 0.649 12.842 90244 Z= 0.343 Chirality : 0.043 0.206 10230 Planarity : 0.005 0.059 11573 Dihedral : 4.974 83.036 9103 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.59 % Favored : 95.36 % Rotamer: Outliers : 0.30 % Allowed : 3.79 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.09), residues: 8314 helix: 1.01 (0.07), residues: 4680 sheet: -1.49 (0.19), residues: 671 loop : -1.52 (0.11), residues: 2963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP 2 450 HIS 0.011 0.001 HIS a 803 PHE 0.055 0.002 PHE e 16 TYR 0.050 0.002 TYR h 144 ARG 0.011 0.001 ARG h 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1842 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 1821 time to evaluate : 5.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 119 LEU cc_start: 0.9171 (tp) cc_final: 0.8519 (mt) REVERT: 8 120 VAL cc_start: 0.9431 (t) cc_final: 0.9215 (p) REVERT: 8 122 GLN cc_start: 0.8054 (tt0) cc_final: 0.7615 (tp-100) REVERT: 8 181 VAL cc_start: 0.9152 (p) cc_final: 0.8849 (t) REVERT: 9 81 LEU cc_start: 0.8647 (tp) cc_final: 0.8381 (mm) REVERT: 9 120 VAL cc_start: 0.9441 (p) cc_final: 0.9221 (t) REVERT: 9 124 LEU cc_start: 0.8903 (mt) cc_final: 0.8700 (mt) REVERT: 9 132 MET cc_start: 0.7602 (mtt) cc_final: 0.7074 (mtt) REVERT: 9 194 ASN cc_start: 0.8226 (t0) cc_final: 0.7151 (t0) REVERT: 9 197 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6880 (tt0) REVERT: Q 127 LEU cc_start: 0.9040 (tp) cc_final: 0.8351 (tp) REVERT: Q 155 TYR cc_start: 0.7602 (t80) cc_final: 0.7360 (t80) REVERT: Q 201 ASP cc_start: 0.8742 (m-30) cc_final: 0.8417 (m-30) REVERT: Q 206 GLN cc_start: 0.8299 (tt0) cc_final: 0.8037 (mt0) REVERT: R 27 LYS cc_start: 0.6141 (pttp) cc_final: 0.5305 (ptpt) REVERT: R 47 TYR cc_start: 0.7025 (m-10) cc_final: 0.6473 (m-80) REVERT: T 42 MET cc_start: 0.6862 (ptp) cc_final: 0.6416 (ptt) REVERT: V 28 ARG cc_start: 0.6119 (mtt180) cc_final: 0.5654 (mmp-170) REVERT: 6 16 GLN cc_start: 0.5308 (mt0) cc_final: 0.4964 (tt0) REVERT: 6 42 ASP cc_start: 0.4943 (t0) cc_final: 0.4645 (t0) REVERT: 6 157 ASN cc_start: 0.4134 (m-40) cc_final: 0.3860 (m-40) REVERT: 6 207 MET cc_start: 0.0114 (mmp) cc_final: -0.0106 (mmp) REVERT: 6 275 GLN cc_start: 0.4948 (tp-100) cc_final: 0.3499 (pp30) REVERT: U 50 ILE cc_start: 0.3914 (mm) cc_final: 0.3670 (mm) REVERT: U 65 MET cc_start: 0.4141 (tpt) cc_final: 0.3931 (tpt) REVERT: U 81 MET cc_start: 0.0488 (ptt) cc_final: 0.0186 (ptt) REVERT: U 263 TYR cc_start: 0.4791 (m-80) cc_final: 0.4414 (m-10) REVERT: a 56 ARG cc_start: 0.7806 (tmm-80) cc_final: 0.7308 (mtt180) REVERT: a 66 ARG cc_start: 0.7343 (mtt90) cc_final: 0.6709 (mtm110) REVERT: a 74 LYS cc_start: 0.6808 (mttt) cc_final: 0.6261 (tptt) REVERT: a 94 MET cc_start: 0.7211 (tpp) cc_final: 0.6430 (ttp) REVERT: a 111 ILE cc_start: 0.6161 (mt) cc_final: 0.5900 (mt) REVERT: a 114 ASN cc_start: 0.7208 (t0) cc_final: 0.6888 (t0) REVERT: a 281 GLN cc_start: 0.6949 (tm-30) cc_final: 0.6277 (pt0) REVERT: a 297 ILE cc_start: 0.7131 (tp) cc_final: 0.6613 (tp) REVERT: a 570 PHE cc_start: 0.8464 (t80) cc_final: 0.8147 (t80) REVERT: a 571 LYS cc_start: 0.8740 (tmtt) cc_final: 0.8260 (tptp) REVERT: a 572 LYS cc_start: 0.7095 (mmpt) cc_final: 0.6589 (mmmt) REVERT: a 597 LEU cc_start: 0.7961 (mt) cc_final: 0.7689 (mt) REVERT: a 624 PHE cc_start: 0.7103 (m-80) cc_final: 0.6700 (m-80) REVERT: a 628 TYR cc_start: 0.3719 (m-80) cc_final: 0.3077 (m-80) REVERT: a 637 TYR cc_start: 0.5039 (p90) cc_final: 0.3758 (t80) REVERT: a 757 LEU cc_start: 0.7952 (tp) cc_final: 0.7557 (tp) REVERT: a 802 LEU cc_start: 0.8967 (mt) cc_final: 0.8747 (mt) REVERT: a 807 LEU cc_start: 0.8418 (tp) cc_final: 0.8138 (tp) REVERT: a 809 TRP cc_start: 0.7286 (t60) cc_final: 0.6939 (t60) REVERT: e 48 CYS cc_start: 0.5739 (t) cc_final: 0.5475 (t) REVERT: X 73 MET cc_start: 0.2865 (mtp) cc_final: 0.2124 (mmm) REVERT: d 83 ARG cc_start: 0.3525 (mtp85) cc_final: 0.2741 (tpt-90) REVERT: d 105 MET cc_start: 0.7249 (ttm) cc_final: 0.6871 (ttt) REVERT: d 120 ARG cc_start: 0.4585 (mmm-85) cc_final: 0.4073 (mtp-110) REVERT: d 152 ASN cc_start: 0.5318 (m110) cc_final: 0.5115 (m110) REVERT: d 160 LEU cc_start: 0.6886 (mt) cc_final: 0.6514 (mt) REVERT: d 262 GLU cc_start: 0.7512 (pp20) cc_final: 0.6790 (pp20) REVERT: p 309 LEU cc_start: 0.7346 (tp) cc_final: 0.7145 (tp) REVERT: b 19 MET cc_start: 0.5878 (mtm) cc_final: 0.5551 (ttt) REVERT: b 116 GLU cc_start: 0.3717 (mp0) cc_final: 0.3416 (mp0) REVERT: b 203 MET cc_start: 0.2737 (tmm) cc_final: 0.2242 (ttt) REVERT: g 44 MET cc_start: 0.5877 (mtt) cc_final: 0.5361 (mtm) REVERT: g 61 MET cc_start: 0.3705 (mtp) cc_final: 0.3419 (mtm) REVERT: g 90 PHE cc_start: 0.5554 (m-80) cc_final: 0.5211 (m-80) REVERT: h 90 PHE cc_start: 0.7048 (t80) cc_final: 0.6831 (t80) REVERT: h 132 ILE cc_start: 0.5321 (mm) cc_final: 0.5094 (mm) REVERT: i 23 MET cc_start: 0.5722 (mmm) cc_final: 0.5404 (mmm) REVERT: k 23 MET cc_start: 0.6973 (mtp) cc_final: 0.6748 (ttp) REVERT: k 24 VAL cc_start: 0.6015 (t) cc_final: 0.5757 (t) REVERT: k 44 MET cc_start: 0.4164 (ttt) cc_final: 0.3930 (ttt) REVERT: k 53 MET cc_start: 0.5523 (mpp) cc_final: 0.5042 (mpp) REVERT: l 72 VAL cc_start: 0.6877 (t) cc_final: 0.6588 (p) REVERT: l 80 LEU cc_start: 0.6337 (mt) cc_final: 0.6090 (mt) REVERT: l 146 LEU cc_start: 0.7492 (tp) cc_final: 0.7253 (tp) REVERT: l 150 LEU cc_start: 0.9008 (mt) cc_final: 0.8749 (mt) REVERT: n 47 MET cc_start: 0.7125 (mtm) cc_final: 0.6658 (tmm) REVERT: n 70 LEU cc_start: 0.7168 (tp) cc_final: 0.6592 (tp) REVERT: n 132 ILE cc_start: 0.5842 (mt) cc_final: 0.5589 (mt) REVERT: o 46 VAL cc_start: 0.6631 (t) cc_final: 0.6410 (t) REVERT: o 61 MET cc_start: 0.7230 (mtt) cc_final: 0.6626 (mtt) REVERT: o 136 ILE cc_start: 0.7859 (mt) cc_final: 0.7614 (mt) REVERT: 1 215 ARG cc_start: 0.7400 (mtp85) cc_final: 0.6779 (mtp85) REVERT: 1 232 ARG cc_start: 0.6739 (mtm-85) cc_final: 0.6313 (ttp-110) REVERT: 1 283 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7827 (mt-10) REVERT: 1 401 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7918 (tm-30) REVERT: 1 484 GLN cc_start: 0.8295 (tp40) cc_final: 0.7782 (tp-100) REVERT: 2 229 THR cc_start: 0.4493 (t) cc_final: 