Starting phenix.real_space_refine on Mon Dec 30 03:51:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfe_40439/12_2024/8sfe_40439.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfe_40439/12_2024/8sfe_40439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sfe_40439/12_2024/8sfe_40439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfe_40439/12_2024/8sfe_40439.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfe_40439/12_2024/8sfe_40439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfe_40439/12_2024/8sfe_40439.cif" } resolution = 3.36 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= 0.004 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 377 5.16 5 C 37846 2.51 5 N 10544 2.21 5 O 11713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 60512 Number of models: 1 Model: "" Number of chains: 32 Chain: "z" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3903 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 13, 'TRANS': 494} Chain: "Z" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3903 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 13, 'TRANS': 494} Chain: "a" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3709 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 11, 'TRANS': 478} Chain breaks: 2 Chain: "b" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3590 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 8, 'TRANS': 469} Chain breaks: 1 Chain: "d" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3673 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 475} Chain breaks: 1 Chain: "e" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3882 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 14, 'TRANS': 490} Chain breaks: 1 Chain: "g" Number of atoms: 3678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3678 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 16, 'TRANS': 460} Chain breaks: 1 Chain: "h" Number of atoms: 3834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3834 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 14, 'TRANS': 485} Chain breaks: 1 Chain: "q" Number of atoms: 3692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3692 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 12, 'TRANS': 470} Chain breaks: 1 Chain: "A" Number of atoms: 3742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3742 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 11, 'TRANS': 482} Chain breaks: 2 Chain: "B" Number of atoms: 3698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3698 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 8, 'TRANS': 483} Chain breaks: 1 Chain: "D" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3655 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 473} Chain breaks: 1 Chain: "E" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3863 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 14, 'TRANS': 488} Chain breaks: 1 Chain: "G" Number of atoms: 3741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3741 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 16, 'TRANS': 468} Chain breaks: 1 Chain: "H" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3825 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 14, 'TRANS': 484} Chain breaks: 1 Chain: "Q" Number of atoms: 3692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3692 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 12, 'TRANS': 470} Chain breaks: 1 Chain: "z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 28.83, per 1000 atoms: 0.48 Number of scatterers: 60512 At special positions: 0 Unit cell: (187.266, 175.628, 190.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 377 16.00 P 32 15.00 O 11713 8.00 N 10544 7.00 C 37846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS h 330 " - pdb=" SG CYS h 349 " distance=2.03 Simple disulfide: pdb=" SG CYS H 326 " - pdb=" SG CYS H 345 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.92 Conformation dependent library (CDL) restraints added in 6.2 seconds 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14680 Finding SS restraints... Secondary structure from input PDB file: 322 helices and 87 sheets defined 55.4% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.33 Creating SS restraints... Processing helix chain 'z' and resid 18 through 35 Processing helix chain 'z' and resid 36 through 38 No H-bonds generated for 'chain 'z' and resid 36 through 38' Processing helix chain 'z' and resid 59 through 67 Processing helix chain 'z' and resid 71 through 86 Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.623A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 4.006A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 158 removed outlier: 3.801A pdb=" N LEU z 148 " --> pdb=" O ASP z 144 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 removed outlier: 4.144A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA z 171 " --> pdb=" O VAL z 167 " (cutoff:3.500A) Processing helix chain 'z' and resid 181 through 183 No H-bonds generated for 'chain 'z' and resid 181 through 183' Processing helix chain 'z' and resid 187 through 189 No H-bonds generated for 'chain 'z' and resid 187 through 189' Processing helix chain 'z' and resid 252 through 259 removed outlier: 4.385A pdb=" N ARG z 256 " --> pdb=" O SER z 252 " (cutoff:3.500A) Processing helix chain 'z' and resid 263 through 282 Processing helix chain 'z' and resid 298 through 307 Processing helix chain 'z' and resid 317 through 328 removed outlier: 3.783A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) Processing helix chain 'z' and resid 340 through 344 removed outlier: 4.213A pdb=" N CYS z 343 " --> pdb=" O SER z 340 " (cutoff:3.500A) Processing helix chain 'z' and resid 380 through 405 Processing helix chain 'z' and resid 413 through 426 Processing helix chain 'z' and resid 427 through 429 No H-bonds generated for 'chain 'z' and resid 427 through 429' Processing helix chain 'z' and resid 430 through 431 No H-bonds generated for 'chain 'z' and resid 430 through 431' Processing helix chain 'z' and resid 432 through 445 removed outlier: 4.080A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.572A pdb=" N LYS z 449 " --> pdb=" O LEU z 445 " (cutoff:3.500A) Processing helix chain 'z' and resid 458 through 474 removed outlier: 3.884A pdb=" N GLU z 472 " --> pdb=" O ALA z 468 " (cutoff:3.500A) Processing helix chain 'z' and resid 488 through 493 Processing helix chain 'z' and resid 498 through 517 Processing helix chain 'Z' and resid 19 through 35 Processing helix chain 'Z' and resid 59 through 64 Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'Z' and resid 91 through 111 removed outlier: 3.867A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 4.047A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU Z 135 " --> pdb=" O LEU Z 131 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU Z 136 " --> pdb=" O GLN Z 132 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL Z 137 " --> pdb=" O PHE Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 158 removed outlier: 3.892A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.816A pdb=" N ASP Z 166 " --> pdb=" O ALA Z 162 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL Z 167 " --> pdb=" O GLU Z 163 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU Z 168 " --> pdb=" O LEU Z 164 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER Z 175 " --> pdb=" O ALA Z 171 " (cutoff:3.500A) Processing helix chain 'Z' and resid 252 through 282 removed outlier: 3.886A pdb=" N ARG Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS Z 273 " --> pdb=" O ASP Z 269 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 308 Processing helix chain 'Z' and resid 320 through 329 removed outlier: 4.249A pdb=" N LEU Z 326 " --> pdb=" O GLU Z 322 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Z 327 " --> pdb=" O ARG Z 323 " (cutoff:3.500A) Processing helix chain 'Z' and resid 380 through 404 removed outlier: 3.698A pdb=" N LEU Z 384 " --> pdb=" O ASN Z 380 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN Z 386 " --> pdb=" O HIS Z 382 " (cutoff:3.500A) Processing helix chain 'Z' and resid 412 through 426 Processing helix chain 'Z' and resid 427 through 429 No H-bonds generated for 'chain 'Z' and resid 427 through 429' Processing helix chain 'Z' and resid 430 through 431 No H-bonds generated for 'chain 'Z' and resid 430 through 431' Processing helix chain 'Z' and resid 432 through 444 Processing helix chain 'Z' and resid 445 through 455 removed outlier: 3.558A pdb=" N SER Z 455 " --> pdb=" O LEU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 473 removed outlier: 3.510A pdb=" N THR Z 462 " --> pdb=" O ASP Z 458 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU Z 463 " --> pdb=" O LEU Z 459 " (cutoff:3.500A) Processing helix chain 'Z' and resid 498 through 517 Processing helix chain 'a' and resid 16 through 34 removed outlier: 3.548A pdb=" N GLN a 20 " --> pdb=" O THR a 16 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 65 removed outlier: 3.888A pdb=" N ILE a 61 " --> pdb=" O ASP a 57 " (cutoff:3.500A) Processing helix chain 'a' and resid 69 through 86 removed outlier: 3.526A pdb=" N VAL a 74 " --> pdb=" O PRO a 70 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 110 Processing helix chain 'a' and resid 113 through 134 removed outlier: 3.556A pdb=" N ASN a 133 " --> pdb=" O VAL a 129 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU a 134 " --> pdb=" O ARG a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 145 through 156 Processing helix chain 'a' and resid 159 through 163 removed outlier: 4.087A pdb=" N ILE a 163 " --> pdb=" O ILE a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 178 removed outlier: 3.949A pdb=" N PHE a 168 " --> pdb=" O ASN a 164 " (cutoff:3.500A) Processing helix chain 'a' and resid 191 through 193 No H-bonds generated for 'chain 'a' and resid 191 through 193' Processing helix chain 'a' and resid 204 through 208 removed outlier: 3.702A pdb=" N GLU a 207 " --> pdb=" O SER a 204 " (cutoff:3.500A) Processing helix chain 'a' and resid 272 through 282 Processing helix chain 'a' and resid 295 through 300 removed outlier: 3.838A pdb=" N TYR a 299 " --> pdb=" O MET a 295 " (cutoff:3.500A) Processing helix chain 'a' and resid 312 through 324 removed outlier: 3.594A pdb=" N ARG a 318 " --> pdb=" O ARG a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 385 through 404 removed outlier: 3.562A pdb=" N VAL a 402 " --> pdb=" O VAL a 398 " (cutoff:3.500A) Processing helix chain 'a' and resid 413 through 428 removed outlier: 3.630A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN a 425 " --> pdb=" O ILE a 421 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 445 Processing helix chain 'a' and resid 446 through 456 Processing helix chain 'a' and resid 459 through 477 removed outlier: 3.587A pdb=" N LEU a 463 " --> pdb=" O ASP a 459 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU a 473 " --> pdb=" O ALA a 469 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN a 475 " --> pdb=" O HIS a 471 " (cutoff:3.500A) Processing helix chain 'a' and resid 478 through 482 removed outlier: 4.661A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 25 through 41 removed outlier: 3.630A pdb=" N VAL b 39 " --> pdb=" O ILE b 35 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER b 41 " --> pdb=" O ASP b 37 " (cutoff:3.500A) Processing helix chain 'b' and resid 67 through 73 removed outlier: 3.599A pdb=" N LYS b 72 " --> pdb=" O ALA b 68 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN b 73 " --> pdb=" O THR b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 94 Processing helix chain 'b' and resid 98 through 119 Processing helix chain 'b' and resid 122 through 144 removed outlier: 3.806A pdb=" N ALA b 136 " --> pdb=" O GLU b 132 " (cutoff:3.500A) Processing helix chain 'b' and resid 156 through 167 removed outlier: 3.706A pdb=" N THR b 166 " --> pdb=" O ILE b 162 " (cutoff:3.500A) Processing helix chain 'b' and resid 175 through 187 removed outlier: 4.126A pdb=" N VAL b 187 " --> pdb=" O ALA b 183 " (cutoff:3.500A) Processing helix chain 'b' and resid 264 through 284 removed outlier: 3.520A pdb=" N LYS b 284 " --> pdb=" O GLU b 280 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 307 removed outlier: 3.987A pdb=" N LEU b 303 " --> pdb=" O TYR b 299 " (cutoff:3.500A) Processing helix chain 'b' and resid 316 through 327 Processing helix chain 'b' and resid 379 through 403 removed outlier: 4.059A pdb=" N LEU b 383 " --> pdb=" O THR b 379 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP b 384 " --> pdb=" O GLN b 380 " (cutoff:3.500A) Processing helix chain 'b' and resid 411 through 428 removed outlier: 3.578A pdb=" N ARG b 427 " --> pdb=" O GLN b 423 " (cutoff:3.500A) Processing helix chain 'b' and resid 431 through 454 removed outlier: 3.977A pdb=" N ALA b 435 " --> pdb=" O LYS b 431 " (cutoff:3.500A) Proline residue: b 447 - end of helix removed outlier: 3.885A pdb=" N ILE b 450 " --> pdb=" O LEU b 446 " (cutoff:3.500A) Processing helix chain 'b' and resid 460 through 470 removed outlier: 3.931A pdb=" N SER b 470 " --> pdb=" O ARG b 466 " (cutoff:3.500A) Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 517 removed outlier: 3.608A pdb=" N VAL b 517 " --> pdb=" O VAL b 513 " (cutoff:3.500A) Processing helix chain 'd' and resid 31 through 47 removed outlier: 3.687A pdb=" N ALA d 47 " --> pdb=" O ALA d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 52 removed outlier: 4.026A pdb=" N LEU d 52 " --> pdb=" O ARG d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 81 removed outlier: 3.558A pdb=" N ILE d 77 " --> pdb=" O ASP d 73 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 102 Processing helix chain 'd' and resid 105 through 126 removed outlier: 4.026A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU d 123 " --> pdb=" O SER d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 129 through 151 removed outlier: 3.601A pdb=" N ILE d 133 " --> pdb=" O HIS d 129 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET d 151 " --> pdb=" O ILE d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 159 through 171 removed outlier: 4.059A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 194 Proline residue: d 185 - end of helix removed outlier: 3.851A pdb=" N VAL d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 217 through 221 Processing helix chain 'd' and resid 279 through 294 Processing helix chain 'd' and resid 310 through 319 removed outlier: 3.507A pdb=" N PHE d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS d 319 " --> pdb=" O HIS d 315 " (cutoff:3.500A) Processing helix chain 'd' and resid 332 through 341 Processing helix chain 'd' and resid 347 through 351 removed outlier: 3.728A pdb=" N PHE d 351 " --> pdb=" O ILE d 348 " (cutoff:3.500A) Processing helix chain 'd' and resid 352 through 356 removed outlier: 3.510A pdb=" N MET d 355 " --> pdb=" O THR d 352 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU d 356 " --> pdb=" O ALA d 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 352 through 356' Processing helix chain 'd' and resid 395 through 418 removed outlier: 4.429A pdb=" N ALA d 401 " --> pdb=" O VAL d 397 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU d 402 " --> pdb=" O ILE d 398 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL d 416 " --> pdb=" O ILE d 412 " (cutoff:3.500A) Processing helix chain 'd' and resid 426 through 443 Processing helix chain 'd' and resid 446 through 457 removed outlier: 4.416A pdb=" N CYS d 450 " --> pdb=" O MET d 446 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 469 Processing helix chain 'd' and resid 472 through 487 Processing helix chain 'd' and resid 504 through 507 Processing helix chain 'd' and resid 512 through 531 Processing helix chain 'e' and resid 29 through 45 Processing helix chain 'e' and resid 48 through 52 Processing helix chain 'e' and resid 73 through 81 Processing helix chain 'e' and resid 85 through 102 Processing helix chain 'e' and resid 105 through 126 removed outlier: 4.599A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU e 123 " --> pdb=" O GLU e 119 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 151 Processing helix chain 'e' and resid 161 through 169 removed outlier: 3.579A pdb=" N ILE e 166 " --> pdb=" O THR e 162 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN e 167 " --> pdb=" O GLU e 163 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA e 169 " --> pdb=" O LEU e 165 " (cutoff:3.500A) Processing helix chain 'e' and resid 169 through 174 Processing helix chain 'e' and resid 177 through 180 removed outlier: 3.616A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 177 through 180' Processing helix chain 'e' and resid 181 through 196 Processing helix chain 'e' and resid 272 through 286 Processing helix chain 'e' and resid 287 through 289 No H-bonds generated for 'chain 'e' and resid 287 through 289' Processing helix chain 'e' and resid 307 through 318 removed outlier: 3.730A pdb=" N ASN e 311 " --> pdb=" O ASP e 307 " (cutoff:3.500A) Processing helix chain 'e' and resid 328 through 334 removed outlier: 4.373A pdb=" N LEU e 332 " --> pdb=" O PRO e 328 " (cutoff:3.500A) Processing helix chain 'e' and resid 391 through 415 Processing helix chain 'e' and resid 423 through 437 Processing helix chain 'e' and resid 438 through 440 No H-bonds generated for 'chain 'e' and resid 438 through 440' Processing helix chain 'e' and resid 441 through 456 Processing helix chain 'e' and resid 456 through 466 removed outlier: 3.655A pdb=" N MET e 460 " --> pdb=" O GLU e 456 " (cutoff:3.500A) Processing helix chain 'e' and resid 471 through 484 Processing helix chain 'e' and resid 500 through 505 removed outlier: 4.136A pdb=" N GLN e 504 " --> pdb=" O ASP e 500 " (cutoff:3.500A) Processing helix chain 'e' and resid 510 through 529 Processing helix chain 'g' and resid 19 through 36 removed outlier: 4.425A pdb=" N ILE g 36 " --> pdb=" O ILE g 32 " (cutoff:3.500A) Processing helix chain 'g' and resid 61 through 69 removed outlier: 3.550A pdb=" N ILE g 65 " --> pdb=" O ASP g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 73 through 91 Processing helix chain 'g' and resid 93 through 113 removed outlier: 3.635A pdb=" N ILE g 98 " --> pdb=" O THR g 94 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU g 109 " --> pdb=" O LEU g 105 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N HIS g 110 " --> pdb=" O SER g 106 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE g 111 " --> pdb=" O VAL g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 140 removed outlier: 3.755A pdb=" N VAL g 121 " --> pdb=" O HIS g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 147 through 159 Processing helix chain 'g' and resid 167 through 181 removed outlier: 3.767A pdb=" N ALA g 171 " --> pdb=" O TRP g 167 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN g 173 " --> pdb=" O SER g 169 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS g 180 " --> pdb=" O LEU g 176 " (cutoff:3.500A) Processing helix chain 'g' and resid 207 through 211 Processing helix chain 'g' and resid 275 through 281 Processing helix chain 'g' and resid 282 through 284 No H-bonds generated for 'chain 'g' and resid 282 through 284' Processing helix chain 'g' and resid 296 through 307 Processing helix chain 'g' and resid 315 through 327 removed outlier: 4.152A pdb=" N ARG g 321 " --> pdb=" O THR g 317 " (cutoff:3.500A) Processing helix chain 'g' and resid 353 through 357 Processing helix chain 'g' and resid 379 through 403 removed outlier: 4.636A pdb=" N LEU g 383 " --> pdb=" O SER g 379 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER g 384 " --> pdb=" O LYS g 380 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLU g 385 " --> pdb=" O GLU g 381 " (cutoff:3.500A) Processing helix chain 'g' and resid 411 through 428 removed outlier: 3.650A pdb=" N LYS g 426 " --> pdb=" O THR g 422 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA g 427 " --> pdb=" O GLU g 423 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET g 428 " --> pdb=" O LYS g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 432 through 443 removed outlier: 3.756A pdb=" N ALA g 440 " --> pdb=" O TYR g 436 " (cutoff:3.500A) Processing helix chain 'g' and resid 444 through 453 Processing helix chain 'g' and resid 457 through 471 removed outlier: 3.683A pdb=" N LEU g 461 " --> pdb=" O SER g 457 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN g 471 " --> pdb=" O ALA g 467 " (cutoff:3.500A) Processing helix chain 'g' and resid 488 through 493 Processing helix chain 'g' and resid 498 through 517 Processing helix chain 'h' and resid 18 through 35 removed outlier: 3.577A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 40 removed outlier: 3.952A pdb=" N LEU h 40 " --> pdb=" O ARG h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 68 Processing helix chain 'h' and resid 73 through 94 removed outlier: 4.172A pdb=" N ILE h 86 " --> pdb=" O THR h 82 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 113 Processing helix chain 'h' and resid 114 through 116 No H-bonds generated for 'chain 'h' and resid 114 through 116' Processing helix chain 'h' and resid 121 through 142 removed outlier: 3.540A pdb=" N ILE h 125 " --> pdb=" O HIS h 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS h 141 " --> pdb=" O VAL h 137 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU h 142 " --> pdb=" O ASN h 138 " (cutoff:3.500A) Processing helix chain 'h' and resid 156 through 164 Processing helix chain 'h' and resid 165 through 168 Processing helix chain 'h' and resid 175 through 190 removed outlier: 3.550A pdb=" N PHE h 179 " --> pdb=" O GLN h 175 " (cutoff:3.500A) Processing helix chain 'h' and resid 268 through 281 Processing helix chain 'h' and resid 282 through 285 Processing helix chain 'h' and resid 300 through 302 No H-bonds generated for 'chain 'h' and resid 300 through 302' Processing helix chain 'h' and resid 303 through 311 removed outlier: 3.727A pdb=" N ARG h 310 " --> pdb=" O TYR h 306 " (cutoff:3.500A) Processing helix chain 'h' and resid 319 through 330 Processing helix chain 'h' and resid 382 through 384 No H-bonds generated for 'chain 'h' and resid 382 through 384' Processing helix chain 'h' and resid 385 through 406 removed outlier: 4.104A pdb=" N HIS h 394 " --> pdb=" O GLU h 390 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP h 395 " --> pdb=" O ARG h 391 " (cutoff:3.500A) Processing helix chain 'h' and resid 414 through 429 removed outlier: 3.846A pdb=" N MET h 418 " --> pdb=" O GLY h 414 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG h 429 " --> pdb=" O ARG h 425 " (cutoff:3.500A) Processing helix chain 'h' and resid 434 through 446 removed outlier: 3.684A pdb=" N LEU h 438 " --> pdb=" O LYS h 434 " (cutoff:3.500A) Processing helix chain 'h' and resid 447 through 457 Processing helix chain 'h' and resid 460 through 475 Processing helix chain 'h' and resid 500 through 519 Processing helix chain 'q' and resid 30 through 42 Processing helix chain 'q' and resid 68 through 76 Processing helix chain 'q' and resid 80 through 97 removed outlier: 3.587A pdb=" N MET q 85 " --> pdb=" O PRO q 81 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE q 86 " --> pdb=" O ALA q 82 " (cutoff:3.500A) Processing helix chain 'q' and resid 100 through 122 Processing helix chain 'q' and resid 124 through 143 removed outlier: 3.549A pdb=" N GLU q 141 " --> pdb=" O ARG q 137 " (cutoff:3.500A) Processing helix chain 'q' and resid 144 through 146 No H-bonds generated for 'chain 'q' and resid 144 through 146' Processing helix chain 'q' and resid 156 through 164 Processing helix chain 'q' and resid 164 through 172 removed outlier: 4.228A pdb=" N ILE q 168 " --> pdb=" O LEU q 164 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 189 removed outlier: 3.950A pdb=" N LEU q 182 " --> pdb=" O PHE q 178 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS q 187 " --> pdb=" O ILE q 183 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL q 188 " --> pdb=" O ALA q 184 " (cutoff:3.500A) Processing helix chain 'q' and resid 198 through 200 No H-bonds generated for 'chain 'q' and resid 198 through 200' Processing helix chain 'q' and resid 211 through 215 Processing helix chain 'q' and resid 263 through 284 Processing helix chain 'q' and resid 298 through 308 Processing helix chain 'q' and resid 319 through 329 removed outlier: 3.755A pdb=" N ARG q 323 " --> pdb=" O TRP q 319 " (cutoff:3.500A) Processing helix chain 'q' and resid 382 through 404 removed outlier: 3.925A pdb=" N ASP q 387 " --> pdb=" O ASN q 383 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR q 398 " --> pdb=" O ASP q 394 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG q 404 " --> pdb=" O LYS q 400 " (cutoff:3.500A) Processing helix chain 'q' and resid 413 through 429 removed outlier: 4.100A pdb=" N GLU q 428 " --> pdb=" O THR q 424 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 434 through 446 Processing helix chain 'q' and resid 446 through 455 removed outlier: 3.711A pdb=" N ARG q 450 " --> pdb=" O GLU q 446 " (cutoff:3.500A) Processing helix chain 'q' and resid 459 through 474 removed outlier: 3.763A pdb=" N GLN q 472 " --> pdb=" O TYR q 468 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU q 473 " --> pdb=" O ALA q 469 " (cutoff:3.500A) Processing helix chain 'q' and resid 492 through 496 Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'A' and resid 16 through 34 removed outlier: 4.543A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.532A pdb=" N ILE A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 86 Processing helix chain 'A' and resid 89 through 109 Processing helix chain 'A' and resid 113 through 135 removed outlier: 3.542A pdb=" N ARG A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 164 through 179 removed outlier: 3.691A pdb=" N ASP A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 175 " --> pdb=" O MET A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 204 through 208 removed outlier: 3.623A pdb=" N GLU A 207 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 208 " --> pdb=" O GLN A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 208' Processing helix chain 'A' and resid 272 through 282 Processing helix chain 'A' and resid 295 through 303 removed outlier: 4.388A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 322 Processing helix chain 'A' and resid 385 through 404 Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.567A pdb=" N ASN A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 445 Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 459 through 477 removed outlier: 3.585A pdb=" N ALA A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 507 through 527 removed outlier: 3.536A pdb=" N ILE A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 41 removed outlier: 4.458A pdb=" N SER B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 73 removed outlier: 3.676A pdb=" N ILE B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 98 through 119 Processing helix chain 'B' and resid 122 through 145 removed outlier: 3.845A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 167 removed outlier: 3.634A pdb=" N THR B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 190 Processing helix chain 'B' and resid 264 through 283 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 316 through 326 Processing helix chain 'B' and resid 380 through 403 removed outlier: 4.025A pdb=" N ASP B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 428 Processing helix chain 'B' and resid 431 through 453 removed outlier: 3.875A pdb=" N ALA B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Proline residue: B 447 - end of helix Processing helix chain 'B' and resid 457 through 472 removed outlier: 4.019A pdb=" N GLU B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.656A pdb=" N SER D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 removed outlier: 3.787A pdb=" N LEU D 52 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 105 through 126 removed outlier: 3.795A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 151 removed outlier: 3.600A pdb=" N ILE D 133 " --> pdb=" O HIS D 129 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET D 151 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 172 removed outlier: 3.510A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 Proline residue: D 185 - end of helix removed outlier: 3.563A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 284 through 294 Processing helix chain 'D' and resid 310 through 317 Processing helix chain 'D' and resid 329 through 341 removed outlier: 4.155A pdb=" N GLU D 334 " --> pdb=" O ARG D 330 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE D 335 " --> pdb=" O GLU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 395 through 418 removed outlier: 4.245A pdb=" N ALA D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 443 removed outlier: 3.826A pdb=" N THR D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 458 removed outlier: 4.288A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 468 Processing helix chain 'D' and resid 472 through 486 Processing helix chain 'D' and resid 495 through 498 removed outlier: 3.974A pdb=" N GLY D 498 " --> pdb=" O VAL D 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'D' and resid 503 through 507 Processing helix chain 'D' and resid 512 through 532 Processing helix chain 'E' and resid 30 through 49 removed outlier: 4.086A pdb=" N LEU E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 81 removed outlier: 3.717A pdb=" N ILE E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 96 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 129 through 152 Processing helix chain 'E' and resid 161 through 173 removed outlier: 3.516A pdb=" N ILE E 166 " --> pdb=" O THR E 162 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 195 removed outlier: 4.353A pdb=" N