0.4283 (t) REVERT: 2 264 SER cc_start: 0.7409 (m) cc_final: 0.6993 (p) REVERT: 2 272 ILE cc_start: 0.8760 (mt) cc_final: 0.8489 (mm) REVERT: 2 459 ARG cc_start: 0.7686 (ttp-110) cc_final: 0.7333 (mtm-85) REVERT: 2 462 ASP cc_start: 0.8250 (m-30) cc_final: 0.7974 (m-30) REVERT: 2 540 MET cc_start: 0.3606 (mtm) cc_final: 0.2623 (mtm) REVERT: 2 550 MET cc_start: 0.4212 (mtt) cc_final: 0.3469 (mmt) REVERT: 2 613 ARG cc_start: 0.7687 (mtp180) cc_final: 0.6484 (mtp85) REVERT: 0 104 ARG cc_start: 0.8061 (mmp-170) cc_final: 0.7673 (mtm-85) REVERT: 0 113 THR cc_start: 0.8909 (t) cc_final: 0.8434 (t) REVERT: 0 168 LEU cc_start: 0.8557 (mt) cc_final: 0.7855 (mt) REVERT: 0 284 MET cc_start: 0.7079 (ttm) cc_final: 0.6817 (ttm) REVERT: 0 346 MET cc_start: 0.8913 (ttt) cc_final: 0.8517 (ttt) REVERT: 0 406 ILE cc_start: 0.8627 (mt) cc_final: 0.8293 (mt) REVERT: 4 100 GLU cc_start: 0.8044 (mp0) cc_final: 0.7666 (mp0) REVERT: 4 187 GLN cc_start: 0.8366 (tt0) cc_final: 0.7309 (tp40) REVERT: 4 189 ILE cc_start: 0.9153 (tt) cc_final: 0.8928 (tt) REVERT: 4 214 LYS cc_start: 0.6664 (mmmt) cc_final: 0.6124 (tppt) REVERT: 4 363 HIS cc_start: 0.8035 (t-90) cc_final: 0.7770 (t-90) REVERT: 4 392 ILE cc_start: 0.8723 (mt) cc_final: 0.8511 (mp) REVERT: 4 398 LEU cc_start: 0.8640 (tp) cc_final: 0.8179 (tp) REVERT: 4 414 ASP cc_start: 0.6499 (p0) cc_final: 0.6077 (p0) REVERT: 4 451 TYR cc_start: 0.7244 (m-10) cc_final: 0.6913 (m-10) REVERT: 5 106 ASP cc_start: 0.7958 (t0) cc_final: 0.7648 (t0) REVERT: 5 353 ILE cc_start: 0.9071 (pt) cc_final: 0.8842 (pt) REVERT: 5 386 ARG cc_start: 0.7815 (mmt90) cc_final: 0.7574 (mpt180) REVERT: 3 187 GLN cc_start: 0.8456 (tt0) cc_final: 0.8164 (tt0) REVERT: 3 314 ARG cc_start: 0.7744 (ttm-80) cc_final: 0.7507 (ttm-80) REVERT: 3 401 LEU cc_start: 0.8228 (mt) cc_final: 0.7307 (mt) REVERT: 3 450 LEU cc_start: 0.7159 (mt) cc_final: 0.6957 (mt) REVERT: 3 482 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7777 (tt0) REVERT: 7 33 LEU cc_start: 0.8468 (mt) cc_final: 0.8045 (tp) REVERT: 7 119 TYR cc_start: 0.6216 (m-80) cc_final: 0.5950 (m-80) REVERT: 7 193 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7314 (mm-30) REVERT: 7 196 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7515 (ttp-170) outliers start: 21 outliers final: 3 residues processed: 1832 average time/residue: 0.6086 time to fit residues: 1892.9391 Evaluate side-chains 1500 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1497 time to evaluate : 5.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 145 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 360 optimal weight: 5.9990 chunk 654 optimal weight: 0.7980 chunk 717 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 686 optimal weight: 5.9990 chunk 305 optimal weight: 6.9990 chunk 385 optimal weight: 2.9990 chunk 617 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 39 ASN ** 9 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 77 ASN 9 100 GLN ** 9 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 206 GLN Q 126 GLN R 75 GLN V 35 GLN ** 6 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 GLN ** U 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 41 ASN a 112 ASN ** a 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 722 GLN ** a 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 351 ASN c 364 HIS ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 132 HIS 0 103 GLN ** 0 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 73 HIS 4 465 GLN 5 156 GLN ** 5 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN ** 7 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 174 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.199799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.163276 restraints weight = 141693.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.160340 restraints weight = 102320.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.160797 restraints weight = 77615.483| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 66773 Z= 0.281 Angle : 0.649 11.230 90244 Z= 0.341 Chirality : 0.044 0.222 10230 Planarity : 0.005 0.058 11573 Dihedral : 4.987 82.186 9103 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.34 % Favored : 94.61 % Rotamer: Outliers : 0.14 % Allowed : 3.53 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.09), residues: 8314 helix: 1.03 (0.07), residues: 4700 sheet: -1.18 (0.19), residues: 688 loop : -1.53 (0.12), residues: 2926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP a 602 HIS 0.011 0.001 HIS 0 164 PHE 0.046 0.002 PHE a 301 TYR 0.052 0.002 TYR h 144 ARG 0.039 0.001 ARG 1 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1778 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1768 time to evaluate : 5.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 54 MET cc_start: 0.5109 (mmm) cc_final: 0.4489 (mmm) REVERT: 8 122 GLN cc_start: 0.8059 (tt0) cc_final: 0.7545 (tp-100) REVERT: 8 181 VAL cc_start: 0.9219 (p) cc_final: 0.8757 (t) REVERT: 8 194 ASN cc_start: 0.8101 (t0) cc_final: 0.7776 (t0) REVERT: 9 59 LYS cc_start: 0.8247 (mttt) cc_final: 0.7671 (tptm) REVERT: 9 124 LEU cc_start: 0.8939 (mt) cc_final: 0.8610 (mt) REVERT: 9 132 MET cc_start: 0.7617 (mtt) cc_final: 0.7161 (mtt) REVERT: 9 140 ASP cc_start: 0.7473 (m-30) cc_final: 0.7046 (m-30) REVERT: 9 185 ASN cc_start: 0.9323 (p0) cc_final: 0.9091 (p0) REVERT: 9 194 ASN cc_start: 0.8437 (t0) cc_final: 0.7387 (t0) REVERT: Q 58 GLU cc_start: 0.7290 (mp0) cc_final: 0.7025 (mm-30) REVERT: Q 184 TYR cc_start: 0.8495 (m-10) cc_final: 0.7876 (m-10) REVERT: R 5 THR cc_start: 0.7295 (p) cc_final: 0.7018 (p) REVERT: R 27 LYS cc_start: 0.6365 (pttp) cc_final: 0.5589 (ptpt) REVERT: R 47 TYR cc_start: 0.7142 (m-10) cc_final: 0.6518 (m-80) REVERT: R 102 MET cc_start: 0.5786 (mtm) cc_final: 0.5546 (mtm) REVERT: T 42 MET cc_start: 0.6838 (ptp) cc_final: 0.6304 (ptt) REVERT: V 28 ARG cc_start: 0.6389 (mtt180) cc_final: 0.5784 (mmp-170) REVERT: 6 16 GLN cc_start: 0.5501 (mt0) cc_final: 0.4694 (tt0) REVERT: 6 275 GLN cc_start: 0.5166 (tp-100) cc_final: 0.3698 (pp30) REVERT: 6 331 LEU cc_start: 0.6805 (mt) cc_final: 0.6422 (tt) REVERT: U 50 ILE cc_start: 0.3448 (mm) cc_final: 0.3224 (mm) REVERT: U 65 MET cc_start: 0.3631 (tpt) cc_final: 0.3416 (tpt) REVERT: U 81 MET cc_start: 0.0253 (ptt) cc_final: -0.0141 (ptt) REVERT: a 56 ARG cc_start: 0.7997 (tmm-80) cc_final: 0.7326 (mtt180) REVERT: a 74 LYS cc_start: 0.7261 (mttt) cc_final: 0.6577 (tptt) REVERT: a 94 MET cc_start: 0.7362 (tpp) cc_final: 0.6657 (ttp) REVERT: a 111 ILE cc_start: 0.6007 (mt) cc_final: 0.5739 (mt) REVERT: a 114 ASN cc_start: 0.7393 (t0) cc_final: 0.7185 (t0) REVERT: a 366 GLN cc_start: 0.6025 (mm-40) cc_final: 0.4894 (tm-30) REVERT: a 388 TYR cc_start: 0.6771 (m-80) cc_final: 0.6166 (m-80) REVERT: a 445 GLU cc_start: 0.7573 (tt0) cc_final: 0.7211 (tt0) REVERT: a 491 MET cc_start: 0.4747 (ptt) cc_final: 0.1938 (tmm) REVERT: a 570 PHE cc_start: 0.8739 (t80) cc_final: 0.8445 (t80) REVERT: a 571 LYS cc_start: 0.8709 (tmtt) cc_final: 0.8342 (tptp) REVERT: a 572 LYS cc_start: 0.7165 (mmpt) cc_final: 0.6804 (mmmt) REVERT: a 597 LEU cc_start: 0.7477 (mt) cc_final: 0.7092 (mt) REVERT: a 621 ILE cc_start: 0.8471 (mp) cc_final: 0.8145 (mp) REVERT: a 624 PHE cc_start: 0.7522 (m-80) cc_final: 0.6892 (m-80) REVERT: a 628 TYR cc_start: 0.3556 (m-80) cc_final: 0.2971 (m-80) REVERT: a 757 LEU cc_start: 0.7668 (tp) cc_final: 0.7332 (tp) REVERT: a 809 TRP cc_start: 0.7779 (t60) cc_final: 0.7189 (t60) REVERT: e 16 PHE cc_start: 0.7202 (m-80) cc_final: 0.6844 (m-80) REVERT: X 73 MET cc_start: 0.2824 (mtp) cc_final: 0.2217 (mmm) REVERT: d 83 ARG cc_start: 0.2853 (mtp85) cc_final: 0.2265 (tpt-90) REVERT: d 142 ASN cc_start: 0.7671 (m-40) cc_final: 0.7100 (t0) REVERT: d 160 LEU cc_start: 0.7016 (mt) cc_final: 0.6463 (mt) REVERT: d 262 GLU cc_start: 0.7380 (pp20) cc_final: 0.6827 (pp20) REVERT: b 19 MET cc_start: 0.5891 (mtm) cc_final: 0.5571 (ttt) REVERT: b 203 MET cc_start: 0.2391 (tmm) cc_final: 0.2059 (ttt) REVERT: g 61 MET cc_start: 0.3499 (mtp) cc_final: 0.2847 (mtm) REVERT: g 64 ILE cc_start: 0.7002 (mt) cc_final: 0.6784 (mt) REVERT: h 90 PHE cc_start: 0.7449 (t80) cc_final: 0.6921 (t80) REVERT: h 110 ILE cc_start: 0.7004 (mt) cc_final: 0.6793 (mt) REVERT: i 23 MET cc_start: 0.6230 (mmm) cc_final: 0.5947 (mmm) REVERT: i 67 ILE cc_start: 0.5648 (mt) cc_final: 0.5258 (mt) REVERT: k 17 MET cc_start: 0.8153 (mtm) cc_final: 0.7917 (mtm) REVERT: k 24 VAL cc_start: 0.6077 (t) cc_final: 0.5866 (t) REVERT: k 48 ARG cc_start: 0.7433 (mpp80) cc_final: 0.6736 (ptp90) REVERT: k 53 MET cc_start: 0.4551 (mpp) cc_final: 0.4059 (mpp) REVERT: l 47 MET cc_start: 0.6757 (mtp) cc_final: 0.6534 (mtp) REVERT: l 72 VAL cc_start: 0.6707 (t) cc_final: 0.6473 (p) REVERT: n 47 MET cc_start: 0.7162 (mtm) cc_final: 0.6733 (tmm) REVERT: o 44 MET cc_start: 0.6378 (mmm) cc_final: 0.5179 (ptm) REVERT: o 126 ARG cc_start: 0.7240 (mmp80) cc_final: 0.6960 (mtp180) REVERT: 1 158 GLU cc_start: 0.7617 (mt-10) cc_final: 0.6939 (mm-30) REVERT: 1 401 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7893 (tm-30) REVERT: 1 484 GLN cc_start: 0.8440 (tp40) cc_final: 0.8093 (tp-100) REVERT: 2 165 LYS cc_start: 0.8551 (mptt) cc_final: 0.8124 (mmtp) REVERT: 2 229 THR cc_start: 0.4570 (t) cc_final: 0.3951 (t) REVERT: 2 272 ILE cc_start: 0.8887 (mt) cc_final: 0.8636 (mm) REVERT: 2 284 MET cc_start: 0.6932 (ppp) cc_final: 0.6124 (ppp) REVERT: 2 459 ARG cc_start: 0.7731 (ttp-110) cc_final: 0.7386 (mtt90) REVERT: 2 462 ASP cc_start: 0.8526 (m-30) cc_final: 0.8150 (m-30) REVERT: 2 531 PHE cc_start: 0.6364 (t80) cc_final: 0.6036 (m-80) REVERT: 2 540 MET cc_start: 0.2968 (mtm) cc_final: 0.2565 (mtm) REVERT: 2 550 MET cc_start: 0.3861 (mtt) cc_final: 0.3291 (mmt) REVERT: 2 613 ARG cc_start: 0.7725 (mtp180) cc_final: 0.6465 (mtp85) REVERT: 0 39 MET cc_start: 0.6241 (ptt) cc_final: 0.5928 (ptt) REVERT: 0 104 ARG cc_start: 0.8216 (mmp-170) cc_final: 0.7714 (mtm180) REVERT: 0 113 THR cc_start: 0.8769 (t) cc_final: 0.8292 (t) REVERT: 0 168 LEU cc_start: 0.8581 (mt) cc_final: 0.8085 (mt) REVERT: 0 284 MET cc_start: 0.7179 (ttm) cc_final: 0.6816 (ttm) REVERT: 0 346 MET cc_start: 0.8971 (ttt) cc_final: 0.8565 (ttt) REVERT: 0 406 ILE cc_start: 0.8697 (mt) cc_final: 0.8380 (mt) REVERT: 4 61 ASP cc_start: 0.7636 (t70) cc_final: 0.7315 (t70) REVERT: 4 187 GLN cc_start: 0.8424 (tt0) cc_final: 0.7231 (tp-100) REVERT: 4 193 SER cc_start: 0.7551 (p) cc_final: 0.7257 (p) REVERT: 4 214 LYS cc_start: 0.6757 (mmmt) cc_final: 0.6240 (tppt) REVERT: 4 363 HIS cc_start: 0.8260 (t-90) cc_final: 0.8045 (t-90) REVERT: 4 392 ILE cc_start: 0.8756 (mt) cc_final: 0.8451 (mp) REVERT: 4 414 ASP cc_start: 0.6437 (p0) cc_final: 0.6133 (p0) REVERT: 4 426 TYR cc_start: 0.7556 (t80) cc_final: 0.7315 (t80) REVERT: 4 451 TYR cc_start: 0.7380 (m-10) cc_final: 0.7148 (m-10) REVERT: 5 106 ASP cc_start: 0.8037 (t0) cc_final: 0.7731 (t0) REVERT: 5 180 MET cc_start: 0.8300 (tpt) cc_final: 0.8034 (tpt) REVERT: 5 300 MET cc_start: 0.8267 (mmm) cc_final: 0.7964 (mtp) REVERT: 5 335 TYR cc_start: 0.8484 (m-10) cc_final: 0.8179 (m-80) REVERT: 5 353 ILE cc_start: 0.9127 (pt) cc_final: 0.8863 (pt) REVERT: 5 365 ILE cc_start: 0.9217 (mt) cc_final: 0.8969 (mt) REVERT: 5 463 ILE cc_start: 0.7320 (mm) cc_final: 0.6959 (mp) REVERT: 5 490 GLU cc_start: 0.5989 (mp0) cc_final: 0.5713 (mp0) REVERT: 3 187 GLN cc_start: 0.8478 (tt0) cc_final: 0.8122 (tt0) REVERT: 3 401 LEU cc_start: 0.8091 (mt) cc_final: 0.7409 (mt) REVERT: 7 33 LEU cc_start: 0.8155 (mt) cc_final: 0.7922 (tp) REVERT: 7 193 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7530 (mm-30) outliers start: 10 outliers final: 3 residues processed: 1772 average time/residue: 0.6466 time to fit residues: 1956.9460 Evaluate side-chains 1482 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1479 time to evaluate : 5.