ARG E 183 " --> pdb=" O ASN E 179 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLN E 184 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLU E 187 " --> pdb=" O ARG E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 209 removed outlier: 3.767A pdb=" N ILE E 209 " --> pdb=" O PHE E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 296 Processing helix chain 'E' and resid 307 through 317 removed outlier: 3.790A pdb=" N ASN E 311 " --> pdb=" O ASP E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 335 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.696A pdb=" N LEU E 353 " --> pdb=" O ALA E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 415 Processing helix chain 'E' and resid 423 through 437 Processing helix chain 'E' and resid 443 through 456 removed outlier: 3.612A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.625A pdb=" N MET E 460 " --> pdb=" O GLU E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 484 Processing helix chain 'E' and resid 500 through 505 removed outlier: 3.973A pdb=" N GLN E 504 " --> pdb=" O ASP E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 529 Processing helix chain 'G' and resid 18 through 34 removed outlier: 4.182A pdb=" N GLN G 22 " --> pdb=" O GLY G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 69 Processing helix chain 'G' and resid 73 through 91 Processing helix chain 'G' and resid 93 through 113 removed outlier: 3.814A pdb=" N GLU G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N HIS G 110 " --> pdb=" O SER G 106 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE G 111 " --> pdb=" O VAL G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 140 removed outlier: 3.683A pdb=" N VAL G 121 " --> pdb=" O HIS G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 158 Processing helix chain 'G' and resid 167 through 179 removed outlier: 4.174A pdb=" N ASN G 173 " --> pdb=" O SER G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 211 Processing helix chain 'G' and resid 275 through 285 removed outlier: 3.512A pdb=" N GLN G 283 " --> pdb=" O GLU G 279 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU G 284 " --> pdb=" O ASP G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 306 removed outlier: 3.728A pdb=" N ALA G 306 " --> pdb=" O TYR G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 327 removed outlier: 4.231A pdb=" N ARG G 321 " --> pdb=" O THR G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 342 removed outlier: 4.142A pdb=" N VAL G 342 " --> pdb=" O GLU G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 403 removed outlier: 4.440A pdb=" N LEU G 383 " --> pdb=" O SER G 379 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER G 384 " --> pdb=" O LYS G 380 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU G 385 " --> pdb=" O GLU G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 425 Processing helix chain 'G' and resid 432 through 444 removed outlier: 3.636A pdb=" N ALA G 440 " --> pdb=" O TYR G 436 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU G 444 " --> pdb=" O ALA G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 453 Processing helix chain 'G' and resid 459 through 471 removed outlier: 3.940A pdb=" N GLN G 471 " --> pdb=" O ALA G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 493 Processing helix chain 'G' and resid 498 through 517 Processing helix chain 'H' and resid 17 through 35 Processing helix chain 'H' and resid 36 through 40 removed outlier: 3.534A pdb=" N THR H 39 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU H 40 " --> pdb=" O ARG H 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 36 through 40' Processing helix chain 'H' and resid 61 through 69 removed outlier: 3.772A pdb=" N ILE H 65 " --> pdb=" O ASP H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 90 removed outlier: 3.741A pdb=" N GLU H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL H 90 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 114 removed outlier: 3.739A pdb=" N LEU H 99 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU H 100 " --> pdb=" O SER H 96 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 117 through 137 removed outlier: 3.817A pdb=" N LYS H 137 " --> pdb=" O VAL H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 161 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 168 through 186 removed outlier: 4.027A pdb=" N PHE H 174 " --> pdb=" O GLN H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 266 through 285 removed outlier: 3.926A pdb=" N ILE H 281 " --> pdb=" O LYS H 277 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N HIS H 282 " --> pdb=" O LEU H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 298 No H-bonds generated for 'chain 'H' and resid 296 through 298' Processing helix chain 'H' and resid 299 through 304 Processing helix chain 'H' and resid 305 through 307 No H-bonds generated for 'chain 'H' and resid 305 through 307' Processing helix chain 'H' and resid 315 through 324 removed outlier: 4.087A pdb=" N MET H 324 " --> pdb=" O LYS H 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 389 removed outlier: 3.891A pdb=" N GLU H 384 " --> pdb=" O GLN H 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 389 through 402 Processing helix chain 'H' and resid 410 through 425 removed outlier: 3.811A pdb=" N ARG H 425 " --> pdb=" O ARG H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 442 removed outlier: 3.805A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 454 removed outlier: 3.594A pdb=" N ARG H 447 " --> pdb=" O GLU H 443 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 471 removed outlier: 4.086A pdb=" N ILE H 460 " --> pdb=" O ASP H 456 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 516 removed outlier: 3.668A pdb=" N VAL H 516 " --> pdb=" O LEU H 512 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 45 removed outlier: 3.684A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 76 Processing helix chain 'Q' and resid 80 through 98 Processing helix chain 'Q' and resid 100 through 122 Processing helix chain 'Q' and resid 124 through 143 removed outlier: 3.533A pdb=" N GLU Q 141 " --> pdb=" O ARG Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 146 No H-bonds generated for 'chain 'Q' and resid 144 through 146' Processing helix chain 'Q' and resid 156 through 172 removed outlier: 3.736A pdb=" N SER Q 162 " --> pdb=" O ASP Q 158 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE Q 168 " --> pdb=" O LEU Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 189 removed outlier: 3.875A pdb=" N LEU Q 182 " --> pdb=" O PHE Q 178 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL Q 188 " --> pdb=" O ALA Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 198 through 200 No H-bonds generated for 'chain 'Q' and resid 198 through 200' Processing helix chain 'Q' and resid 211 through 215 removed outlier: 3.563A pdb=" N SER Q 214 " --> pdb=" O GLY Q 211 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 285 Processing helix chain 'Q' and resid 286 through 288 No H-bonds generated for 'chain 'Q' and resid 286 through 288' Processing helix chain 'Q' and resid 298 through 308 Processing helix chain 'Q' and resid 320 through 329 Processing helix chain 'Q' and resid 354 through 358 removed outlier: 4.038A pdb=" N THR Q 358 " --> pdb=" O VAL Q 355 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 383 No H-bonds generated for 'chain 'Q' and resid 381 through 383' Processing helix chain 'Q' and resid 384 through 405 removed outlier: 3.945A pdb=" N ILE Q 388 " --> pdb=" O LEU Q 384 " (cutoff:3.500A) Processing helix chain 'Q' and resid 413 through 428 removed outlier: 4.234A pdb=" N GLU Q 428 " --> pdb=" O THR Q 424 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 455 removed outlier: 4.548A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE Q 448 " --> pdb=" O ALA Q 444 " (cutoff:3.500A) Proline residue: Q 449 - end of helix Processing helix chain 'Q' and resid 459 through 471 Processing helix chain 'Q' and resid 501 through 520 Processing sheet with id=AA1, first strand: chain 'z' and resid 45 through 48 Processing sheet with id=AA2, first strand: chain 'z' and resid 191 through 193 removed outlier: 6.886A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N ARG z 208 " --> pdb=" O LYS z 365 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS z 365 " --> pdb=" O ARG z 208 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR z 361 " --> pdb=" O LEU z 212 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N CYS z 366 " --> pdb=" O ALA z 347 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA z 347 " --> pdb=" O CYS z 366 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ILE z 292 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'z' and resid 191 through 193 removed outlier: 6.886A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N ARG z 208 " --> pdb=" O LYS z 365 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS z 365 " --> pdb=" O ARG z 208 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR z 361 " --> pdb=" O LEU z 212 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU z 358 " --> pdb=" O LEU z 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'z' and resid 407 through 409 Processing sheet with id=AA5, first strand: chain 'z' and resid 478 through 479 Processing sheet with id=AA6, first strand: chain 'z' and resid 521 through 523 removed outlier: 6.666A pdb=" N MET z 522 " --> pdb=" O LEU g 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id=AA8, first strand: chain 'Z' and resid 139 through 140 Processing sheet with id=AA9, first strand: chain 'Z' and resid 206 through 207 Processing sheet with id=AB1, first strand: chain 'Z' and resid 211 through 212 removed outlier: 3.625A pdb=" N THR Z 361 " --> pdb=" O LEU Z 212 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N CYS Z 366 " --> pdb=" O ALA Z 347 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA Z 347 " --> pdb=" O CYS Z 366 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU Z 349 " --> pdb=" O GLU Z 226 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLU Z 226 " --> pdb=" O LEU Z 349 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Z' and resid 232 through 233 Processing sheet with id=AB3, first strand: chain 'Z' and resid 478 through 479 Processing sheet with id=AB4, first strand: chain 'Z' and resid 518 through 522 removed outlier: 4.219A pdb=" N VAL Z 518 " --> pdb=" O MET G 46 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N MET G 48 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU Z 520 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU G 50 " --> pdb=" O GLU Z 520 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N MET Z 522 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR G 59 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU G 49 " --> pdb=" O VAL G 57 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 54 through 55 removed outlier: 3.645A pdb=" N THR a 55 " --> pdb=" O LYS a 43 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASP a 42 " --> pdb=" O ASP g 519 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'a' and resid 195 through 199 removed outlier: 6.697A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'a' and resid 213 through 214 removed outlier: 3.633A pdb=" N TYR a 214 " --> pdb=" O ILE a 364 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE a 364 " --> pdb=" O TYR a 214 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU a 360 " --> pdb=" O ARG a 355 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ARG a 355 " --> pdb=" O GLU a 360 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N ILE a 362 " --> pdb=" O GLN a 353 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLN a 353 " --> pdb=" O ILE a 362 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE a 364 " --> pdb=" O VAL a 351 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL a 351 " --> pdb=" O ILE a 364 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ASN a 366 " --> pdb=" O GLU a 349 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY a 346 " --> pdb=" O ILE a 234 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYS a 233 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU a 287 " --> pdb=" O LYS a 233 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA a 235 " --> pdb=" O LEU a 287 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'a' and resid 408 through 410 Processing sheet with id=AB9, first strand: chain 'a' and resid 486 through 489 removed outlier: 3.788A pdb=" N LYS a 494 " --> pdb=" O ASP a 489 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 527 through 528 Processing sheet with id=AC2, first strand: chain 'b' and resid 63 through 64 removed outlier: 3.587A pdb=" N THR b 64 " --> pdb=" O LYS b 50 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS b 50 " --> pdb=" O THR b 64 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AC4, first strand: chain 'b' and resid 200 through 205 removed outlier: 3.657A pdb=" N LYS b 204 " --> pdb=" O LEU b 375 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'b' and resid 289 through 292 removed outlier: 3.572A pdb=" N PHE b 290 " --> pdb=" O MET b 310 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b' and resid 476 through 479 removed outlier: 3.594A pdb=" N THR b 484 " --> pdb=" O ASP b 479 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'd' and resid 153 through 154 Processing sheet with id=AC8, first strand: chain 'd' and resid 212 through 214 removed outlier: 4.314A pdb=" N GLY d 392 " --> pdb=" O LYS d 213 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'd' and resid 228 through 229 removed outlier: 3.599A pdb=" N LYS d 375 " --> pdb=" O GLU d 363 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU d 363 " --> pdb=" O LYS d 375 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR d 377 " --> pdb=" O LEU d 361 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU d 361 " --> pdb=" O THR d 377 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 248 through 249 removed outlier: 5.699A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'd' and resid 366 through 367 Processing sheet with id=AD3, first strand: chain 'd' and resid 491 through 494 removed outlier: 3.914A pdb=" N GLY d 492 " --> pdb=" O SER d 501 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER d 501 " --> pdb=" O GLY d 492 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'e' and resid 59 through 62 Processing sheet with id=AD5, first strand: chain 'e' and resid 248 through 250 Processing sheet with id=AD6, first strand: chain 'e' and resid 418 through 419 Processing sheet with id=AD7, first strand: chain 'e' and resid 530 through 534 removed outlier: 6.354A pdb=" N ASP h 46 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP e 532 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL h 50 " --> pdb=" O ARG e 534 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'g' and resid 141 through 142 Processing sheet with