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 687 optimal weight: 2.9990 chunk 588 optimal weight: 0.4980 chunk 166 optimal weight: 4.9990 chunk 329 optimal weight: 6.9990 chunk 453 optimal weight: 2.9990 chunk 346 optimal weight: 4.9990 chunk 762 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 605 optimal weight: 2.9990 chunk 416 optimal weight: 10.0000 chunk 726 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 11 GLN ** 9 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 126 GLN T 75 GLN ** 6 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 336 HIS ** U 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 722 GLN ** a 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 130 HIS ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 132 HIS b 197 GLN 1 231 GLN ** 1 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 522 GLN ** 0 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 156 GLN 5 205 GLN ** 5 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 161 GLN 7 46 GLN ** 7 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.201547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.166291 restraints weight = 142554.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.162498 restraints weight = 112839.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.162794 restraints weight = 88988.295| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 66773 Z= 0.214 Angle : 0.612 11.951 90244 Z= 0.322 Chirality : 0.042 0.238 10230 Planarity : 0.004 0.059 11573 Dihedral : 4.852 83.228 9103 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.75 % Favored : 95.20 % Rotamer: Outliers : 0.10 % Allowed : 2.95 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.09), residues: 8314 helix: 1.17 (0.07), residues: 4696 sheet: -0.95 (0.19), residues: 698 loop : -1.44 (0.12), residues: 2920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP a 602 HIS 0.012 0.001 HIS a 803 PHE 0.038 0.002 PHE a 301 TYR 0.048 0.002 TYR h 144 ARG 0.015 0.001 ARG b 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1773 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1766 time to evaluate : 5.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 119 LEU cc_start: 0.9205 (tp) cc_final: 0.8677 (tp) REVERT: 8 122 GLN cc_start: 0.8021 (tt0) cc_final: 0.7546 (tp40) REVERT: 8 181 VAL cc_start: 0.9160 (p) cc_final: 0.8934 (t) REVERT: 9 124 LEU cc_start: 0.8948 (mt) cc_final: 0.8694 (mt) REVERT: 9 132 MET cc_start: 0.7586 (mtt) cc_final: 0.7146 (mtt) REVERT: 9 140 ASP cc_start: 0.7447 (m-30) cc_final: 0.7011 (m-30) REVERT: 9 194 ASN cc_start: 0.8312 (t0) cc_final: 0.7439 (t0) REVERT: Q 127 LEU cc_start: 0.8819 (tp) cc_final: 0.7749 (tp) REVERT: Q 141 PHE cc_start: 0.7907 (t80) cc_final: 0.7331 (t80) REVERT: Q 184 TYR cc_start: 0.8219 (m-10) cc_final: 0.7755 (m-10) REVERT: R 5 THR cc_start: 0.7355 (p) cc_final: 0.7048 (p) REVERT: R 27 LYS cc_start: 0.6296 (pttp) cc_final: 0.5506 (mttm) REVERT: R 47 TYR cc_start: 0.7085 (m-10) cc_final: 0.6533 (m-80) REVERT: R 51 ARG cc_start: 0.2893 (mmt-90) cc_final: 0.1454 (mpt-90) REVERT: R 52 GLU cc_start: 0.6774 (mm-30) cc_final: 0.5946 (tm-30) REVERT: R 84 MET cc_start: 0.7232 (mtm) cc_final: 0.6874 (mtm) REVERT: R 104 CYS cc_start: 0.7741 (m) cc_final: 0.7450 (m) REVERT: V 28 ARG cc_start: 0.6374 (mtt180) cc_final: 0.5797 (mmp-170) REVERT: 6 275 GLN cc_start: 0.5208 (tp-100) cc_final: 0.3699 (pp30) REVERT: U 50 ILE cc_start: 0.3510 (mm) cc_final: 0.3290 (mm) REVERT: U 57 ARG cc_start: 0.4540 (ptp90) cc_final: 0.3690 (mmt180) REVERT: a 56 ARG cc_start: 0.8030 (tmm-80) cc_final: 0.7304 (mtt180) REVERT: a 74 LYS cc_start: 0.7138 (mttt) cc_final: 0.6575 (tptt) REVERT: a 111 ILE cc_start: 0.6051 (mt) cc_final: 0.5845 (mt) REVERT: a 114 ASN cc_start: 0.7175 (t0) cc_final: 0.6931 (t0) REVERT: a 306 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7272 (mptt) REVERT: a 388 TYR cc_start: 0.6687 (m-80) cc_final: 0.6104 (m-80) REVERT: a 445 GLU cc_start: 0.7861 (tt0) cc_final: 0.7459 (tt0) REVERT: a 491 MET cc_start: 0.5112 (ptt) cc_final: 0.2536 (tmm) REVERT: a 551 LEU cc_start: 0.6279 (tp) cc_final: 0.6013 (tp) REVERT: a 570 PHE cc_start: 0.8643 (t80) cc_final: 0.8435 (t80) REVERT: a 571 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8335 (tptp) REVERT: a 572 LYS cc_start: 0.7244 (mmpt) cc_final: 0.6993 (mmmt) REVERT: a 597 LEU cc_start: 0.7501 (mt) cc_final: 0.7104 (mt) REVERT: a 602 TRP cc_start: 0.6316 (m-90) cc_final: 0.5214 (m-10) REVERT: a 621 ILE cc_start: 0.8381 (mp) cc_final: 0.8067 (mp) REVERT: a 624 PHE cc_start: 0.7274 (m-80) cc_final: 0.6749 (m-10) REVERT: a 628 TYR cc_start: 0.3512 (m-80) cc_final: 0.3033 (m-80) REVERT: a 757 LEU cc_start: 0.7757 (tp) cc_final: 0.7406 (tp) REVERT: a 795 MET cc_start: 0.8108 (tpt) cc_final: 0.7832 (tpt) REVERT: a 809 TRP cc_start: 0.7607 (t60) cc_final: 0.7100 (t60) REVERT: e 16 PHE cc_start: 0.7245 (m-80) cc_final: 0.6763 (m-80) REVERT: X 73 MET cc_start: 0.2688 (mtp) cc_final: 0.2080 (mmm) REVERT: d 83 ARG cc_start: 0.2817 (mtp85) cc_final: 0.2191 (tpt-90) REVERT: d 105 MET cc_start: 0.6743 (ttt) cc_final: 0.6091 (ttt) REVERT: d 142 ASN cc_start: 0.7343 (m-40) cc_final: 0.6835 (t0) REVERT: d 152 ASN cc_start: 0.5193 (m110) cc_final: 0.4939 (m110) REVERT: d 160 LEU cc_start: 0.7138 (mt) cc_final: 0.6831 (mt) REVERT: d 262 GLU cc_start: 0.7478 (pp20) cc_final: 0.6926 (pp20) REVERT: p 331 MET cc_start: -0.0162 (tpt) cc_final: -0.0370 (mmt) REVERT: b 19 MET cc_start: 0.5826 (mtm) cc_final: 0.5557 (ttt) REVERT: g 32 TYR cc_start: 0.5645 (t80) cc_final: 0.3919 (t80) REVERT: g 41 ILE cc_start: 0.6417 (mt) cc_final: 0.5806 (mt) REVERT: g 44 MET cc_start: 0.6607 (mtt) cc_final: 0.6014 (mtt) REVERT: g 61 MET cc_start: 0.3378 (mtp) cc_final: 0.3043 (mtp) REVERT: h 90 PHE cc_start: 0.7345 (t80) cc_final: 0.6749 (t80) REVERT: i 23 MET cc_start: 0.6098 (mmm) cc_final: 0.5858 (mmm) REVERT: i 67 ILE cc_start: 0.5560 (mt) cc_final: 0.5145 (mt) REVERT: j 44 MET cc_start: 0.0145 (tmm) cc_final: -0.0058 (tmm) REVERT: k 23 MET cc_start: 0.7393 (mtp) cc_final: 0.7089 (mtp) REVERT: k 24 VAL cc_start: 0.5885 (t) cc_final: 0.5580 (t) REVERT: l 72 VAL cc_start: 0.6709 (t) cc_final: 0.6501 (p) REVERT: l 150 LEU cc_start: 0.9041 (mt) cc_final: 0.8833 (mt) REVERT: m 47 MET cc_start: 0.7884 (mmp) cc_final: 0.6768 (mmt) REVERT: n 47 MET cc_start: 0.7031 (mtm) cc_final: 0.6813 (ptm) REVERT: o 44 MET cc_start: 0.5565 (mmm) cc_final: 0.5304 (ptm) REVERT: o 48 ARG cc_start: 0.5462 (mmm160) cc_final: 0.5179 (mmm160) REVERT: 1 158 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7302 (mm-30) REVERT: 1 171 ARG cc_start: 0.7850 (mpt-90) cc_final: 0.7495 (tpp80) REVERT: 1 315 THR cc_start: 0.8476 (t) cc_final: 0.8110 (t) REVERT: 1 401 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7900 (tm-30) REVERT: 1 435 LEU cc_start: 0.8523 (mt) cc_final: 0.8244 (mt) REVERT: 1 484 GLN cc_start: 0.8330 (tp40) cc_final: 0.7727 (tp-100) REVERT: 2 50 LEU cc_start: 0.8465 (mt) cc_final: 0.8247 (mt) REVERT: 2 66 VAL cc_start: 0.8360 (p) cc_final: 0.8010 (m) REVERT: 2 165 LYS cc_start: 0.8577 (mptt) cc_final: 0.8088 (mmtp) REVERT: 2 229 THR cc_start: 0.4615 (t) cc_final: 0.4046 (t) REVERT: 2 272 ILE cc_start: 0.8853 (mt) cc_final: 0.8631 (mm) REVERT: 2 284 MET cc_start: 0.7096 (ppp) cc_final: 0.6203 (ppp) REVERT: 2 462 ASP cc_start: 0.8323 (m-30) cc_final: 0.8060 (m-30) REVERT: 2 531 PHE cc_start: 0.6550 (t80) cc_final: 0.6089 (m-80) REVERT: 2 550 MET cc_start: 0.4017 (mtt) cc_final: 0.3326 (mmt) REVERT: 2 613 ARG cc_start: 0.7713 (mtp180) cc_final: 0.6459 (mtp85) REVERT: 0 39 MET cc_start: 0.6214 (ptt) cc_final: 0.5959 (ptt) REVERT: 0 104 ARG cc_start: 0.8113 (mmp-170) cc_final: 0.7625 (mtm-85) REVERT: 0 113 THR cc_start: 0.8812 (t) cc_final: 0.8394 (t) REVERT: 0 168 LEU cc_start: 0.8566 (mt) cc_final: 0.8174 (mt) REVERT: 0 314 ASN cc_start: 0.7883 (p0) cc_final: 0.7665 (p0) REVERT: 0 315 THR cc_start: 0.8685 (p) cc_final: 0.8465 (p) REVERT: 0 346 MET cc_start: 0.8930 (ttt) cc_final: 0.8514 (ttt) REVERT: 0 406 ILE cc_start: 0.8749 (mt) cc_final: 0.8420 (mt) REVERT: 4 187 GLN cc_start: 0.8441 (tt0) cc_final: 0.7503 (tp-100) REVERT: 4 214 LYS cc_start: 0.6651 (mmmt) cc_final: 0.6248 (tppt) REVERT: 4 268 THR cc_start: 0.8739 (p) cc_final: 0.8224 (p) REVERT: 4 392 ILE cc_start: 0.8726 (mt) cc_final: 0.8410 (mp) REVERT: 4 410 MET cc_start: 0.7871 (mmm) cc_final: 0.7264 (mtm) REVERT: 4 414 ASP cc_start: 0.6386 (p0) cc_final: 0.6090 (p0) REVERT: 4 426 TYR cc_start: 0.7737 (t80) cc_final: 0.7101 (t80) REVERT: 4 451 TYR cc_start: 0.7302 (m-10) cc_final: 0.6982 (m-10) REVERT: 5 106 ASP cc_start: 0.7983 (t0) cc_final: 0.7696 (t0) REVERT: 5 167 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7388 (pm20) REVERT: 5 300 MET cc_start: 0.8111 (mmm) cc_final: 0.7733 (mtp) REVERT: 5 302 SER cc_start: 0.9154 (m) cc_final: 0.8913 (m) REVERT: 5 335 TYR cc_start: 0.8548 (m-10) cc_final: 0.8142 (m-80) REVERT: 5 353 ILE cc_start: 0.9111 (pt) cc_final: 0.8856 (pt) REVERT: 5 365 ILE cc_start: 0.9109 (mt) cc_final: 0.8878 (mt) REVERT: 5 383 LEU cc_start: 0.8728 (mt) cc_final: 0.8449 (mm) REVERT: 5 463 ILE cc_start: 0.7506 (mm) cc_final: 0.7086 (mp) REVERT: 3 354 LEU cc_start: 0.9146 (pt) cc_final: 0.8945 (pt) REVERT: 3 401 LEU cc_start: 0.8230 (mt) cc_final: 0.7622 (mt) REVERT: 7 193 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7303 (mm-30) outliers start: 7 outliers final: 3 residues processed: 1767 average time/residue: 0.6076 time to fit residues: 1826.2865 Evaluate side-chains 1466 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1463 time to evaluate : 5.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 17 optimal weight: 9.9990 chunk 782 optimal weight: 4.9990 chunk 284 optimal weight: 2.9990 chunk 718 optimal weight: 0.7980 chunk 608 optimal weight: 5.9990 chunk 581 optimal weight: 8.9990 chunk 247 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 534 optimal weight: 6.9990 chunk 780 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 71 GLN 9 169 GLN T 75 GLN ** 6 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 317 GLN U 38 GLN U 259 HIS ** U 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 442 HIS ** a 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 531 ASN a 736 ASN ** a 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 GLN d 35 ASN d 108 ASN d 137 GLN d 328 ASN ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 7 ASN 2 261 GLN ** 0 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 97 GLN 5 156 GLN 5 171 GLN 5 382 GLN 3 482 GLN 7 46 GLN ** 7 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.199482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.167056 restraints weight = 142894.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.163555 restraints weight = 145550.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.165313 restraints weight = 108314.470| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 66773 Z= 0.274 Angle : 0.653 11.408 90244 Z= 0.343 Chirality : 0.044 0.202 10230 Planarity : 0.005 0.069 11573 Dihedral : 4.952 83.394 9103 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.50 % Favored : 94.46 % Rotamer: Outliers : 0.07 % Allowed : 2.65 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.09), residues: 8314 helix: 1.10 (0.07), residues: 4709 sheet: -0.96 (0.20), residues: 694 loop : -1.49 (0.12), residues: 2911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP 0 450 HIS 0.011 0.002 HIS a 803 PHE 0.036 0.002 PHE b 150 TYR 0.049 0.002 TYR h 144 ARG 0.013 0.001 ARG T 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1719 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1714 time to evaluate : 5.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 54 MET cc_start: 0.4970 (mmm) cc_final: 0.4312 (mmm) REVERT: 8 119 LEU cc_start: 0.9253 (tp) cc_final: 0.8783 (mt) REVERT: 8 122 GLN cc_start: 0.8019 (tt0) cc_final: 0.7557 (tp40) REVERT: 8 156 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8331 (ptmm) REVERT: 9 59 LYS cc_start: 0.8180 (mttt) cc_final: 0.7632 (tptm) REVERT: 9 140 ASP cc_start: 0.7398 (m-30) cc_final: 0.6913 (m-30) REVERT: 9 194 ASN cc_start: 0.8464 (t0) cc_final: 0.7594 (t0) REVERT: Q 124 LEU cc_start: 0.8798 (mm) cc_final: 0.8284 (pp) REVERT: Q 127 LEU cc_start: 0.8973 (tp) cc_final: 0.8051 (tp) REVERT: Q 184 TYR cc_start: 0.8037 (m-10) cc_final: 0.7549 (m-10) REVERT: R 5 THR cc_start: 0.7081 (p) cc_final: 0.6811 (p) REVERT: R 27 LYS cc_start: 0.6103 (pttp) cc_final: 0.5359 (mttm) REVERT: R 47 TYR cc_start: 0.7068 (m-10) cc_final: 0.6488 (m-80) REVERT: R 51 ARG cc_start: 0.2764 (mmt-90) cc_final: 0.1216 (mpt-90) REVERT: R 52 GLU cc_start: 0.6726 (mm-30) cc_final: 0.5975 (tm-30) REVERT: V 28 ARG cc_start: 0.6362 (mtt180) cc_final: 0.5778 (mmp-170) REVERT: V 