id=AD9, first strand: chain 'g' and resid 199 through 204 removed outlier: 6.098A pdb=" N ARG g 199 " --> pdb=" O ILE g 373 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU g 375 " --> pdb=" O ARG g 199 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU g 201 " --> pdb=" O LEU g 375 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLY g 377 " --> pdb=" O GLU g 201 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE g 203 " --> pdb=" O GLY g 377 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'g' and resid 218 through 219 removed outlier: 3.582A pdb=" N PHE g 359 " --> pdb=" O LYS g 352 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS g 352 " --> pdb=" O PHE g 359 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU g 348 " --> pdb=" O THR g 363 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'g' and resid 238 through 239 Processing sheet with id=AE3, first strand: chain 'g' and resid 478 through 479 Processing sheet with id=AE4, first strand: chain 'h' and resid 145 through 146 Processing sheet with id=AE5, first strand: chain 'h' and resid 202 through 203 removed outlier: 7.592A pdb=" N LYS h 202 " --> pdb=" O LEU h 378 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'h' and resid 220 through 221 removed outlier: 3.658A pdb=" N THR h 355 " --> pdb=" O TYR h 362 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'h' and resid 313 through 316 removed outlier: 6.134A pdb=" N VAL h 293 " --> pdb=" O ALA h 315 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA h 242 " --> pdb=" O LEU h 294 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'h' and resid 479 through 481 removed outlier: 3.693A pdb=" N ALA h 489 " --> pdb=" O GLY h 480 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'h' and resid 523 through 524 Processing sheet with id=AF1, first strand: chain 'q' and resid 202 through 208 removed outlier: 3.947A pdb=" N GLY q 379 " --> pdb=" O ILE q 207 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER q 216 " --> pdb=" O VAL q 376 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'q' and resid 221 through 223 removed outlier: 3.573A pdb=" N PHE q 223 " --> pdb=" O VAL q 361 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'q' and resid 239 through 242 removed outlier: 6.412A pdb=" N ALA q 240 " --> pdb=" O VAL q 292 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL q 291 " --> pdb=" O VAL q 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'q' and resid 408 through 410 Processing sheet with id=AF5, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AF6, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.601A pdb=" N THR A 55 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP A 42 " --> pdb=" O ILE G 518 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP G 520 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 197 through 199 removed outlier: 6.393A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 213 through 214 removed outlier: 3.576A pdb=" N TYR A 214 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 287 through 288 removed outlier: 6.913A pdb=" N MET A 306 " --> pdb=" O THR A 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'A' and resid 355 through 356 Processing sheet with id=AG2, first strand: chain 'A' and resid 408 through 410 Processing sheet with id=AG3, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.588A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 62 through 64 removed outlier: 4.100A pdb=" N MET B 62 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AG6, first strand: chain 'B' and resid 201 through 205 removed outlier: 6.633A pdb=" N ILE B 202 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLY B 377 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LYS B 204 " --> pdb=" O GLY B 377 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 374 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR B 213 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 231 through 232 Processing sheet with id=AG8, first strand: chain 'B' and resid 477 through 479 removed outlier: 3.522A pdb=" N THR B 484 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AH1, first strand: chain 'D' and resid 228 through 229 removed outlier: 3.601A pdb=" N VAL D 365 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS D 375 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU D 363 " --> pdb=" O LYS D 375 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 246 through 249 removed outlier: 3.549A pdb=" N GLY D 247 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU D 299 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE D 249 " --> pdb=" O LEU D 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.672A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 59 through 62 Processing sheet with id=AH5, first strand: chain 'E' and resid 248 through 251 removed outlier: 3.683A pdb=" N ILE E 301 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 418 through 419 Processing sheet with id=AH7, first strand: chain 'E' and resid 530 through 534 removed outlier: 4.030A pdb=" N ILE E 530 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU H 48 " --> pdb=" O ILE E 530 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP E 532 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS H 47 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER H 59 " --> pdb=" O LYS H 47 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AH9, first strand: chain 'G' and resid 183 through 184 removed outlier: 3.764A pdb=" N ILE G 192 " --> pdb=" O PHE G 184 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 199 through 204 removed outlier: 6.114A pdb=" N ARG G 199 " --> pdb=" O ILE G 373 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU G 375 " --> pdb=" O ARG G 199 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU G 201 " --> pdb=" O LEU G 375 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLY G 377 " --> pdb=" O GLU G 201 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE G 203 " --> pdb=" O GLY G 377 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 216 through 219 removed outlier: 3.682A pdb=" N LEU G 348 " --> pdb=" O THR G 363 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 288 through 290 removed outlier: 5.963A pdb=" N VAL G 238 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG G 329 " --> pdb=" O ILE G 237 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 478 through 479 Processing sheet with id=AI5, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AI6, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.577A pdb=" N GLY H 196 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU H 374 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LYS H 198 " --> pdb=" O LEU H 374 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLY H 376 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL H 200 " --> pdb=" O GLY H 376 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'H' and resid 216 through 217 Processing sheet with id=AI8, first strand: chain 'H' and resid 309 through 310 removed outlier: 6.045A pdb=" N ALA H 238 " --> pdb=" O LEU H 290 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE H 237 " --> pdb=" O SER H 329 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLN H 331 " --> pdb=" O ILE H 237 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU H 239 " --> pdb=" O GLN H 331 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'H' and resid 475 through 477 Processing sheet with id=AJ1, first strand: chain 'H' and resid 519 through 520 Processing sheet with id=AJ2, first strand: chain 'Q' and resid 202 through 208 removed outlier: 3.520A pdb=" N ARG Q 203 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY Q 379 " --> pdb=" O ILE Q 207 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'Q' and resid 221 through 223 removed outlier: 3.896A pdb=" N TYR Q 351 " --> pdb=" O VAL Q 362 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS Q 364 " --> pdb=" O SER Q 349 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER Q 349 " --> pdb=" O LYS Q 364 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Q' and resid 290 through 292 removed outlier: 5.759A pdb=" N VAL Q 291 " --> pdb=" O VAL Q 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'Q' and resid 408 through 410 Processing sheet with id=AJ6, first strand: chain 'Q' and resid 478 through 480 3131 hydrogen bonds defined for protein. 9099 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: 24.87 Time building geometry restraints manager: 14.00 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: 20351 1.34 - 1.46: 9744 1.46 - 1.58: 30446 1.58 - 1.70: 48 1.70 - 1.82: 618 Bond restraints: 61207 Sorted by residual: bond pdb=" CA PRO Q 192 " pdb=" CB PRO Q 192 " ideal model delta sigma weight residual 1.531 1.519 0.012 6.20e-03 2.60e+04 4.06e+00 bond pdb=" C4 ADP Q5000 " pdb=" C5 ADP Q5000 " ideal model delta sigma weight residual 1.490 1.462 0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C4 ADP G 601 " pdb=" C5 ADP G 601 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C ARG H 152 " pdb=" O ARG H 152 " ideal model delta sigma weight residual 1.236 1.254 -0.019 1.47e-02 4.63e+03 1.60e+00 bond pdb=" C4 ADP q5000 " pdb=" C5 ADP q5000 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.52e+00 ... (remaining 61202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 81147 2.08 - 4.16: 1201 4.16 - 6.24: 273 6.24 - 8.32: 38 8.32 - 10.40: 5 Bond angle restraints: 82664 Sorted by residual: angle pdb=" N ILE E 159 " pdb=" CA ILE E 159 " pdb=" C ILE E 159 " ideal model delta sigma weight residual 111.62 107.61 4.01 7.90e-01 1.60e+00 2.58e+01 angle pdb=" N VAL h 147 " pdb=" CA VAL h 147 " pdb=" C VAL h 147 " ideal model delta sigma weight residual 113.20 108.90 4.30 9.60e-01 1.09e+00 2.01e+01 angle pdb=" N THR a 371 " pdb=" CA THR a 371 " pdb=" C THR a 371 " ideal model delta sigma weight residual 114.75 109.21 5.54 1.26e+00 6.30e-01 1.93e+01 angle pdb=" C GLN H 151 " pdb=" N ARG H 152 " pdb=" CA ARG H 152 " ideal model delta sigma weight residual 122.31 129.69 -7.38 2.00e+00 2.50e-01 1.36e+01 angle pdb=" C VAL D 508 " pdb=" N VAL D 509 " pdb=" CA VAL D 509 " ideal model delta sigma weight residual 121.97 128.59 -6.62 1.80e+00 3.09e-01 1.35e+01 ... (remaining 82659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 37108 35.93 - 71.86: 658 71.86 - 107.79: 52 107.79 - 143.72: 14 143.72 - 179.65: 4 Dihedral angle restraints: 37836 sinusoidal: 15184 harmonic: 22652 Sorted by residual: dihedral pdb=" C5' ADP D 601 " pdb=" O5' ADP D 601 " pdb=" PA ADP D 601 " pdb=" O2A ADP D 601 " ideal model delta sinusoidal sigma weight residual 300.00 120.35 179.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PB ADP z 601 " pdb=" PA ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 111.88 -171.88 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP Q5000 " pdb=" O3A ADP Q5000 " pdb=" PB ADP Q5000 " pdb=" PA ADP Q5000 " ideal model delta sinusoidal sigma weight residual 300.00 152.23 147.77 1 2.00e+01 2.50e-03 4.43e+01 ... (remaining 37833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 7166 0.043 - 0.086: 2013 0.086 - 0.129: 685 0.129 - 0.172: 43 0.172 - 0.215: 7 Chirality restraints: 9914 Sorted by residual: chirality pdb=" CB ILE h 172 " pdb=" CA ILE h 172 " pdb=" CG1 ILE h 172 " pdb=" CG2 ILE h 172 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE E 209 " pdb=" CA ILE E 209 " pdb=" CG1 ILE E 209 " pdb=" CG2 ILE E 209 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CA MET g 304 " pdb=" N MET g 304 " pdb=" C MET g 304 " pdb=" CB MET g 304 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 9911 not shown) Planarity restraints: 10525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO Q 338 " 0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO Q 339 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO Q 339 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO Q 339 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU Z 184 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO Z 185 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO Z 185 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO Z 185 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS e 535 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO e 536 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO e 536 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO e 536 " -0.028 5.00e-02 4.00e+02 ... (remaining 10522 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 962 2.64 - 3.20: 59390 3.20 - 3.77: 98927 3.77 - 4.33: 128314 4.33 - 4.90: 206893 Nonbonded interactions: 494486 Sorted by model distance: nonbonded pdb=" OH TYR d 449 " pdb=" OE1 GLU E 456 " model vdw 2.072 3.040 nonbonded pdb=" OH TYR a 181 " pdb=" OG1 THR a 371 " model vdw 2.093 3.040 nonbonded pdb=" OE2 GLU Q 273 " pdb=" OH TYR Q 304 " model vdw 2.097 3.040 nonbonded pdb=" OG SER q 215 " pdb=" O VAL q 376 " model vdw 2.113 3.040 nonbonded pdb=" O LYS q 400 " pdb=" OG1 THR q 403 " model vdw 2.132 3.040 ... (remaining 494481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 528 or resid 601)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 24 through 243 or resid 263 through 520 or resid 601)) selection = chain 'b' } ncs_group { reference = chain 'D' selection = (chain 'd' and (resid 30 through 256 or resid 280 through 539 or resid 601)) } ncs_group { reference = (chain 'E' and (resid 25 through 540 or resid 601)) selection = (chain 'e' and (resid 25 through 540 or resid 601)) } ncs_group { reference = (chain 'G' and (resid 17 through 241 or resid 274 through 525 or resid 601)) selection = chain 'g' } ncs_group { reference = chain 'H' selection = (chain 'h' and (resid 12 through 250 or resid 266 through 529 or resid 601)) } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'z' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 1.820 Check model and map are aligned: 0.350 Set scattering table: 0.440 Process input model: 108.440 Find NCS groups from input model: 4.920 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 61207 Z= 0.213 Angle : 0.653 10.398 82664 Z= 0.325 Chirality : 0.044 0.215 9914 Planarity : 0.003 0.081 10525 Dihedral : 14.918 179.654 23150 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.56 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.39 (0.10), residues: 7817 helix: 1.20 (0.08), residues: 3955 sheet: -1.45 (0.24), residues: 506 loop : -1.92 (0.10), residues: 3356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 130 HIS 0.010 0.001 HIS z 214 PHE 0.024 0.001 PHE Q 223 TYR 0.024 0.001 TYR A 131 ARG 0.011 0.000 ARG d 539 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 548 time to evaluate : 5.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: z 196 MET cc_start: 0.8414 (ppp) cc_final: 0.8098 (ppp) REVERT: Z 190 MET cc_start: 0.8085 (ttt) cc_final: 0.7881 (ttt) REVERT: Z 212 LEU cc_start: 0.9192 (tp) cc_final: 0.8991 (tp) REVERT: Z 213 ASP cc_start: 0.8075 (m-30) cc_final: 0.7470 (m-30) REVERT: a 105 ASP cc_start: 0.8571 (t0) cc_final: 0.8111 (t70) REVERT: a 171 MET cc_start: 0.7457 (ttt) cc_final: 0.6792 (tmm) REVERT: b 391 HIS cc_start: 0.9200 (t-90) cc_final: 0.8881 (t70) REVERT: b 445 MET cc_start: 0.8597 (ttm) cc_final: 0.8229 (ttm) REVERT: b 480 MET cc_start: 0.7901 (mpp) cc_final: 0.7389 (mmm) REVERT: d 81 MET cc_start: 0.7618 (tpt) cc_final: 0.7189 (tpt) REVERT: d 458 MET cc_start: 0.9344 (mmt) cc_final: 0.9090 (mmt) REVERT: e 29 MET cc_start: 0.8160 (ppp) cc_final: 0.7782 (ppp) REVERT: e 39 MET cc_start: 0.8573 (mmp) cc_final: 0.8145 (mmp) REVERT: e 42 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8481 (mtmm) REVERT: g 396 VAL cc_start: 0.8787 (t) cc_final: 0.8503 (t) REVERT: q 164 LEU cc_start: 0.9166 (mm) cc_final: 0.8886 (tp) REVERT: q 300 MET cc_start: 0.5136 (ttt) cc_final: 0.4089 (tmm) REVERT: A 239 PHE cc_start: 0.5709 (m-10) cc_final: 0.5474 (m-80) REVERT: B 310 MET cc_start: 0.5052 (tmm) cc_final: 0.4323 (ptp) REVERT: B 353 MET cc_start: 0.7344 (mmp) cc_final: 0.5387 (tpp) REVERT: E 119 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8477 (mm-30) REVERT: E 122 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8699 (tm-30) REVERT: E 474 MET cc_start: 0.8758 (tmm) cc_final: 0.8384 (tmm) REVERT: E 526 MET cc_start: 0.8945 (ttp) cc_final: 0.8354 (tmm) REVERT: G 228 MET cc_start: 0.2323 (ppp) cc_final: 0.1788 (ppp) REVERT: G 359 PHE cc_start: 0.8298 (m-10) cc_final: 0.7954 (m-80) REVERT: H 160 MET cc_start: 0.8885 (ptt) cc_final: 0.8588 (ppp) REVERT: Q 95 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8305 (tm-30) outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.5175 time to fit residues: 498.6313 Evaluate side-chains 452 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 5.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 658 optimal weight: 0.7980 chunk 591 optimal weight: 0.9990 chunk 328 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 chunk 398 optimal weight: 0.6980 chunk 315 optimal weight: 50.0000 chunk 611 optimal weight: 50.0000 chunk 236 optimal weight: 2.9990 chunk 371 optimal weight: 30.0000 chunk 455 optimal weight: 6.9990 chunk 708 optimal weight: 30.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 214 HIS ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 GLN b 426 ASN d 347 HIS d 406 HIS ** d 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 384 GLN h 526 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 110 HIS ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 399 ASN ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 523 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 61207 Z= 0.218 Angle : 0.647 14.056 82664 Z= 0.317 Chirality : 0.044 0.309 9914 Planarity : 0.004 0.081 10525 Dihedral : 8.236 161.192 8522 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.22 % Favored : 93.71 % Rotamer: Outliers : 0.67 % Allowed : 8.46 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.44 (0.10), residues: 7817 helix: 1.17 (0.08), residues: 4002 sheet: -1.49 (0.23), residues: 545 loop : -1.99 (0.10), residues: 3270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 319 HIS 0.010 0.001 HIS z 214 PHE 0.030 0.001 PHE B 179 TYR 0.019 0.001 TYR Z 229 ARG 0.006 0.000 ARG d 539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 483 time to evaluate : 5.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 190 MET cc_start: 0.8237 (ttt) cc_final: 0.7851 (ttt) REVERT: Z 212 LEU cc_start: 0.9182 (tp) cc_final: 0.8919 (tp) REVERT: Z 221 MET cc_start: 0.2100 (mmp) cc_final: 0.1749 (mmm) REVERT: a 105 ASP cc_start: 0.8603 (t0) cc_final: 0.8155 (t70) REVERT: a 110 GLN cc_start: 0.8973 (mt0) cc_final: 0.8749 (mt0) REVERT: b 445 MET cc_start: 0.8645 (ttm) cc_final: 0.8242 (ttm) REVERT: d 81 MET cc_start: 0.7615 (tpt) cc_final: 0.7148 (tpt) REVERT: d 192 MET cc_start: 0.7186 (mmm) cc_final: 0.6555 (mtm) REVERT: e 39 MET cc_start: 0.8579 (mmp) cc_final: 0.8123 (mmp) REVERT: e 42 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8470 (mtmm) REVERT: e 61 MET cc_start: 0.8018 (mmm) cc_final: 0.7620 (mmm) REVERT: e 468 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7763 (ptp) REVERT: e 474 MET cc_start: 0.9168 (tmm) cc_final: 0.8910 (tmm) REVERT: e 501 MET cc_start: 0.8225 (mpp) cc_final: 0.7830 (mpp) REVERT: g 53 MET cc_start: 0.7806 (ppp) cc_final: 0.7503 (ppp) REVERT: q 146 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8537 (pp) REVERT: q 300 MET cc_start: 0.5191 (ttt) cc_final: 0.4083 (tmm) REVERT: A 225 MET cc_start: 0.0139 (tpp) cc_final: -0.0090 (tpp) REVERT: A 239 PHE cc_start: 0.5647 (m-10) cc_final: 0.5431 (m-80) REVERT: B 213 TYR cc_start: 0.8698 (p90) cc_final: 0.8261 (p90) REVERT: B 310 MET cc_start: 0.5303 (tmm) cc_final: 0.4787 (ptp) REVERT: B 353 MET cc_start: 0.7465 (mmp) cc_final: 0.5504 (tpp) REVERT: E 93 GLU cc_start: 0.7874 (mp0) cc_final: 0.7450 (mp0) REVERT: E 119 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8644 (mm-30) REVERT: E 122 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8694 (tm-30) REVERT: E 239 MET cc_start: -0.0651 (ppp) cc_final: -0.1229 (ppp) REVERT: E 288 MET cc_start: -0.2601 (tpt) cc_final: -0.3241 (ptt) REVERT: E 474 MET cc_start: 0.8828 (tmm) cc_final: 0.8441 (tmm) REVERT: E 526 MET cc_start: 0.8906 (ttp) cc_final: 0.8654 (tmm) REVERT: G 228 MET cc_start: 0.3794 (ppp) cc_final: 0.3250 (ppp) REVERT: G 359 PHE cc_start: 0.8253 (m-10) cc_final: 0.7879 (m-80) REVERT: H 160 MET cc_start: 0.8880 (ptt) cc_final: 0.8602 (ppp) outliers start: 44 outliers final: 29 residues processed: 506 average time/residue: 0.5574 time to fit residues: 496.6489 Evaluate side-chains 461 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 430 time to evaluate : 5.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 214 HIS Chi-restraints excluded: chain z residue 360 PHE Chi-restraints excluded: chain Z residue 360 PHE Chi-restraints excluded: chain Z residue 376 ILE Chi-restraints excluded: chain a residue 62 LEU Chi-restraints excluded: chain a residue 132 ILE Chi-restraints excluded: chain a residue 181 TYR Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 462 VAL Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain e residue 468 MET Chi-restraints excluded: chain e residue 523 MET Chi-restraints excluded: chain g residue 59 THR Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 162 CYS Chi-restraints excluded: chain h residue 399 ILE Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 419 TYR Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 300 MET Chi-restraints excluded: chain Q residue 303 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 393 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 589 optimal weight: 9.9990 chunk 482 optimal weight: 0.9990 chunk 195 optimal weight: 8.9990 chunk 709 optimal weight: 0.6980 chunk 766 optimal weight: 4.9990 chunk 631 optimal weight: 7.9990 chunk 703 optimal weight: 30.0000 chunk 241 optimal weight: 6.9990 chunk 569 optimal weight: 50.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 497 ASN ** a 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 500 GLN b 124 GLN b 391 HIS ** d 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 389 ASN ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 384 GLN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 484 HIS ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 390 HIS ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 523 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 61207 Z= 0.259 Angle : 0.641 13.243 82664 Z= 0.314 Chirality : 0.044 0.162 9914 Planarity : 0.003 0.076 10525 Dihedral : 8.039 156.662 8522 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.23 % Favored : 93.69 % Rotamer: Outliers : 1.05 % Allowed : 12.15 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.45 (0.10), residues: 7817 helix: 1.17 (0.08), residues: 3997 sheet: -1.69 (0.23), residues: 530 loop : -1.98 (0.10), residues: 3290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP q 506 HIS 0.006 0.001 HIS b 148 PHE 0.027 0.001 PHE b 155 TYR 0.017 0.001 TYR h 236 ARG 0.004 0.000 ARG d 539 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 463 time to evaluate : 5.185 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: z 321 MET cc_start: 0.9073 (ptp) cc_final: 0.8790 (ptp) REVERT: Z 190 MET cc_start: 0.8262 (ttt) cc_final: 0.7952 (ttt) REVERT: Z 194 MET cc_start: 0.8078 (ppp) cc_final: 0.7825 (ppp) REVERT: Z 212 LEU cc_start: 0.9195 (tp) cc_final: 0.8994 (tp) REVERT: Z 221 MET cc_start: 0.1947 (mmp) cc_final: 0.1559 (mmm) REVERT: a 105 ASP cc_start: 0.8627 (t0) cc_final: 0.8177 (t70) REVERT: b 445 MET cc_start: 0.8645 (ttm) cc_final: 0.8177 (ttm) REVERT: d 81 MET cc_start: 0.7572 (tpt) cc_final: 0.7132 (tpt) REVERT: d 192 MET cc_start: 0.7320 (mmm) cc_final: 0.6720 (mtm) REVERT: e 29 MET cc_start: 0.7804 (ppp) cc_final: 0.7445 (pmm) REVERT: e 39 MET cc_start: 0.8581 (mmp) cc_final: 0.8074 (mmp) REVERT: e 48 MET cc_start: 0.6993 (ppp) cc_final: 0.6774 (ttp) REVERT: e 118 GLU cc_start: 0.8599 (pp20) cc_final: 0.8255 (pp20) REVERT: e 468 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7699 (ptp) REVERT: e 474 MET cc_start: 0.9211 (tmm) cc_final: 0.8917 (tmm) REVERT: e 501 MET cc_start: 0.8343 (mpp) cc_final: 0.8006 (mpp) REVERT: g 46 MET cc_start: 0.8461 (mtp) cc_final: 0.8229 (mtp) REVERT: q 146 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8575 (pp) REVERT: q 181 LYS cc_start: 0.8116 (pttt) cc_final: 0.7678 (pttm) REVERT: q 223 PHE cc_start: 0.8347 (p90) cc_final: 0.8099 (p90) REVERT: q 300 MET cc_start: 0.5180 (ttt) cc_final: 0.4050 (tmm) REVERT: A 239 PHE cc_start: 0.5679 (m-10) cc_final: 0.5459 (m-80) REVERT: B 310 MET cc_start: 0.5196 (tmm) cc_final: 0.4916 (ptp) REVERT: B 353 MET cc_start: 0.7526 (mmp) cc_final: 0.5623 (tpp) REVERT: E 122 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8625 (tm-30) REVERT: E 239 MET cc_start: -0.0626 (ppp) cc_final: -0.1186 (ppp) REVERT: E 288 MET cc_start: -0.3105 (tpt) cc_final: -0.3609 (ptt) REVERT: E 474 MET cc_start: 0.8756 (tmm) cc_final: 0.8388 (tmm) REVERT: E 526 MET cc_start: 0.8912 (ttp) cc_final: 0.8512 (tmm) REVERT: G 359 PHE cc_start: 0.8237 (m-10) cc_final: 0.7823 (m-80) REVERT: H 156 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7818 (mm-30) REVERT: H 160 MET cc_start: 0.8899 (ptt) cc_final: 0.8043 (ppp) outliers start: 69 outliers final: 39 residues processed: 508 average time/residue: 0.5654 time to fit residues: 507.8082 Evaluate side-chains 471 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 429 time to evaluate : 5.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 48 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 302 LEU Chi-restraints excluded: chain z residue 360 PHE Chi-restraints excluded: chain Z residue 360 PHE Chi-restraints excluded: chain a residue 62 LEU Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 132 ILE Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 391 HIS Chi-restraints excluded: chain b residue 462 VAL Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain e residue 373 VAL Chi-restraints excluded: chain e residue 468 MET Chi-restraints excluded: chain e residue 523 MET Chi-restraints excluded: chain g residue 59 THR Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 162 CYS Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 169 MET Chi-restraints excluded: chain q residue 325 CYS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 419 TYR Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 290 VAL Chi-restraints excluded: chain Q residue 300 MET Chi-restraints excluded: chain Q residue 303 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 701 optimal weight: 30.0000 chunk 533 optimal weight: 0.0470 chunk 368 optimal weight: 50.0000 chunk 78 optimal weight: 8.9990 chunk 338 optimal weight: 5.9990 chunk 476 optimal weight: 0.9990 chunk 712 optimal weight: 10.0000 chunk 753 optimal weight: 30.0000 chunk 372 optimal weight: 3.9990 chunk 674 optimal weight: 0.0010 chunk 203 optimal weight: 6.9990 overall best weight: 2.2090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 214 HIS ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 GLN ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS ** d 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 147 HIS e 191 ASN g 389 ASN ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 17 GLN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 523 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 61207 Z= 0.196 Angle : 0.613 12.052 82664 Z= 0.298 Chirality : 0.043 0.175 9914 Planarity : 0.003 0.078 10525 Dihedral : 7.797 155.682 8522 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 1.65 % Allowed : 14.09 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.40 (0.10), residues: 7817 helix: 1.23 (0.08), residues: 4001 sheet: -1.72 (0.23), residues: 520 loop : -1.97 (0.10), residues: 3296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP h 497 HIS 0.016 0.001 HIS b 391 PHE 0.023 0.001 PHE b 155 TYR 0.022 0.001 TYR D 439 ARG 0.003 0.000 ARG d 539 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 479 time to evaluate : 5.211 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: Z 190 MET cc_start: 0.8255 (ttt) cc_final: 0.7835 (ttt) REVERT: Z 194 MET cc_start: 0.8214 (ppp) cc_final: 0.7988 (ppp) REVERT: Z 212 LEU cc_start: 0.9217 (tp) cc_final: 0.8992 (tp) REVERT: Z 221 MET cc_start: 0.1917 (mmp) cc_final: 0.1560 (mmm) REVERT: a 105 ASP cc_start: 0.8584 (t0) cc_final: 0.8185 (t70) REVERT: b 445 MET cc_start: 0.8660 (ttm) cc_final: 0.8160 (ttm) REVERT: d 81 MET cc_start: 0.7570 (tpt) cc_final: 0.7141 (tpt) REVERT: d 192 MET cc_start: 0.7460 (mmm) cc_final: 0.6871 (mtm) REVERT: e 29 MET cc_start: 0.7836 (ppp) cc_final: 0.7514 (pmm) REVERT: e 61 MET cc_start: 0.8015 (mmm) cc_final: 0.7456 (mmm) REVERT: e 118 GLU cc_start: 0.8544 (pp20) cc_final: 0.8024 (pp20) REVERT: e 119 GLU cc_start: 0.8452 (pp20) cc_final: 0.8238 (pp20) REVERT: e 474 MET cc_start: 0.9231 (tmm) cc_final: 0.8910 (tmm) REVERT: e 501 MET cc_start: 0.8364 (mpp) cc_final: 0.8065 (mpp) REVERT: g 53 MET cc_start: 0.7715 (ppp) cc_final: 0.7453 (ppp) REVERT: q 146 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8572 (pp) REVERT: q 181 LYS cc_start: 0.8168 (pttt) cc_final: 0.7770 (pttm) REVERT: q 223 PHE cc_start: 0.8385 (p90) cc_final: 0.8016 (p90) REVERT: q 300 MET cc_start: 0.5102 (ttt) cc_final: 0.3994 (tmm) REVERT: q 454 GLU cc_start: 0.7868 (pt0) cc_final: 0.7619 (pt0) REVERT: B 275 MET cc_start: 0.3069 (tmm) cc_final: 0.1505 (ttt) REVERT: B 310 MET cc_start: 0.5208 (tmm) cc_final: 0.4794 (ptp) REVERT: E 93 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7474 (mp0) REVERT: E 122 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8605 (tm-30) REVERT: E 239 MET cc_start: -0.0602 (ppp) cc_final: -0.1217 (ppp) REVERT: E 288 MET cc_start: -0.3059 (tpt) cc_final: -0.3551 (ptt) REVERT: E 474 MET cc_start: 0.8721 (tmm) cc_final: 0.8311 (tmm) REVERT: E 501 MET cc_start: 0.8088 (mpp) cc_final: 0.7857 (mpp) REVERT: E 526 MET cc_start: 0.8877 (ttp) cc_final: 0.8458 (tmm) REVERT: G 89 GLU cc_start: 0.8286 (tp30) cc_final: 0.7985 (tp30) REVERT: G 228 MET cc_start: 0.4490 (ppp) cc_final: 0.4231 (ppp) REVERT: G 359 PHE cc_start: 0.8192 (m-10) cc_final: 0.7724 (m-80) REVERT: G 394 MET cc_start: 0.7797 (tpp) cc_final: 0.7517 (mmt) REVERT: H 156 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7763 (mm-30) REVERT: H 160 MET cc_start: 0.8881 (ptt) cc_final: 0.8011 (ppp) outliers start: 108 outliers final: 55 residues processed: 561 average time/residue: 0.5230 time to fit residues: 519.7260 Evaluate side-chains 501 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 444 time to evaluate : 5.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 48 VAL Chi-restraints excluded: chain z residue 114 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 214 HIS Chi-restraints excluded: chain z residue 302 LEU Chi-restraints excluded: chain z residue 322 GLU Chi-restraints excluded: chain z residue 360 PHE Chi-restraints excluded: chain z residue 479 VAL Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 195 GLU Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 360 PHE Chi-restraints excluded: chain a residue 62 LEU Chi-restraints excluded: chain a residue 132 ILE Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 391 HIS Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 462 VAL Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 297 VAL Chi-restraints excluded: chain d residue 536 VAL Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 523 MET Chi-restraints excluded: chain g residue 59 THR Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 162 CYS Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 169 MET Chi-restraints excluded: chain q residue 468 TYR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 419 TYR Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 86 ILE Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 290 VAL Chi-restraints excluded: chain Q residue 303 HIS Chi-restraints excluded: chain Q residue 362 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 627 optimal weight: 0.9980 chunk 427 optimal weight: 0.0970 chunk 10 optimal weight: 5.9990 chunk 561 optimal weight: 20.0000 chunk 311 optimal weight: 20.0000 chunk 643 optimal weight: 2.9990 chunk 521 optimal weight: 0.0020 chunk 0 optimal weight: 8.9990 chunk 384 optimal weight: 2.9990 chunk 676 optimal weight: 3.9990 chunk 190 optimal weight: 9.9990 overall best weight: 1.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 214 HIS ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS ** d 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 394 HIS ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 ASN ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 390 HIS Q 523 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 61207 Z= 0.169 Angle : 0.605 11.652 82664 Z= 0.293 Chirality : 0.042 0.272 9914 Planarity : 0.003 0.077 10525 Dihedral : 7.599 157.785 8522 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.90 % Favored : 94.04 % Rotamer: Outliers : 1.85 % Allowed : 15.02 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.36 (0.10), residues: 7817 helix: 1.27 (0.08), residues: 4015 sheet: -1.72 (0.23), residues: 529 loop : -1.97 (0.10), residues: 3273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP h 497 HIS 0.014 0.001 HIS z 214 PHE 0.021 0.001 PHE b 155 TYR 0.020 0.001 TYR h 236 ARG 0.003 0.000 ARG q 323 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 471 time to evaluate : 5.153 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: z 194 MET cc_start: 0.7525 (ppp) cc_final: 0.6836 (ppp) REVERT: z 196 MET cc_start: 0.8240 (ppp) cc_final: 0.6532 (ppp) REVERT: Z 44 MET cc_start: 0.8716 (mtm) cc_final: 0.8496 (mtm) REVERT: Z 190 MET cc_start: 0.8237 (ttt) cc_final: 0.7788 (ttt) REVERT: Z 194 MET cc_start: 0.8241 (ppp) cc_final: 0.7944 (ppp) REVERT: Z 212 LEU cc_start: 0.9238 (tp) cc_final: 0.8969 (tp) REVERT: Z 213 ASP cc_start: 0.8894 (t0) cc_final: 0.8597 (p0) REVERT: a 105 ASP cc_start: 0.8562 (t0) cc_final: 0.8189 (t70) REVERT: b 310 MET cc_start: -0.0832 (tpt) cc_final: -0.1216 (tpt) REVERT: b 445 MET cc_start: 0.8639 (ttm) cc_final: 0.8139 (ttm) REVERT: d 81 MET cc_start: 0.7552 (tpt) cc_final: 0.7113 (tpt) REVERT: d 192 MET cc_start: 0.7419 (mmm) cc_final: 0.6826 (mtm) REVERT: e 29 MET cc_start: 0.7941 (ppp) cc_final: 0.7688 (pmm) REVERT: e 61 MET cc_start: 0.8071 (mmm) cc_final: 0.7620 (mmm) REVERT: e 118 GLU cc_start: 0.8543 (pp20) cc_final: 0.7998 (pp20) REVERT: e 119 GLU cc_start: 0.8414 (pp20) cc_final: 0.8198 (pp20) REVERT: e 501 MET cc_start: 0.8389 (mpp) cc_final: 0.8097 (mpp) REVERT: g 53 MET cc_start: 0.7718 (ppp) cc_final: 0.7444 (ppp) REVERT: g 443 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9352 (tt) REVERT: q 146 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8564 (pp) REVERT: q 181 LYS cc_start: 0.8161 (pttt) cc_final: 0.7829 (pttm) REVERT: q 223 PHE cc_start: 0.8324 (p90) cc_final: 0.7953 (p90) REVERT: q 300 MET cc_start: 0.5117 (ttt) cc_final: 0.3968 (tmm) REVERT: q 454 GLU cc_start: 0.7830 (pt0) cc_final: 0.7578 (pt0) REVERT: A 111 LYS cc_start: 0.8876 (mppt) cc_final: 0.8616 (mptt) REVERT: A 306 MET cc_start: 0.6328 (ppp) cc_final: 0.5867 (ppp) REVERT: B 275 MET cc_start: 0.3088 (tmm) cc_final: 0.1627 (ttt) REVERT: B 310 MET cc_start: 0.5373 (tmm) cc_final: 0.4893 (ptp) REVERT: B 518 ASP cc_start: 0.8319 (p0) cc_final: 0.8012 (p0) REVERT: E 90 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8907 (tt) REVERT: E 93 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7607 (mt-10) REVERT: E 122 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8607 (tm-30) REVERT: E 239 MET cc_start: -0.0802 (ppp) cc_final: -0.1336 (ppp) REVERT: E 288 MET cc_start: -0.3269 (tpt) cc_final: -0.3667 (ptt) REVERT: E 474 MET cc_start: 0.8684 (tmm) cc_final: 0.8237 (tmm) REVERT: E 526 MET cc_start: 0.8851 (ttp) cc_final: 0.8435 (tmm) REVERT: G 359 PHE cc_start: 0.8168 (m-10) cc_final: 0.7698 (m-80) REVERT: G 394 MET cc_start: 0.7929 (tpp) cc_final: 0.7607 (mmt) REVERT: H 156 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7854 (mm-30) REVERT: H 160 MET cc_start: 0.8890 (ptt) cc_final: 0.8031 (ppp) REVERT: Q 276 MET cc_start: 0.3444 (tpt) cc_final: 0.3225 (tmm) outliers start: 121 outliers final: 65 residues processed: 565 average time/residue: 0.5240 time to fit residues: 525.8486 Evaluate side-chains 513 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 444 time to evaluate : 5.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 48 VAL Chi-restraints excluded: chain z residue 114 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 214 HIS Chi-restraints excluded: chain z residue 302 LEU Chi-restraints excluded: chain z residue 322 GLU Chi-restraints excluded: chain z residue 351 TYR Chi-restraints excluded: chain z residue 360 PHE Chi-restraints excluded: chain z residue 479 VAL Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 139 VAL Chi-restraints excluded: chain Z residue 195 GLU Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 360 PHE Chi-restraints excluded: chain a residue 62 LEU Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 415 VAL Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 391 HIS Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 297 VAL Chi-restraints excluded: chain d residue 536 VAL Chi-restraints excluded: chain e residue 48 MET Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain e residue 373 VAL Chi-restraints excluded: chain e residue 457 VAL Chi-restraints excluded: chain g residue 59 THR Chi-restraints excluded: chain g residue 443 LEU Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 162 CYS Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 169 MET Chi-restraints excluded: chain q residue 468 TYR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 419 TYR Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 86 ILE Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 290 VAL Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain Q residue 376 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 253 optimal weight: 0.9990 chunk 678 optimal weight: 0.4980 chunk 149 optimal weight: 8.9990 chunk 442 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 754 optimal weight: 7.9990 chunk 626 optimal weight: 3.9990 chunk 349 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 249 optimal weight: 7.9990 chunk 396 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 384 GLN h 394 HIS ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 523 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 61207 Z= 0.170 Angle : 0.608 11.092 82664 Z= 0.293 Chirality : 0.042 0.364 9914 Planarity : 0.003 0.076 10525 Dihedral : 7.452 161.789 8522 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.77 % Favored : 94.17 % Rotamer: Outliers : 1.75 % Allowed : 16.38 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.32 (0.10), residues: 7817 helix: 1.30 (0.08), residues: 4022 sheet: -1.70 (0.22), residues: 531 loop : -1.95 (0.10), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP h 497 HIS 0.010 0.001 HIS b 391 PHE 0.020 0.001 PHE b 155 TYR 0.026 0.001 TYR Q 304 ARG 0.003 0.000 ARG G 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 461 time to evaluate : 5.183 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: z 196 MET cc_start: 0.8292 (ppp) cc_final: 0.7166 (ppp) REVERT: Z 44 MET cc_start: 0.8704 (mtm) cc_final: 0.8484 (mtt) REVERT: Z 190 MET cc_start: 0.8257 (ttt) cc_final: 0.7792 (ttt) REVERT: Z 194 MET cc_start: 0.8228 (ppp) cc_final: 0.7864 (ppp) REVERT: Z 212 LEU cc_start: 0.9229 (tp) cc_final: 0.8960 (tp) REVERT: Z 213 ASP cc_start: 0.8931 (t0) cc_final: 0.8636 (p0) REVERT: Z 221 MET cc_start: 0.2093 (mmp) cc_final: 0.1659 (mmm) REVERT: a 105 ASP cc_start: 0.8570 (t0) cc_final: 0.8187 (t70) REVERT: a 171 MET cc_start: 0.7821 (ttm) cc_final: 0.6974 (tmm) REVERT: a 181 TYR cc_start: 0.7395 (t80) cc_final: 0.7193 (m-10) REVERT: a 209 MET cc_start: 0.6342 (tpt) cc_final: 0.6042 (tpt) REVERT: b 310 MET cc_start: -0.0908 (tpt) cc_final: -0.1257 (tpt) REVERT: b 445 MET cc_start: 0.8607 (ttm) cc_final: 0.8159 (ttm) REVERT: d 81 MET cc_start: 0.7558 (tpt) cc_final: 0.7127 (tpt) REVERT: e 29 MET cc_start: 0.7964 (ppp) cc_final: 0.7618 (pmm) REVERT: e 61 MET cc_start: 0.8041 (mmm) cc_final: 0.7651 (mmm) REVERT: e 118 GLU cc_start: 0.8560 (pp20) cc_final: 0.8002 (pp20) REVERT: e 119 GLU cc_start: 0.8430 (pp20) cc_final: 0.8207 (pp20) REVERT: e 191 ASN cc_start: 0.8611 (t0) cc_final: 0.8298 (m110) REVERT: e 501 MET cc_start: 0.8391 (mpp) cc_final: 0.8105 (mpp) REVERT: g 53 MET cc_start: 0.7823 (ppp) cc_final: 0.7517 (ppp) REVERT: g 181 MET cc_start: 0.6116 (ppp) cc_final: 0.5895 (ppp) REVERT: g 443 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9376 (tt) REVERT: q 52 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8057 (mtp) REVERT: q 146 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8607 (pp) REVERT: q 181 LYS cc_start: 0.8162 (pttt) cc_final: 0.7833 (pttm) REVERT: q 223 PHE cc_start: 0.8322 (p90) cc_final: 0.7934 (p90) REVERT: q 300 MET cc_start: 0.5221 (ttt) cc_final: 0.4083 (tmm) REVERT: q 454 GLU cc_start: 0.7795 (pt0) cc_final: 0.7552 (pt0) REVERT: A 111 LYS cc_start: 0.8884 (mppt) cc_final: 0.8595 (mptt) REVERT: A 384 MET cc_start: 0.5186 (tmm) cc_final: 0.4461 (pmm) REVERT: B 310 MET cc_start: 0.5330 (tmm) cc_final: 0.4808 (ptp) REVERT: B 488 MET cc_start: 0.8161 (mmm) cc_final: 0.7707 (mmm) REVERT: B 518 ASP cc_start: 0.8362 (p0) cc_final: 0.8015 (p0) REVERT: E 90 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8868 (tt) REVERT: E 93 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7705 (mt-10) REVERT: E 119 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8491 (mm-30) REVERT: E 122 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8349 (tm-30) REVERT: E 239 MET cc_start: -0.0650 (ppp) cc_final: -0.1152 (ppp) REVERT: E 288 MET cc_start: -0.3276 (tpt) cc_final: -0.3691 (ptt) REVERT: E 474 MET cc_start: 0.8704 (tmm) cc_final: 0.8258 (tmm) REVERT: E 526 MET cc_start: 0.8830 (ttp) cc_final: 0.8356 (tmm) REVERT: G 46 MET cc_start: 0.8273 (mmm) cc_final: 0.7938 (mmt) REVERT: G 89 GLU cc_start: 0.8299 (tp30) cc_final: 0.7996 (tp30) REVERT: G 359 PHE cc_start: 0.8100 (m-10) cc_final: 0.7629 (m-80) REVERT: G 394 MET cc_start: 0.7961 (tpp) cc_final: 0.7608 (mmt) REVERT: H 156 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7875 (mm-30) REVERT: H 160 MET cc_start: 0.8909 (ptt) cc_final: 0.8047 (ppp) REVERT: Q 492 MET cc_start: 0.8626 (mmm) cc_final: 0.8286 (mmm) outliers start: 115 outliers final: 78 residues processed: 549 average time/residue: 0.5111 time to fit residues: 499.1165 Evaluate side-chains 524 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 441 time to evaluate : 5.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 48 VAL Chi-restraints excluded: chain z residue 114 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 302 LEU Chi-restraints excluded: chain z residue 322 GLU Chi-restraints excluded: chain z residue 351 TYR Chi-restraints excluded: chain z residue 360 PHE Chi-restraints excluded: chain z residue 479 VAL Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 139 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 360 PHE Chi-restraints excluded: chain Z residue 522 MET Chi-restraints excluded: chain a residue 62 LEU Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 371 THR Chi-restraints excluded: chain a residue 415 VAL Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 391 HIS Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 297 VAL Chi-restraints excluded: chain d residue 474 ILE Chi-restraints excluded: chain d residue 536 VAL Chi-restraints excluded: chain e residue 48 MET Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain e residue 373 VAL Chi-restraints excluded: chain g residue 59 THR Chi-restraints excluded: chain g residue 443 LEU Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 147 VAL Chi-restraints excluded: chain h residue 162 CYS Chi-restraints excluded: chain h residue 172 ILE Chi-restraints excluded: chain q residue 52 MET Chi-restraints excluded: chain q residue 60 LEU Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 169 MET Chi-restraints excluded: chain q residue 171 LYS Chi-restraints excluded: chain q residue 362 VAL Chi-restraints excluded: chain q residue 468 TYR Chi-restraints excluded: chain q residue 471 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 181 MET Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 419 TYR Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 86 ILE Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 290 VAL Chi-restraints excluded: chain Q residue 300 MET Chi-restraints excluded: chain Q residue 303 HIS Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain Q residue 521 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 727 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 429 optimal weight: 2.9990 chunk 551 optimal weight: 9.9990 chunk 427 optimal weight: 4.9990 chunk 635 optimal weight: 4.9990 chunk 421 optimal weight: 7.9990 chunk 751 optimal weight: 9.9990 chunk 470 optimal weight: 6.9990 chunk 458 optimal weight: 6.9990 chunk 347 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 214 HIS ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 482 ASN ** d 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 191 ASN e 481 GLN ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 394 HIS A 30 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 306 ASN Q 523 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 61207 Z= 0.297 Angle : 0.669 11.239 82664 Z= 0.325 Chirality : 0.044 0.338 9914 Planarity : 0.003 0.075 10525 Dihedral : 7.496 159.784 8522 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.55 % Favored : 93.39 % Rotamer: Outliers : 2.01 % Allowed : 17.08 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.39 (0.10), residues: 7817 helix: 1.22 (0.08), residues: 4036 sheet: -1.74 (0.23), residues: 494 loop : -1.97 (0.10), residues: 3287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 130 HIS 0.007 0.001 HIS b 391 PHE 0.029 0.001 PHE H 455 TYR 0.021 0.001 TYR Q 304 ARG 0.006 0.000 ARG h 325 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 449 time to evaluate : 5.379 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: Z 44 MET cc_start: 0.8733 (mtm) cc_final: 0.8530 (mtm) REVERT: Z 190 MET cc_start: 0.8385 (ttt) cc_final: 0.7847 (ttt) REVERT: Z 194 MET cc_start: 0.8278 (ppp) cc_final: 0.7881 (ppp) REVERT: Z 212 LEU cc_start: 0.9254 (tp) cc_final: 0.8981 (tp) REVERT: Z 213 ASP cc_start: 0.8969 (t0) cc_final: 0.8683 (p0) REVERT: Z 221 MET cc_start: 0.2452 (mmp) cc_final: 0.2072 (mmm) REVERT: a 105 ASP cc_start: 0.8634 (t0) cc_final: 0.8210 (t70) REVERT: a 171 MET cc_start: 0.7778 (ttm) cc_final: 0.6951 (tmm) REVERT: a 181 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.7028 (t80) REVERT: a 209 MET cc_start: 0.6454 (tpt) cc_final: 0.6218 (tpt) REVERT: b 310 MET cc_start: -0.0779 (tpt) cc_final: -0.1154 (tpt) REVERT: b 445 MET cc_start: 0.8670 (ttm) cc_final: 0.8178 (ttm) REVERT: d 48 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8892 (mm) REVERT: d 81 MET cc_start: 0.7668 (tpt) cc_final: 0.7259 (tpt) REVERT: e 29 MET cc_start: 0.7944 (ppp) cc_final: 0.7673 (pmm) REVERT: e 80 MET cc_start: 0.8779 (mmp) cc_final: 0.8560 (mmt) REVERT: e 118 GLU cc_start: 0.8620 (pp20) cc_final: 0.8214 (pp20) REVERT: e 501 MET cc_start: 0.8434 (mpp) cc_final: 0.8084 (mpp) REVERT: g 53 MET cc_start: 0.7855 (ppp) cc_final: 0.7643 (ppp) REVERT: g 443 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9369 (tt) REVERT: h 164 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7247 (pmm) REVERT: h 472 HIS cc_start: 0.8332 (OUTLIER) cc_final: 0.7937 (t70) REVERT: q 52 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8212 (mtp) REVERT: q 146 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8640 (pp) REVERT: q 223 PHE cc_start: 0.8365 (p90) cc_final: 0.7932 (p90) REVERT: q 300 MET cc_start: 0.5064 (ttt) cc_final: 0.3964 (tmm) REVERT: q 454 GLU cc_start: 0.7932 (pt0) cc_final: 0.7675 (pt0) REVERT: q 468 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7993 (t80) REVERT: A 111 LYS cc_start: 0.8931 (mppt) cc_final: 0.8633 (mptt) REVERT: A 306 MET cc_start: 0.6600 (ppp) cc_final: 0.6098 (ppp) REVERT: A 384 MET cc_start: 0.4762 (tmm) cc_final: 0.4251 (pmm) REVERT: B 310 MET cc_start: 0.5332 (tmm) cc_final: 0.4905 (ptm) REVERT: E 90 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8973 (tt) REVERT: E 93 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7821 (mt-10) REVERT: E 119 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8570 (mm-30) REVERT: E 122 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8613 (tm-30) REVERT: E 239 MET cc_start: -0.0651 (ppp) cc_final: -0.1230 (ppp) REVERT: E 288 MET cc_start: -0.3376 (tpt) cc_final: -0.3830 (ptt) REVERT: G 113 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7868 (tm-30) REVERT: G 469 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.8089 (t-170) REVERT: H 160 MET cc_start: 0.8921 (ptt) cc_final: 0.8031 (ppp) REVERT: Q 276 MET cc_start: 0.3411 (tmm) cc_final: 0.2955 (tpt) outliers start: 132 outliers final: 86 residues processed: 554 average time/residue: 0.5205 time to fit residues: 509.1603 Evaluate side-chains 525 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 429 time to evaluate : 5.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 48 VAL Chi-restraints excluded: chain z residue 114 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 214 HIS Chi-restraints excluded: chain z residue 302 LEU Chi-restraints excluded: chain z residue 322 GLU Chi-restraints excluded: chain z residue 351 TYR Chi-restraints excluded: chain z residue 360 PHE Chi-restraints excluded: chain z residue 479 VAL Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 139 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 360 PHE Chi-restraints excluded: chain Z residue 522 MET Chi-restraints excluded: chain a residue 62 LEU Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 181 TYR Chi-restraints excluded: chain a residue 371 THR Chi-restraints excluded: chain a residue 415 VAL Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 391 HIS Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 297 VAL Chi-restraints excluded: chain d residue 474 ILE Chi-restraints excluded: chain d residue 536 VAL Chi-restraints excluded: chain e residue 48 MET Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain e residue 373 VAL Chi-restraints excluded: chain e residue 403 HIS Chi-restraints excluded: chain e residue 457 VAL Chi-restraints excluded: chain g residue 59 THR Chi-restraints excluded: chain g residue 443 LEU Chi-restraints excluded: chain g residue 479 VAL Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 147 VAL Chi-restraints excluded: chain h residue 162 CYS Chi-restraints excluded: chain h residue 164 MET Chi-restraints excluded: chain h residue 172 ILE Chi-restraints excluded: chain h residue 192 ASP Chi-restraints excluded: chain h residue 472 HIS Chi-restraints excluded: chain q residue 52 MET Chi-restraints excluded: chain q residue 60 LEU Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 160 VAL Chi-restraints excluded: chain q residue 362 VAL Chi-restraints excluded: chain q residue 468 TYR Chi-restraints excluded: chain q residue 471 HIS Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain G residue 469 HIS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 419 TYR Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 86 ILE Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 290 VAL Chi-restraints excluded: chain Q residue 303 HIS Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain Q residue 521 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 465 optimal weight: 0.0040 chunk 300 optimal weight: 6.9990 chunk 449 optimal weight: 3.9990 chunk 226 optimal weight: 0.0000 chunk 147 optimal weight: 0.9990 chunk 145 optimal weight: 0.0000 chunk 477 optimal weight: 0.8980 chunk 512 optimal weight: 9.9990 chunk 371 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 590 optimal weight: 8.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 214 HIS ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS ** d 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 481 GLN ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 394 HIS ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 61207 Z= 0.155 Angle : 0.628 10.831 82664 Z= 0.302 Chirality : 0.043 0.310 9914 Planarity : 0.003 0.079 10525 Dihedral : 7.302 163.846 8522 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.59 % Favored : 94.35 % Rotamer: Outliers : 1.71 % Allowed : 17.74 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.28 (0.10), residues: 7817 helix: 1.31 (0.08), residues: 4021 sheet: -1.73 (0.23), residues: 492 loop : -1.91 (0.10), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP h 497 HIS 0.007 0.001 HIS b 391 PHE 0.022 0.001 PHE H 455 TYR 0.019 0.001 TYR D 439 ARG 0.011 0.000 ARG z 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 477 time to evaluate : 5.372 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: z 143 MET cc_start: 0.7515 (tpp) cc_final: 0.7294 (tpp) REVERT: z 194 MET cc_start: 0.7388 (ppp) cc_final: 0.6784 (ppp) REVERT: z 196 MET cc_start: 0.8212 (ppp) cc_final: 0.7728 (ppp) REVERT: Z 44 MET cc_start: 0.8685 (mtm) cc_final: 0.8468 (mtt) REVERT: Z 190 MET cc_start: 0.8251 (ttt) cc_final: 0.7845 (ttt) REVERT: Z 194 MET cc_start: 0.8410 (ppp) cc_final: 0.7885 (ppp) REVERT: Z 212 LEU cc_start: 0.9262 (tp) cc_final: 0.8979 (tp) REVERT: Z 213 ASP cc_start: 0.9011 (t0) cc_final: 0.8711 (p0) REVERT: Z 221 MET cc_start: 0.2294 (mmp) cc_final: 0.1967 (mmm) REVERT: a 105 ASP cc_start: 0.8562 (t0) cc_final: 0.8181 (t70) REVERT: a 171 MET cc_start: 0.7777 (ttm) cc_final: 0.6935 (tmm) REVERT: b 310 MET cc_start: -0.0884 (tpt) cc_final: -0.1247 (tpt) REVERT: b 445 MET cc_start: 0.8623 (ttm) cc_final: 0.8146 (ttm) REVERT: d 81 MET cc_start: 0.7574 (tpt) cc_final: 0.7157 (tpt) REVERT: e 61 MET cc_start: 0.7868 (mmm) cc_final: 0.7224 (mmm) REVERT: e 80 MET cc_start: 0.8708 (mmp) cc_final: 0.8492 (mmt) REVERT: e 118 GLU cc_start: 0.8562 (pp20) cc_final: 0.7966 (pp20) REVERT: e 191 ASN cc_start: 0.8579 (t0) cc_final: 0.8310 (m110) REVERT: e 501 MET cc_start: 0.8296 (mpp) cc_final: 0.8082 (mpp) REVERT: g 53 MET cc_start: 0.7888 (ppp) cc_final: 0.7673 (ppp) REVERT: g 181 MET cc_start: 0.6035 (ppp) cc_final: 0.5771 (ppp) REVERT: q 52 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8050 (mtp) REVERT: q 146 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8583 (pp) REVERT: q 181 LYS cc_start: 0.7952 (pttt) cc_final: 0.7643 (pttm) REVERT: q 187 CYS cc_start: 0.8638 (t) cc_final: 0.8288 (t) REVERT: q 223 PHE cc_start: 0.8354 (p90) cc_final: 0.7900 (p90) REVERT: q 300 MET cc_start: 0.5029 (ttt) cc_final: 0.4102 (tmm) REVERT: q 454 GLU cc_start: 0.7770 (pt0) cc_final: 0.7517 (pt0) REVERT: q 468 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7865 (t80) REVERT: A 111 LYS cc_start: 0.8892 (mppt) cc_final: 0.8575 (mptt) REVERT: A 384 MET cc_start: 0.4626 (tmm) cc_final: 0.4078 (pmm) REVERT: B 310 MET cc_start: 0.5198 (tmm) cc_final: 0.4894 (ptm) REVERT: D 141 LEU cc_start: 0.9161 (tp) cc_final: 0.8955 (tp) REVERT: D 355 MET cc_start: -0.2411 (mmm) cc_final: -0.2679 (mmm) REVERT: E 93 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7816 (mt-10) REVERT: E 118 GLU cc_start: 0.8207 (pp20) cc_final: 0.7970 (pp20) REVERT: E 119 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8159 (mm-30) REVERT: E 122 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8452 (tm-30) REVERT: E 239 MET cc_start: -0.0647 (ppp) cc_final: -0.1133 (ppp) REVERT: E 288 MET cc_start: -0.3244 (tpt) cc_final: -0.3686 (ptt) REVERT: E 474 MET cc_start: 0.8634 (tmm) cc_final: 0.8193 (tmm) REVERT: E 526 MET cc_start: 0.8837 (ttp) cc_final: 0.8342 (tmm) REVERT: G 46 MET cc_start: 0.8238 (mmm) cc_final: 0.7907 (mmt) REVERT: H 156 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7988 (pm20) REVERT: H 160 MET cc_start: 0.8889 (ptt) cc_final: 0.7968 (ppp) outliers start: 112 outliers final: 77 residues processed: 564 average time/residue: 0.5262 time to fit residues: 526.5757 Evaluate side-chains 524 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 443 time to evaluate : 5.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 114 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 302 LEU Chi-restraints excluded: chain z residue 322 GLU Chi-restraints excluded: chain z residue 360 PHE Chi-restraints excluded: chain z residue 479 VAL Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 139 VAL Chi-restraints excluded: chain Z residue 202 THR Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 360 PHE Chi-restraints excluded: chain Z residue 522 MET Chi-restraints excluded: chain a residue 62 LEU Chi-restraints excluded: chain a residue 371 THR Chi-restraints excluded: chain a residue 415 VAL Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 391 HIS Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 297 VAL Chi-restraints excluded: chain d residue 474 ILE Chi-restraints excluded: chain d residue 536 VAL Chi-restraints excluded: chain e residue 48 MET Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain e residue 373 VAL Chi-restraints excluded: chain e residue 457 VAL Chi-restraints excluded: chain e residue 510 LEU Chi-restraints excluded: chain g residue 59 THR Chi-restraints excluded: chain g residue 479 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 147 VAL Chi-restraints excluded: chain h residue 162 CYS Chi-restraints excluded: chain h residue 164 MET Chi-restraints excluded: chain h residue 172 ILE Chi-restraints excluded: chain q residue 52 MET Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 160 VAL Chi-restraints excluded: chain q residue 171 LYS Chi-restraints excluded: chain q residue 362 VAL Chi-restraints excluded: chain q residue 468 TYR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 419 TYR Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 86 ILE Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 290 VAL Chi-restraints excluded: chain Q residue 300 MET Chi-restraints excluded: chain Q residue 303 HIS Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain Q residue 385 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 683 optimal weight: 0.1980 chunk 720 optimal weight: 8.9990 chunk 657 optimal weight: 5.9990 chunk 700 optimal weight: 4.9990 chunk 421 optimal weight: 40.0000 chunk 305 optimal weight: 5.9990 chunk 550 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 633 optimal weight: 7.9990 chunk 662 optimal weight: 0.0980 chunk 698 optimal weight: 0.7980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS d 406 HIS ** d 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 394 HIS ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 61207 Z= 0.209 Angle : 0.647 10.773 82664 Z= 0.311 Chirality : 0.043 0.300 9914 Planarity : 0.003 0.075 10525 Dihedral : 7.241 166.318 8522 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.87 % Favored : 94.06 % Rotamer: Outliers : 1.60 % Allowed : 18.21 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.28 (0.10), residues: 7817 helix: 1.31 (0.08), residues: 4030 sheet: -1.71 (0.23), residues: 488 loop : -1.92 (0.10), residues: 3299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 130 HIS 0.006 0.001 HIS b 391 PHE 0.021 0.001 PHE H 455 TYR 0.019 0.001 TYR d 439 ARG 0.013 0.000 ARG Z 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 445 time to evaluate : 5.221 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: z 194 MET cc_start: 0.7613 (ppp) cc_final: 0.6797 (ppp) REVERT: z 196 MET cc_start: 0.8295 (ppp) cc_final: 0.6516 (ppp) REVERT: Z 44 MET cc_start: 0.8704 (mtm) cc_final: 0.8492 (mtm) REVERT: Z 190 MET cc_start: 0.8281 (ttt) cc_final: 0.7741 (ttt) REVERT: Z 194 MET cc_start: 0.8460 (ppp) cc_final: 0.8117 (ppp) REVERT: Z 212 LEU cc_start: 0.9288 (tp) cc_final: 0.8998 (tp) REVERT: Z 213 ASP cc_start: 0.9012 (t0) cc_final: 0.8744 (p0) REVERT: Z 221 MET cc_start: 0.2310 (mmp) cc_final: 0.1953 (mmm) REVERT: Z 487 MET cc_start: 0.7837 (ppp) cc_final: 0.7584 (ppp) REVERT: a 105 ASP cc_start: 0.8592 (t0) cc_final: 0.8193 (t70) REVERT: a 171 MET cc_start: 0.7768 (ttm) cc_final: 0.6930 (tmm) REVERT: b 87 MET cc_start: 0.9408 (tpt) cc_final: 0.9022 (tmm) REVERT: b 310 MET cc_start: -0.0855 (tpt) cc_final: -0.1210 (tpt) REVERT: b 445 MET cc_start: 0.8668 (ttm) cc_final: 0.8182 (ttm) REVERT: d 81 MET cc_start: 0.7624 (tpt) cc_final: 0.7212 (tpt) REVERT: e 61 MET cc_start: 0.7851 (mmm) cc_final: 0.7304 (mmm) REVERT: e 80 MET cc_start: 0.8663 (mmp) cc_final: 0.8456 (mmt) REVERT: e 118 GLU cc_start: 0.8594 (pp20) cc_final: 0.8012 (pp20) REVERT: e 191 ASN cc_start: 0.8580 (t0) cc_final: 0.8320 (m110) REVERT: e 501 MET cc_start: 0.8309 (mpp) cc_final: 0.8065 (mpp) REVERT: g 53 MET cc_start: 0.7837 (ppp) cc_final: 0.7628 (ppp) REVERT: g 68 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8645 (mp0) REVERT: g 181 MET cc_start: 0.6038 (ppp) cc_final: 0.5816 (ppp) REVERT: g 394 MET cc_start: 0.8510 (mtm) cc_final: 0.8165 (mtm) REVERT: q 52 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8077 (mtp) REVERT: q 146 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8656 (pp) REVERT: q 181 LYS cc_start: 0.8021 (pttt) cc_final: 0.7724 (pttm) REVERT: q 221 MET cc_start: 0.5120 (tmm) cc_final: 0.4695 (tmm) REVERT: q 223 PHE cc_start: 0.8374 (p90) cc_final: 0.7930 (p90) REVERT: q 300 MET cc_start: 0.5055 (ttt) cc_final: 0.4141 (tmm) REVERT: q 454 GLU cc_start: 0.7824 (pt0) cc_final: 0.7564 (pt0) REVERT: q 468 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7901 (t80) REVERT: A 111 LYS cc_start: 0.8912 (mppt) cc_final: 0.8599 (mptt) REVERT: A 384 MET cc_start: 0.4423 (tmm) cc_final: 0.3498 (pmm) REVERT: B 310 MET cc_start: 0.5197 (tmm) cc_final: 0.4940 (ptm) REVERT: B 488 MET cc_start: 0.8148 (mmm) cc_final: 0.7542 (mmm) REVERT: D 355 MET cc_start: -0.2436 (mmm) cc_final: -0.2695 (mmm) REVERT: E 90 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8878 (tt) REVERT: E 93 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7807 (mt-10) REVERT: E 119 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8491 (mm-30) REVERT: E 122 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8474 (tm-30) REVERT: E 239 MET cc_start: -0.0615 (ppp) cc_final: -0.1133 (ppp) REVERT: E 288 MET cc_start: -0.3209 (tpt) cc_final: -0.3729 (ptt) REVERT: E 474 MET cc_start: 0.8711 (tmm) cc_final: 0.8286 (tmm) REVERT: G 46 MET cc_start: 0.8281 (mmm) cc_final: 0.7945 (mmt) REVERT: H 156 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7935 (pm20) REVERT: H 160 MET cc_start: 0.8920 (ptt) cc_final: 0.7987 (ppp) outliers start: 105 outliers final: 84 residues processed: 526 average time/residue: 0.5416 time to fit residues: 508.4815 Evaluate side-chains 528 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 438 time to evaluate : 5.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 48 VAL Chi-restraints excluded: chain z residue 73 THR Chi-restraints excluded: chain z residue 114 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 302 LEU Chi-restraints excluded: chain z residue 322 GLU Chi-restraints excluded: chain z residue 360 PHE Chi-restraints excluded: chain z residue 479 VAL Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 139 VAL Chi-restraints excluded: chain Z residue 202 THR Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 360 PHE Chi-restraints excluded: chain Z residue 522 MET Chi-restraints excluded: chain a residue 62 LEU Chi-restraints excluded: chain a residue 371 THR Chi-restraints excluded: chain a residue 415 VAL Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 391 HIS Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 297 VAL Chi-restraints excluded: chain d residue 536 VAL Chi-restraints excluded: chain e residue 48 MET Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain e residue 373 VAL Chi-restraints excluded: chain e residue 393 MET Chi-restraints excluded: chain e residue 457 VAL Chi-restraints excluded: chain e residue 510 LEU Chi-restraints excluded: chain g residue 59 THR Chi-restraints excluded: chain g residue 68 GLU Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain g residue 479 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 147 VAL Chi-restraints excluded: chain h residue 162 CYS Chi-restraints excluded: chain h residue 164 MET Chi-restraints excluded: chain h residue 172 ILE Chi-restraints excluded: chain h residue 523 THR Chi-restraints excluded: chain q residue 52 MET Chi-restraints excluded: chain q residue 60 LEU Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 160 VAL Chi-restraints excluded: chain q residue 362 VAL Chi-restraints excluded: chain q residue 468 TYR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 419 TYR Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 86 ILE Chi-restraints excluded: chain Q residue 290 VAL Chi-restraints excluded: chain Q residue 303 HIS Chi-restraints excluded: chain Q residue 362 VAL Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain Q residue 385 MET Chi-restraints excluded: chain Q residue 521 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 460 optimal weight: 4.9990 chunk 740 optimal weight: 0.9990 chunk 452 optimal weight: 0.0070 chunk 351 optimal weight: 0.7980 chunk 514 optimal weight: 7.9990 chunk 777 optimal weight: 0.7980 chunk 715 optimal weight: 10.0000 chunk 618 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 477 optimal weight: 0.9980 chunk 379 optimal weight: 0.8980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 60 ASN ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 394 HIS ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 ASN ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 61207 Z= 0.157 Angle : 0.640 10.857 82664 Z= 0.306 Chirality : 0.043 0.294 9914 Planarity : 0.003 0.078 10525 Dihedral : 7.061 169.389 8522 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.59 % Favored : 94.35 % Rotamer: Outliers : 1.43 % Allowed : 18.65 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.10), residues: 7817 helix: 1.33 (0.08), residues: 4020 sheet: -1.67 (0.23), residues: 500 loop : -1.90 (0.10), residues: 3297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP h 497 HIS 0.006 0.001 HIS b 391 PHE 0.028 0.001 PHE H 175 TYR 0.020 0.001 TYR B 456 ARG 0.010 0.000 ARG d 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 459 time to evaluate : 5.305 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: z 143 MET cc_start: 0.7255 (tpp) cc_final: 0.6909 (tpp) REVERT: z 194 MET cc_start: 0.7290 (ppp) cc_final: 0.6568 (ppp) REVERT: z 196 MET cc_start: 0.8258 (ppp) cc_final: 0.6474 (ppp) REVERT: Z 44 MET cc_start: 0.8669 (mtm) cc_final: 0.8450 (mtm) REVERT: Z 46 MET cc_start: 0.8017 (tpt) cc_final: 0.7639 (tpp) REVERT: Z 190 MET cc_start: 0.8281 (ttt) cc_final: 0.7735 (ttt) REVERT: Z 194 MET cc_start: 0.8417 (ppp) cc_final: 0.7953 (ppp) REVERT: Z 212 LEU cc_start: 0.9293 (tp) cc_final: 0.9002 (tp) REVERT: Z 221 MET cc_start: 0.2318 (mmp) cc_final: 0.1910 (mmm) REVERT: Z 360 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8533 (m-80) REVERT: a 105 ASP cc_start: 0.8528 (t0) cc_final: 0.8166 (t70) REVERT: a 171 MET cc_start: 0.7747 (ttm) cc_final: 0.6934 (tmm) REVERT: a 209 MET cc_start: 0.6439 (tpt) cc_final: 0.6172 (tpt) REVERT: b 87 MET cc_start: 0.9360 (tpt) cc_final: 0.9024 (tmm) REVERT: b 310 MET cc_start: -0.0974 (tpt) cc_final: -0.1328 (tpt) REVERT: b 445 MET cc_start: 0.8595 (ttm) cc_final: 0.8154 (ttm) REVERT: b 469 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.5395 (t-90) REVERT: d 81 MET cc_start: 0.7542 (tpt) cc_final: 0.7116 (tpt) REVERT: e 37 HIS cc_start: 0.9046 (m170) cc_final: 0.8492 (m90) REVERT: e 61 MET cc_start: 0.7892 (mmm) cc_final: 0.7452 (mmm) REVERT: e 80 MET cc_start: 0.8665 (mmp) cc_final: 0.8442 (mmt) REVERT: e 118 GLU cc_start: 0.8592 (pp20) cc_final: 0.7984 (pp20) REVERT: e 191 ASN cc_start: 0.8616 (t0) cc_final: 0.8354 (m110) REVERT: e 474 MET cc_start: 0.9090 (tmm) cc_final: 0.8636 (tmm) REVERT: g 53 MET cc_start: 0.7864 (ppp) cc_final: 0.7643 (ppp) REVERT: g 68 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8630 (mp0) REVERT: g 181 MET cc_start: 0.6037 (ppp) cc_final: 0.5801 (ppp) REVERT: g 394 MET cc_start: 0.8522 (mtm) cc_final: 0.8152 (mtm) REVERT: q 52 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8081 (mtp) REVERT: q 146 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8615 (pp) REVERT: q 181 LYS cc_start: 0.8030 (pttt) cc_final: 0.7742 (pttm) REVERT: q 206 LYS cc_start: 0.9079 (mttm) cc_final: 0.8223 (mmtt) REVERT: q 221 MET cc_start: 0.5019 (tmm) cc_final: 0.4595 (tmm) REVERT: q 223 PHE cc_start: 0.8388 (p90) cc_final: 0.7913 (p90) REVERT: q 300 MET cc_start: 0.5041 (ttt) cc_final: 0.4121 (tmm) REVERT: q 344 MET cc_start: 0.4511 (tmm) cc_final: 0.3925 (tmm) REVERT: q 385 MET cc_start: 0.8803 (mmt) cc_final: 0.7113 (mmt) REVERT: q 454 GLU cc_start: 0.7826 (pt0) cc_final: 0.7584 (pt0) REVERT: q 468 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7875 (t80) REVERT: A 111 LYS cc_start: 0.8936 (mppt) cc_final: 0.8591 (mptt) REVERT: A 384 MET cc_start: 0.4329 (tmm) cc_final: 0.3381 (pmm) REVERT: B 310 MET cc_start: 0.5204 (tmm) cc_final: 0.4921 (ptm) REVERT: B 488 MET cc_start: 0.8087 (mmm) cc_final: 0.7459 (mmm) REVERT: D 355 MET cc_start: -0.2501 (mmm) cc_final: -0.2757 (mmm) REVERT: E 39 MET cc_start: 0.8115 (tpp) cc_final: 0.7910 (tpp) REVERT: E 90 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8825 (tt) REVERT: E 93 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7806 (mt-10) REVERT: E 118 GLU cc_start: 0.8204 (pp20) cc_final: 0.7956 (pp20) REVERT: E 119 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8201 (mm-30) REVERT: E 122 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8484 (tm-30) REVERT: E 239 MET cc_start: -0.0718 (ppp) cc_final: -0.1191 (ppp) REVERT: E 288 MET cc_start: -0.3159 (tpt) cc_final: -0.3666 (ptt) REVERT: E 474 MET cc_start: 0.8642 (tmm) cc_final: 0.8204 (tmm) REVERT: E 526 MET cc_start: 0.8843 (ttp) cc_final: 0.8377 (tmm) REVERT: G 46 MET cc_start: 0.8249 (mmm) cc_final: 0.7912 (mmt) REVERT: H 156 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: H 160 MET cc_start: 0.8880 (ptt) cc_final: 0.7930 (ppp) outliers start: 94 outliers final: 79 residues processed: 527 average time/residue: 0.5289 time to fit residues: 493.9814 Evaluate side-chains 530 residues out of total 6557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 443 time to evaluate : 5.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 48 VAL Chi-restraints excluded: chain z residue 114 LEU Chi-restraints excluded: chain z residue 149 ILE Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 302 LEU Chi-restraints excluded: chain z residue 322 GLU Chi-restraints excluded: chain z residue 360 PHE Chi-restraints excluded: chain z residue 479 VAL Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 139 VAL Chi-restraints excluded: chain Z residue 202 THR Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 360 PHE Chi-restraints excluded: chain Z residue 522 MET Chi-restraints excluded: chain a residue 62 LEU Chi-restraints excluded: chain a residue 371 THR Chi-restraints excluded: chain a residue 415 VAL Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 391 HIS Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 469 HIS Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 297 VAL Chi-restraints excluded: chain d residue 536 VAL Chi-restraints excluded: chain e residue 48 MET Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 90 LEU Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain e residue 373 VAL Chi-restraints excluded: chain e residue 393 MET Chi-restraints excluded: chain e residue 457 VAL Chi-restraints excluded: chain e residue 510 LEU Chi-restraints excluded: chain g residue 59 THR Chi-restraints excluded: chain g residue 68 GLU Chi-restraints excluded: chain g residue 479 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain h residue 147 VAL Chi-restraints excluded: chain h residue 162 CYS Chi-restraints excluded: chain h residue 164 MET Chi-restraints excluded: chain h residue 172 ILE Chi-restraints excluded: chain h residue 312 MET Chi-restraints excluded: chain q residue 52 MET Chi-restraints excluded: chain q residue 60 LEU Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 160 VAL Chi-restraints excluded: chain q residue 171 LYS Chi-restraints excluded: chain q residue 362 VAL Chi-restraints excluded: chain q residue 468 TYR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 289 CYS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 387 GLU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 156 GLU Chi-restraints excluded: chain H residue 419 TYR Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 86 ILE Chi-restraints excluded: chain Q residue 290 VAL Chi-restraints excluded: chain Q residue 303 HIS Chi-restraints excluded: chain Q residue 376 VAL Chi-restraints excluded: chain Q residue 385 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 491 optimal weight: 3.9990 chunk 659 optimal weight: 5.9990 chunk 189 optimal weight: 0.0570 chunk 570 optimal weight: 50.0000 chunk 91 optimal weight: 0.0670 chunk 171 optimal weight: 20.0000 chunk 619 optimal weight: 20.0000 chunk 259 optimal weight: 0.0070 chunk 636 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 overall best weight: 2.0258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 406 HIS ** d 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 60 ASN ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.140852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.087882 restraints weight = 156270.791| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 5.25 r_work: 0.3253 rms_B_bonded: 5.25 restraints_weight: 2.0000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 61207 Z= 0.192 Angle : 0.651 12.746 82664 Z= 0.311 Chirality : 0.043 0.288 9914 Planarity : 0.003 0.076 10525 Dihedral : 7.011 173.107 8522 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 1.53 % Allowed : 18.70 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.24 (0.10), residues: 7817 helix: 1.35 (0.08), residues: 4030 sheet: -1.69 (0.23), residues: 502 loop : -1.90 (0.10), residues: 3285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 130 HIS 0.005 0.001 HIS G 110 PHE 0.035 0.001 PHE H 175 TYR 0.019 0.001 TYR d 439 ARG 0.007 0.000 ARG Z 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11887.91 seconds wall clock time: 211 minutes 7.92 seconds (12667.92 seconds total)