47 TYR cc_start: 0.6982 (m-10) cc_final: 0.6337 (m-80) REVERT: 6 333 GLU cc_start: 0.7877 (pt0) cc_final: 0.7575 (pt0) REVERT: U 50 ILE cc_start: 0.3774 (mm) cc_final: 0.3429 (mm) REVERT: U 55 MET cc_start: 0.1196 (tpt) cc_final: 0.0739 (tpt) REVERT: U 57 ARG cc_start: 0.4392 (ptp90) cc_final: 0.3591 (mmt180) REVERT: U 316 LYS cc_start: 0.5885 (pttt) cc_final: 0.5598 (mmmt) REVERT: U 317 GLN cc_start: 0.5623 (mp10) cc_final: 0.5224 (mp10) REVERT: U 360 LYS cc_start: 0.7429 (mttt) cc_final: 0.6953 (mtpt) REVERT: a 56 ARG cc_start: 0.7888 (tmm-80) cc_final: 0.7311 (mtt180) REVERT: a 74 LYS cc_start: 0.7172 (mttt) cc_final: 0.6510 (tptt) REVERT: a 306 LYS cc_start: 0.7379 (mmtt) cc_final: 0.6551 (mptt) REVERT: a 363 GLN cc_start: 0.5759 (tp40) cc_final: 0.5370 (tt0) REVERT: a 388 TYR cc_start: 0.6595 (m-80) cc_final: 0.5725 (m-80) REVERT: a 445 GLU cc_start: 0.8194 (tt0) cc_final: 0.7631 (tt0) REVERT: a 454 ARG cc_start: 0.6714 (ttp80) cc_final: 0.4814 (ptt-90) REVERT: a 571 LYS cc_start: 0.8693 (tmtt) cc_final: 0.8157 (tptp) REVERT: a 597 LEU cc_start: 0.7585 (mt) cc_final: 0.7194 (mt) REVERT: a 624 PHE cc_start: 0.7118 (m-80) cc_final: 0.6760 (m-10) REVERT: a 628 TYR cc_start: 0.3412 (m-80) cc_final: 0.2939 (m-80) REVERT: a 719 MET cc_start: 0.3608 (mmt) cc_final: 0.3209 (mmm) REVERT: a 757 LEU cc_start: 0.7929 (tp) cc_final: 0.7582 (tp) REVERT: a 809 TRP cc_start: 0.7354 (t60) cc_final: 0.6974 (t60) REVERT: e 16 PHE cc_start: 0.6895 (m-80) cc_final: 0.6452 (m-80) REVERT: e 40 MET cc_start: 0.6195 (ptt) cc_final: 0.5984 (ptm) REVERT: f 63 GLU cc_start: 0.4630 (pt0) cc_final: 0.3025 (tt0) REVERT: X 72 GLU cc_start: 0.6325 (mt-10) cc_final: 0.4967 (tp30) REVERT: X 73 MET cc_start: 0.2799 (mtp) cc_final: 0.2154 (mmm) REVERT: d 67 VAL cc_start: 0.5535 (t) cc_final: 0.5100 (t) REVERT: d 72 ASP cc_start: 0.6067 (m-30) cc_final: 0.5116 (t70) REVERT: d 78 MET cc_start: 0.6629 (tmm) cc_final: 0.6356 (tmm) REVERT: d 83 ARG cc_start: 0.3280 (mtp85) cc_final: 0.2542 (tpt-90) REVERT: d 105 MET cc_start: 0.6990 (ttt) cc_final: 0.6635 (ttt) REVERT: d 160 LEU cc_start: 0.6984 (mt) cc_final: 0.6763 (mt) REVERT: d 262 GLU cc_start: 0.7595 (pp20) cc_final: 0.6981 (pp20) REVERT: d 328 ASN cc_start: 0.5719 (m-40) cc_final: 0.5352 (m-40) REVERT: p 331 MET cc_start: 0.0009 (tpt) cc_final: -0.0368 (mmt) REVERT: b 19 MET cc_start: 0.5675 (mtm) cc_final: 0.5377 (ttt) REVERT: g 28 MET cc_start: 0.8094 (tpt) cc_final: 0.7614 (tpt) REVERT: g 32 TYR cc_start: 0.4667 (t80) cc_final: 0.4164 (t80) REVERT: g 41 ILE cc_start: 0.6446 (mt) cc_final: 0.5755 (mt) REVERT: g 44 MET cc_start: 0.6729 (mtt) cc_final: 0.6363 (mtt) REVERT: h 17 MET cc_start: 0.7885 (mtt) cc_final: 0.7645 (mtt) REVERT: h 90 PHE cc_start: 0.7178 (t80) cc_final: 0.6670 (t80) REVERT: i 23 MET cc_start: 0.5767 (mmm) cc_final: 0.5536 (mmm) REVERT: i 67 ILE cc_start: 0.5305 (mt) cc_final: 0.4906 (mt) REVERT: i 132 ILE cc_start: 0.7592 (mt) cc_final: 0.7273 (mt) REVERT: j 53 MET cc_start: 0.6493 (mmm) cc_final: 0.3128 (ttt) REVERT: k 23 MET cc_start: 0.7225 (mtp) cc_final: 0.6918 (mtp) REVERT: k 24 VAL cc_start: 0.5810 (t) cc_final: 0.5530 (t) REVERT: k 53 MET cc_start: 0.4466 (mpp) cc_final: 0.4020 (mpp) REVERT: l 72 VAL cc_start: 0.6942 (t) cc_final: 0.6663 (p) REVERT: l 150 LEU cc_start: 0.9000 (mt) cc_final: 0.8796 (mt) REVERT: m 112 ILE cc_start: 0.6536 (pt) cc_final: 0.6296 (pt) REVERT: o 44 MET cc_start: 0.5631 (mmm) cc_final: 0.5157 (ptm) REVERT: o 48 ARG cc_start: 0.5233 (mmm160) cc_final: 0.4392 (mmm160) REVERT: o 50 GLU cc_start: 0.6623 (pt0) cc_final: 0.4935 (mp0) REVERT: 1 158 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7134 (mm-30) REVERT: 1 171 ARG cc_start: 0.7941 (mpt-90) cc_final: 0.7703 (tpp80) REVERT: 1 283 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7920 (mt-10) REVERT: 1 401 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8039 (tm-30) REVERT: 1 484 GLN cc_start: 0.8458 (tp40) cc_final: 0.8000 (tp-100) REVERT: 2 66 VAL cc_start: 0.8353 (p) cc_final: 0.8011 (m) REVERT: 2 165 LYS cc_start: 0.8706 (mptt) cc_final: 0.8228 (mmtp) REVERT: 2 229 THR cc_start: 0.4663 (t) cc_final: 0.4223 (t) REVERT: 2 272 ILE cc_start: 0.8907 (mt) cc_final: 0.8635 (mm) REVERT: 2 531 PHE cc_start: 0.6475 (t80) cc_final: 0.6216 (m-80) REVERT: 2 550 MET cc_start: 0.4388 (mtt) cc_final: 0.3588 (mmt) REVERT: 2 608 MET cc_start: 0.2203 (tmm) cc_final: 0.1808 (ttp) REVERT: 2 613 ARG cc_start: 0.7850 (mtp180) cc_final: 0.6654 (mtp85) REVERT: 0 39 MET cc_start: 0.6753 (ptt) cc_final: 0.6413 (ptt) REVERT: 0 104 ARG cc_start: 0.8192 (mmp-170) cc_final: 0.7678 (mtm180) REVERT: 0 113 THR cc_start: 0.8743 (t) cc_final: 0.8353 (t) REVERT: 0 168 LEU cc_start: 0.8441 (mt) cc_final: 0.8037 (mt) REVERT: 0 346 MET cc_start: 0.8873 (ttt) cc_final: 0.8493 (ttt) REVERT: 4 61 ASP cc_start: 0.7727 (t70) cc_final: 0.7475 (t70) REVERT: 4 100 GLU cc_start: 0.7525 (mp0) cc_final: 0.7005 (mp0) REVERT: 4 127 MET cc_start: 0.8532 (mtm) cc_final: 0.8151 (mtm) REVERT: 4 187 GLN cc_start: 0.8410 (tt0) cc_final: 0.7444 (tp-100) REVERT: 4 214 LYS cc_start: 0.6777 (mmmt) cc_final: 0.6310 (tppt) REVERT: 4 294 LEU cc_start: 0.9063 (tt) cc_final: 0.8759 (tt) REVERT: 4 392 ILE cc_start: 0.8719 (mt) cc_final: 0.8456 (mp) REVERT: 4 398 LEU cc_start: 0.8783 (tp) cc_final: 0.8429 (tp) REVERT: 4 402 MET cc_start: 0.8008 (mmm) cc_final: 0.7673 (mmt) REVERT: 4 410 MET cc_start: 0.7918 (mmm) cc_final: 0.7348 (mtm) REVERT: 4 414 ASP cc_start: 0.6507 (p0) cc_final: 0.6166 (p0) REVERT: 4 451 TYR cc_start: 0.7215 (m-10) cc_final: 0.6950 (m-10) REVERT: 5 106 ASP cc_start: 0.8001 (t0) cc_final: 0.7730 (t0) REVERT: 5 189 ILE cc_start: 0.8966 (mm) cc_final: 0.8718 (mm) REVERT: 5 300 MET cc_start: 0.8142 (mmm) cc_final: 0.7769 (mtp) REVERT: 5 302 SER cc_start: 0.9101 (m) cc_final: 0.8858 (m) REVERT: 5 327 MET cc_start: 0.8459 (ttp) cc_final: 0.8242 (ttm) REVERT: 5 335 TYR cc_start: 0.8652 (m-10) cc_final: 0.8304 (m-80) REVERT: 5 353 ILE cc_start: 0.8889 (pt) cc_final: 0.8672 (pt) REVERT: 5 365 ILE cc_start: 0.9129 (mt) cc_final: 0.8902 (mt) REVERT: 5 371 TYR cc_start: 0.8056 (m-80) cc_final: 0.7851 (m-80) REVERT: 5 463 ILE cc_start: 0.7070 (mm) cc_final: 0.6724 (mp) REVERT: 3 118 ILE cc_start: 0.9220 (pt) cc_final: 0.9001 (pt) REVERT: 3 168 GLU cc_start: 0.6723 (pt0) cc_final: 0.5966 (pt0) REVERT: 3 185 ARG cc_start: 0.8464 (mpp80) cc_final: 0.7905 (mtt180) REVERT: 3 187 GLN cc_start: 0.8517 (tt0) cc_final: 0.8260 (tt0) REVERT: 3 234 MET cc_start: 0.7858 (ptm) cc_final: 0.7618 (ptp) REVERT: 3 300 MET cc_start: 0.8978 (mmt) cc_final: 0.8777 (mmm) REVERT: 3 315 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7923 (tm-30) REVERT: 3 354 LEU cc_start: 0.9068 (pt) cc_final: 0.8840 (pt) REVERT: 3 401 LEU cc_start: 0.8280 (mt) cc_final: 0.7698 (mt) REVERT: 3 435 MET cc_start: 0.7729 (tpt) cc_final: 0.7494 (tpt) REVERT: 7 193 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7241 (mm-30) outliers start: 5 outliers final: 1 residues processed: 1717 average time/residue: 0.6071 time to fit residues: 1766.4715 Evaluate side-chains 1440 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1439 time to evaluate : 5.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 805 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 671 optimal weight: 7.9990 chunk 452 optimal weight: 0.8980 chunk 59 optimal weight: 0.1980 chunk 164 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 524 optimal weight: 1.9990 chunk 347 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 126 GLN ** 6 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 239 HIS 6 336 HIS ** U 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 509 GLN a 531 ASN ** a 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 67 GLN ** d 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 108 ASN d 130 HIS ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 78 ASN 0 172 ASN ** 0 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 465 GLN 7 46 GLN ** 7 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 206 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.201787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.165001 restraints weight = 141575.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.161430 restraints weight = 108769.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.162399 restraints weight = 85557.663| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 66773 Z= 0.194 Angle : 0.610 10.638 90244 Z= 0.318 Chirality : 0.042 0.219 10230 Planarity : 0.004 0.120 11573 Dihedral : 4.825 83.981 9103 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.42 % Rotamer: Outliers : 0.06 % Allowed : 1.53 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.09), residues: 8314 helix: 1.26 (0.07), residues: 4696 sheet: -0.76 (0.20), residues: 680 loop : -1.39 (0.12), residues: 2938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP 6 19 HIS 0.013 0.001 HIS a 803 PHE 0.027 0.002 PHE a 301 TYR 0.056 0.002 TYR j 68 ARG 0.007 0.000 ARG m 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1714 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1710 time to evaluate : 6.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 54 MET cc_start: 0.5345 (mmm) cc_final: 0.4927 (mmm) REVERT: 8 122 GLN cc_start: 0.8104 (tt0) cc_final: 0.7537 (tp40) REVERT: 8 156 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8428 (ptmm) REVERT: 9 59 LYS cc_start: 0.8404 (mttt) cc_final: 0.8137 (tptm) REVERT: 9 120 VAL cc_start: 0.9481 (t) cc_final: 0.9273 (p) REVERT: 9 121 LEU cc_start: 0.8934 (tp) cc_final: 0.8585 (tp) REVERT: 9 125 TYR cc_start: 0.8138 (m-10) cc_final: 0.7862 (m-80) REVERT: 9 140 ASP cc_start: 0.7525 (m-30) cc_final: 0.7082 (m-30) REVERT: 9 185 ASN cc_start: 0.9255 (p0) cc_final: 0.9017 (p0) REVERT: Q 127 LEU cc_start: 0.8908 (tp) cc_final: 0.7907 (tp) REVERT: Q 184 TYR cc_start: 0.7974 (m-10) cc_final: 0.7499 (m-10) REVERT: R 5 THR cc_start: 0.6978 (p) cc_final: 0.6764 (p) REVERT: R 27 LYS cc_start: 0.6409 (pttp) cc_final: 0.5694 (mttm) REVERT: R 44 VAL cc_start: 0.4243 (t) cc_final: 0.3998 (t) REVERT: R 47 TYR cc_start: 0.7210 (m-10) cc_final: 0.6653 (m-80) REVERT: R 51 ARG cc_start: 0.2989 (mmt-90) cc_final: 0.1747 (mpt-90) REVERT: R 52 GLU cc_start: 0.6827 (mm-30) cc_final: 0.5935 (tm-30) REVERT: R 84 MET cc_start: 0.7283 (mtm) cc_final: 0.6923 (mtm) REVERT: R 104 CYS cc_start: 0.7718 (m) cc_final: 0.7497 (m) REVERT: V 28 ARG cc_start: 0.6595 (mtt180) cc_final: 0.5911 (mmp-170) REVERT: V 35 GLN cc_start: 0.6709 (tm-30) cc_final: 0.6324 (tm-30) REVERT: V 42 MET cc_start: 0.1857 (mmp) cc_final: 0.1007 (mmp) REVERT: V 47 TYR cc_start: 0.7085 (m-10) cc_final: 0.6322 (m-80) REVERT: 6 76 MET cc_start: 0.7011 (tpt) cc_final: 0.5577 (ttm) REVERT: U 50 ILE cc_start: 0.3070 (mm) cc_final: 0.2830 (mm) REVERT: U 55 MET cc_start: 0.1238 (tpt) cc_final: 0.0929 (tpt) REVERT: U 57 ARG cc_start: 0.3912 (ptp90) cc_final: 0.3352 (mmt180) REVERT: a 56 ARG cc_start: 0.8067 (tmm-80) cc_final: 0.7354 (mtt180) REVERT: a 73 ARG cc_start: 0.7042 (mtt-85) cc_final: 0.6334 (mmp-170) REVERT: a 74 LYS cc_start: 0.7323 (mttt) cc_final: 0.6727 (tptt) REVERT: a 114 ASN cc_start: 0.7575 (t0) cc_final: 0.7275 (t0) REVERT: a 306 LYS cc_start: 0.7438 (mmtt) cc_final: 0.6795 (tptt) REVERT: a 314 LEU cc_start: 0.8705 (mt) cc_final: 0.8492 (mt) REVERT: a 363 GLN cc_start: 0.5670 (tp40) cc_final: 0.5420 (tt0) REVERT: a 388 TYR cc_start: 0.6396 (m-80) cc_final: 0.5625 (m-80) REVERT: a 445 GLU cc_start: 0.7339 (tt0) cc_final: 0.6966 (tt0) REVERT: a 491 MET cc_start: 0.5392 (ptt) cc_final: 0.2691 (tmm) REVERT: a 571 LYS cc_start: 0.8871 (tmtt) cc_final: 0.8495 (tptp) REVERT: a 597 LEU cc_start: 0.7422 (mt) cc_final: 0.7018 (mt) REVERT: a 624 PHE cc_start: 0.7425 (m-80) cc_final: 0.6751 (m-10) REVERT: a 645 CYS cc_start: 0.7013 (t) cc_final: 0.6805 (p) REVERT: a 757 LEU cc_start: 0.7650 (tp) cc_final: 0.7396 (tp) REVERT: a 795 MET cc_start: 0.8313 (tpt) cc_final: 0.7866 (tpt) REVERT: a 809 TRP cc_start: 0.7780 (t60) cc_final: 0.7144 (t60) REVERT: e 16 PHE cc_start: 0.6771 (m-80) cc_final: 0.6365 (m-80) REVERT: f 63 GLU cc_start: 0.4694 (pt0) cc_final: 0.3545 (tt0) REVERT: X 55 PHE cc_start: 0.7543 (m-80) cc_final: 0.7269 (m-80) REVERT: X 73 MET cc_start: 0.2587 (mtp) cc_final: 0.1983 (mmm) REVERT: d 72 ASP cc_start: 0.6512 (m-30) cc_final: 0.5475 (t70) REVERT: d 83 ARG cc_start: 0.2269 (mtp85) cc_final: 0.1677 (tpt-90) REVERT: d 105 MET cc_start: 0.6730 (ttt) cc_final: 0.6099 (ttt) REVERT: d 160 LEU cc_start: 0.7090 (mt) cc_final: 0.6825 (mt) REVERT: d 262 GLU cc_start: 0.7503 (pp20) cc_final: 0.7035 (pp20) REVERT: d 328 ASN cc_start: 0.5592 (m-40) cc_final: 0.5362 (m-40) REVERT: c 446 MET cc_start: 0.3653 (ptt) cc_final: 0.2857 (ppp) REVERT: b 19 MET cc_start: 0.5796 (mtm) cc_final: 0.5486 (ttt) REVERT: g 28 MET cc_start: 0.7794 (tpt) cc_final: 0.7414 (tpt) REVERT: g 41 ILE cc_start: 0.6383 (mt) cc_final: 0.5631 (mt) REVERT: g 44 MET cc_start: 0.6285 (mtt) cc_final: 0.5875 (mtt) REVERT: h 90 PHE cc_start: 0.7517 (t80) cc_final: 0.6959 (t80) REVERT: i 23 MET cc_start: 0.6259 (mmm) cc_final: 0.6020 (mmm) REVERT: k 23 MET cc_start: 0.7427 (mtp) cc_final: 0.7176 (mtp) REVERT: k 24 VAL cc_start: 0.6052 (t) cc_final: 0.5831 (t) REVERT: k 41 ILE cc_start: 0.4926 (mt) cc_final: 0.4402 (mt) REVERT: k 53 MET cc_start: 0.3577 (mpp) cc_final: 0.3103 (mpp) REVERT: l 47 MET cc_start: 0.6551 (mtp) cc_final: 0.6041 (mtp) REVERT: l 72 VAL cc_start: 0.6486 (t) cc_final: 0.6282 (p) REVERT: m 25 PHE cc_start: 0.7744 (m-80) cc_final: 0.7499 (m-80) REVERT: o 44 MET cc_start: 0.5722 (mmm) cc_final: 0.5419 (ptm) REVERT: 1 95 MET cc_start: 0.8476 (tmm) cc_final: 0.8241 (tmm) REVERT: 1 158 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7249 (mm-30) REVERT: 1 171 ARG cc_start: 0.7957 (mpt-90) cc_final: 0.7621 (tpp80) REVERT: 1 401 GLU cc_start: 0.8559 (tm-30) cc_final: 0.7992 (tm-30) REVERT: 1 456 LYS cc_start: 0.7987 (mtmm) cc_final: 0.7787 (mtmt) REVERT: 1 484 GLN cc_start: 0.8538 (tp40) cc_final: 0.7957 (tp-100) REVERT: 1 608 MET cc_start: 0.7315 (mpp) cc_final: 0.7045 (mpp) REVERT: 2 66 VAL cc_start: 0.8282 (p) cc_final: 0.7969 (m) REVERT: 2 67 TYR cc_start: 0.7051 (m-80) cc_final: 0.6522 (m-80) REVERT: 2 165 LYS cc_start: 0.8619 (mptt) cc_final: 0.8198 (mmtp) REVERT: 2 229 THR cc_start: 0.4844 (t) cc_final: 0.3944 (t) REVERT: 2 284 MET cc_start: 0.7249 (ppp) cc_final: 0.6255 (ppp) REVERT: 2 349 ASP cc_start: 0.7910 (t0) cc_final: 0.7688 (t0) REVERT: 2 462 ASP cc_start: 0.8200 (m-30) cc_final: 0.7993 (m-30) REVERT: 2 531 PHE cc_start: 0.6665 (t80) cc_final: 0.6149 (m-80) REVERT: 2 550 MET cc_start: 0.3766 (mtt) cc_final: 0.3261 (mmp) REVERT: 2 613 ARG cc_start: 0.7642 (mtp180) cc_final: 0.6456 (mtp85) REVERT: 0 39 MET cc_start: 0.6449 (ptt) cc_final: 0.6110 (ptt) REVERT: 0 104 ARG cc_start: 0.8159 (mmp-170) cc_final: 0.7693 (mtm180) REVERT: 0 113 THR cc_start: 0.8898 (t) cc_final: 0.8391 (t) REVERT: 0 168 LEU cc_start: 0.8481 (mt) cc_final: 0.7995 (mt) REVERT: 0 291 PHE cc_start: 0.7410 (m-10) cc_final: 0.6237 (m-80) REVERT: 0 346 MET cc_start: 0.8883 (ttt) cc_final: 0.8600 (ttt) REVERT: 0 406 ILE cc_start: 0.8707 (mt) cc_final: 0.8424 (mt) REVERT: 4 127 MET cc_start: 0.8382 (mtm) cc_final: 0.8151 (mtm) REVERT: 4 187 GLN cc_start: 0.8422 (tt0) cc_final: 0.7384 (tp-100) REVERT: 4 189 ILE cc_start: 0.9131 (tt) cc_final: 0.8882 (tt) REVERT: 4 214 LYS cc_start: 0.6700 (mmmt) cc_final: 0.6419 (tptt) REVERT: 4 268 THR cc_start: 0.8772 (p) cc_final: 0.8313 (p) REVERT: 4 294 LEU cc_start: 0.8914 (tt) cc_final: 0.8507 (tt) REVERT: 4 392 ILE cc_start: 0.8686 (mt) cc_final: 0.8399 (mp) REVERT: 4 398 LEU cc_start: 0.8853 (tp) cc_final: 0.8524 (tp) REVERT: 4 402 MET cc_start: 0.7947 (mmm) cc_final: 0.7648 (mmt) REVERT: 4 410 MET cc_start: 0.8126 (mmm) cc_final: 0.7566 (mtm) REVERT: 4 414 ASP cc_start: 0.6506 (p0) cc_final: 0.6252 (p0) REVERT: 4 451 TYR cc_start: 0.7219 (m-10) cc_final: 0.7007 (m-10) REVERT: 5 106 ASP cc_start: 0.8061 (t0) cc_final: 0.7783 (t0) REVERT: 5 167 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7389 (pm20) REVERT: 5 300 MET cc_start: 0.8170 (mmm) cc_final: 0.7758 (mtp) REVERT: 5 302 SER cc_start: 0.9155 (m) cc_final: 0.8897 (m) REVERT: 5 327 MET cc_start: 0.8331 (ttp) cc_final: 0.8100 (ttm) REVERT: 5 335 TYR cc_start: 0.8563 (m-10) cc_final: 0.8198 (m-80) REVERT: 5 353 ILE cc_start: 0.9076 (pt) cc_final: 0.8819 (pt) REVERT: 5 365 ILE cc_start: 0.8991 (mt) cc_final: 0.8769 (mt) REVERT: 5 402 MET cc_start: 0.7509 (mtp) cc_final: 0.7118 (ttt) REVERT: 3 71 ILE cc_start: 0.9302 (mm) cc_final: 0.9011 (mt) REVERT: 3 87 LEU cc_start: 0.8643 (tp) cc_final: 0.8396 (tp) REVERT: 3 205 GLN cc_start: 0.7253 (tm-30) cc_final: 0.5796 (tm-30) REVERT: 3 234 MET cc_start: 0.8033 (ptm) cc_final: 0.7561 (ptm) REVERT: 3 314 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7341 (ttm-80) REVERT: 3 354 LEU cc_start: 0.9044 (pt) cc_final: 0.8842 (pt) REVERT: 3 401 LEU cc_start: 0.8363 (mt) cc_final: 0.7643 (mt) REVERT: 7 193 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7300 (mm-30) outliers start: 4 outliers final: 1 residues processed: 1713 average time/residue: 0.6212 time to fit residues: 1823.0604 Evaluate side-chains 1450 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1449 time to evaluate : 5.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 388 optimal weight: 5.9990 chunk 267 optimal weight: 0.9980 chunk 365 optimal weight: 6.9990 chunk 425 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 554 optimal weight: 0.7980 chunk 285 optimal weight: 0.8980 chunk 343 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 749 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 71 GLN Q 126 GLN ** 6 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 531 ASN a 803 HIS ** a 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 108 ASN d 130 HIS ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 164 HIS 0 242 GLN 0 343 HIS 4 420 ASN ** 5 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 46 GLN ** 7 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.201902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.167837 restraints weight = 142428.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.164430 restraints weight = 127302.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.166336 restraints weight = 94118.172| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.3432 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: