Starting phenix.real_space_refine on Sat Sep 28 05:49:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shp_40491/09_2024/8shp_40491.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shp_40491/09_2024/8shp_40491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shp_40491/09_2024/8shp_40491.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shp_40491/09_2024/8shp_40491.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shp_40491/09_2024/8shp_40491.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shp_40491/09_2024/8shp_40491.cif" } resolution = 3.0 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= 0.046 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: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 423 5.16 5 C 42515 2.51 5 N 11828 2.21 5 O 13171 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 68049 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1408 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 1 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4132 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Conformer: "C" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} bond proxies already assigned to first conformer: 4158 Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1507 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 9 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N BPHE E 9 " occ=0.38 ... (20 atoms not shown) pdb=" CZ CPHE E 9 " occ=0.62 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 35.39, per 1000 atoms: 0.52 Number of scatterers: 68049 At special positions: 0 Unit cell: (181.976, 176.686, 180.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 423 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13171 8.00 N 11828 7.00 C 42515 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM67956 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67572 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67700 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67636 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67828 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.34 Conformation dependent library (CDL) restraints added in 7.7 seconds 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16458 Finding SS restraints... Secondary structure from input PDB file: 363 helices and 101 sheets defined 55.7% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.61 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.683A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 86 removed outlier: 3.887A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 removed outlier: 3.675A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'A' and resid 144 through 157 removed outlier: 4.238A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 180 removed outlier: 4.278A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 259 through 281 removed outlier: 3.864A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 381 through 405 Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 433 through 445 Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.943A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 484 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 66 through 73 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 Processing helix chain 'B' and resid 151 through 169 removed outlier: 4.422A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.702A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 260 through 284 Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.685A pdb=" N VAL B 341 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 Processing helix chain 'B' and resid 411 through 427 removed outlier: 3.801A pdb=" N ARG B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 454 Proline residue: B 447 - end of helix removed outlier: 3.639A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 472 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'D' and resid 28 through 49 Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' 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: 4.114A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 Processing helix chain 'D' and resid 159 through 173 removed outlier: 3.683A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 Proline residue: D 185 - end of helix removed outlier: 3.703A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 268 through 292 removed outlier: 3.947A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 341 Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 442 Processing helix chain 'D' and resid 446 through 459 removed outlier: 4.026A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 3.753A pdb=" N SER D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 486 Processing helix chain 'D' and resid 504 through 507 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 21 through 25 removed outlier: 3.621A pdb=" N LYS E 25 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 49 removed outlier: 3.600A pdb=" N LEU E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 73 through 80 Processing helix chain 'E' and resid 85 through 102 Processing helix chain 'E' and resid 107 through 125 removed outlier: 3.830A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 151 Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'E' and resid 175 through 180 removed outlier: 6.682A pdb=" N VAL E 178 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 196 Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 218 through 222 Processing helix chain 'E' and resid 270 through 295 removed outlier: 3.826A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 391 through 415 Processing helix chain 'E' and resid 423 through 438 Processing helix chain 'E' and resid 441 through 456 removed outlier: 3.942A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 467 removed outlier: 3.744A 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 Processing helix chain 'E' and resid 510 through 529 Processing helix chain 'G' and resid 19 through 38 removed outlier: 3.707A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 62 through 69 Processing helix chain 'G' and resid 74 through 91 Processing helix chain 'G' and resid 94 through 114 removed outlier: 3.755A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 141 removed outlier: 3.595A pdb=" N VAL G 122 " --> pdb=" O HIS G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 161 Processing helix chain 'G' and resid 163 through 167 removed outlier: 4.218A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 194 through 198 Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 262 through 284 Processing helix chain 'G' and resid 297 through 307 removed outlier: 3.683A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 328 Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 380 through 404 Processing helix chain 'G' and resid 412 through 427 Processing helix chain 'G' and resid 433 through 444 Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'G' and resid 458 through 472 removed outlier: 3.598A pdb=" N LEU G 462 " --> pdb=" O SER G 458 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN G 472 " --> pdb=" O ALA G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 18 through 35 removed outlier: 3.613A pdb=" N LEU H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 40 Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.638A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 4.117A pdb=" N THR H 98 " --> pdb=" O THR H 94 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 117 through 140 removed outlier: 3.696A pdb=" N ILE H 121 " --> pdb=" O HIS H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 164 Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'H' and resid 171 through 186 removed outlier: 3.694A pdb=" N MET H 185 " --> pdb=" O ASP H 181 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU H 186 " --> pdb=" O ALA H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 259 through 284 removed outlier: 3.529A pdb=" N SER H 284 " --> pdb=" O LYS H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 378 through 402 Processing helix chain 'H' and resid 410 through 425 Processing helix chain 'H' and resid 429 through 442 removed outlier: 3.527A pdb=" N LEU H 433 " --> pdb=" O GLY H 429 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 454 Processing helix chain 'H' and resid 456 through 471 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 10 through 15 Processing helix chain 'Q' and resid 24 through 45 removed outlier: 4.378A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 75 Processing helix chain 'Q' and resid 80 through 97 Processing helix chain 'Q' and resid 100 through 122 Processing helix chain 'Q' and resid 124 through 143 Processing helix chain 'Q' and resid 144 through 147 Processing helix chain 'Q' and resid 157 through 168 removed outlier: 4.338A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 190 removed outlier: 3.517A pdb=" N ILE Q 190 " --> pdb=" O ALA Q 186 " (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 261 through 286 removed outlier: 4.884A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 308 Processing helix chain 'Q' and resid 317 through 329 Processing helix chain 'Q' and resid 381 through 405 Processing helix chain 'Q' and resid 413 through 429 removed outlier: 3.811A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 445 removed outlier: 4.251A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 457 Processing helix chain 'Q' and resid 459 through 474 removed outlier: 3.648A pdb=" N VAL Q 463 " --> pdb=" O LYS Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 492 through 496 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Q' and resid 535 through 539 Processing helix chain 'Z' and resid 3 through 8 Processing helix chain 'Z' and resid 16 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 88 Processing helix chain 'Z' and resid 91 through 111 removed outlier: 3.611A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.712A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 4.037A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.672A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE Z 179 " --> pdb=" O SER Z 175 " (cutoff:3.500A) 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 200 through 204 Processing helix chain 'Z' and resid 252 through 263 Processing helix chain 'Z' and resid 264 through 282 removed outlier: 3.579A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 307 Processing helix chain 'Z' and resid 317 through 328 removed outlier: 3.695A pdb=" N MET Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 340 through 344 Processing helix chain 'Z' and resid 380 through 404 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 445 removed outlier: 4.175A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 455 removed outlier: 3.722A pdb=" N LYS Z 449 " --> pdb=" O LEU Z 445 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 474 removed outlier: 3.742A pdb=" N THR Z 462 " --> pdb=" O ASP Z 458 " (cutoff:3.500A) Processing helix chain 'Z' and resid 489 through 493 Processing helix chain 'Z' and resid 498 through 517 Processing helix chain 'a' and resid 14 through 33 removed outlier: 3.684A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 57 through 65 Processing helix chain 'a' and resid 69 through 86 Processing helix chain 'a' and resid 89 through 110 removed outlier: 3.870A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 136 Processing helix chain 'a' and resid 144 through 157 removed outlier: 4.396A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.176A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE a 179 " --> pdb=" O ALA a 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 204 through 208 Processing helix chain 'a' and resid 256 through 258 No H-bonds generated for 'chain 'a' and resid 256 through 258' Processing helix chain 'a' and resid 259 through 281 removed outlier: 3.833A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 304 Processing helix chain 'a' and resid 312 through 324 Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'a' and resid 381 through 405 Processing helix chain 'a' and resid 413 through 427 Processing helix chain 'a' and resid 428 through 430 No H-bonds generated for 'chain 'a' and resid 428 through 430' Processing helix chain 'a' and resid 433 through 445 Processing helix chain 'a' and resid 446 through 456 removed outlier: 3.621A pdb=" N ASN a 450 " --> pdb=" O LEU a 446 " (cutoff:3.500A) Processing helix chain 'a' and resid 459 through 477 Processing helix chain 'a' and resid 480 through 484 Processing helix chain 'a' and resid 498 through 502 Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 20 through 40 Processing helix chain 'b' and resid 66 through 73 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 Processing helix chain 'b' and resid 151 through 169 removed outlier: 4.396A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 174 removed outlier: 3.593A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 175 through 189 Processing helix chain 'b' and resid 195 through 197 No H-bonds generated for 'chain 'b' and resid 195 through 197' Processing helix chain 'b' and resid 208 through 212 Processing helix chain 'b' and resid 260 through 284 Processing helix chain 'b' and resid 297 through 307 Processing helix chain 'b' and resid 316 through 328 Processing helix chain 'b' and resid 337 through 341 removed outlier: 3.575A pdb=" N VAL b 341 " --> pdb=" O PRO b 338 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 403 Processing helix chain 'b' and resid 411 through 427 Processing helix chain 'b' and resid 430 through 454 removed outlier: 4.120A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) Proline residue: b 447 - end of helix removed outlier: 3.832A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 457 through 472 Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 516 Processing helix chain 'd' and resid 28 through 48 Processing helix chain 'd' and resid 73 through 81 removed outlier: 3.596A pdb=" N MET d 81 " --> pdb=" O ILE d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 103 Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.727A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 131 through 152 Processing helix chain 'd' and resid 159 through 172 removed outlier: 3.676A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 178 removed outlier: 6.771A pdb=" N VAL d 176 " --> pdb=" O SER d 173 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 193 Proline residue: d 185 - end of helix Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 217 through 221 Processing helix chain 'd' and resid 268 through 293 removed outlier: 3.726A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 310 through 320 Processing helix chain 'd' and resid 329 through 331 No H-bonds generated for 'chain 'd' and resid 329 through 331' Processing helix chain 'd' and resid 332 through 341 Processing helix chain 'd' and resid 347 through 351 Processing helix chain 'd' and resid 352 through 356 Processing helix chain 'd' and resid 394 through 417 Processing helix chain 'd' and resid 426 through 442 removed outlier: 3.618A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.620A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 removed outlier: 3.650A pdb=" N SER d 463 " --> pdb=" O GLU d 459 " (cutoff:3.500A) Processing helix chain 'd' and resid 472 through 487 Processing helix chain 'd' and resid 512 through 531 removed outlier: 4.947A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 49 removed outlier: 3.533A pdb=" N LEU e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) Processing helix chain 'e' and resid 50 through 52 No H-bonds generated for 'chain 'e' and resid 50 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: 3.868A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG e 126 " --> pdb=" O GLN e 122 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 151 Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'e' and resid 175 through 180 removed outlier: 6.551A pdb=" N VAL e 178 " --> pdb=" O SER e 175 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 181 through 196 Processing helix chain 'e' and resid 205 through 207 No H-bonds generated for 'chain 'e' and resid 205 through 207' Processing helix chain 'e' and resid 218 through 222 Processing helix chain 'e' and resid 270 through 295 removed outlier: 3.873A pdb=" N THR e 295 " --> pdb=" O GLN e 291 " (cutoff:3.500A) Processing helix chain 'e' and resid 307 through 317 Processing helix chain 'e' and resid 326 through 338 Processing helix chain 'e' and resid 344 through 348 Processing helix chain 'e' and resid 349 through 353 Processing helix chain 'e' and resid 391 through 415 Processing helix chain 'e' and resid 423 through 438 Processing helix chain 'e' and resid 441 through 456 removed outlier: 3.840A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 466 Processing helix chain 'e' and resid 469 through 484 Processing helix chain 'e' and resid 500 through 505 Processing helix chain 'e' and resid 510 through 529 Processing helix chain 'g' and resid 19 through 38 removed outlier: 3.663A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 39 through 41 No H-bonds generated for 'chain 'g' and resid 39 through 41' Processing helix chain 'g' and resid 62 through 69 Processing helix chain 'g' and resid 74 through 91 Processing helix chain 'g' and resid 94 through 115 removed outlier: 3.780A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN g 115 " --> pdb=" O HIS g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 141 removed outlier: 3.597A pdb=" N VAL g 122 " --> pdb=" O HIS g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 161 Processing helix chain 'g' and resid 163 through 167 removed outlier: 3.772A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 removed outlier: 3.509A pdb=" N ALA g 172 " --> pdb=" O TRP g 168 " (cutoff:3.500A) Processing helix chain 'g' and resid 208 through 212 Processing helix chain 'g' and resid 262 through 284 Processing helix chain 'g' and resid 297 through 307 removed outlier: 3.697A pdb=" N ALA g 307 " --> pdb=" O TYR g 303 " (cutoff:3.500A) Processing helix chain 'g' and resid 316 through 328 Processing helix chain 'g' and resid 334 through 338 Processing helix chain 'g' and resid 380 through 404 Processing helix chain 'g' and resid 412 through 426 Processing helix chain 'g' and resid 427 through 429 No H-bonds generated for 'chain 'g' and resid 427 through 429' Processing helix chain 'g' and resid 433 through 443 Processing helix chain 'g' and resid 445 through 456 Processing helix chain 'g' and resid 458 through 471 Processing helix chain 'g' and resid 490 through 494 Processing helix chain 'g' and resid 499 through 518 Processing helix chain 'h' and resid 18 through 35 removed outlier: 3.507A pdb=" N LEU h 22 " --> pdb=" O GLY h 18 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 40 removed outlier: 3.558A pdb=" N LEU h 40 " --> pdb=" O ARG h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 69 Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.630A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 114 removed outlier: 4.216A pdb=" N THR h 98 " --> pdb=" O THR h 94 " (cutoff:3.500A) Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 117 through 140 removed outlier: 3.710A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 147 through 164 Processing helix chain 'h' and resid 168 through 170 No H-bonds generated for 'chain 'h' and resid 168 through 170' Processing helix chain 'h' and resid 171 through 186 removed outlier: 3.668A pdb=" N MET h 185 " --> pdb=" O ASP h 181 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU h 186 " --> pdb=" O ALA h 182 " (cutoff:3.500A) Processing helix chain 'h' and resid 191 through 193 No H-bonds generated for 'chain 'h' and resid 191 through 193' Processing helix chain 'h' and resid 204 through 208 Processing helix chain 'h' and resid 224 through 228 Processing helix chain 'h' and resid 259 through 284 removed outlier: 3.543A pdb=" N SER h 284 " --> pdb=" O LYS h 280 " (cutoff:3.500A) Processing helix chain 'h' and resid 296 through 306 Processing helix chain 'h' and resid 315 through 327 Processing helix chain 'h' and resid 378 through 402 Processing helix chain 'h' and resid 410 through 425 Processing helix chain 'h' and resid 429 through 442 removed outlier: 3.571A pdb=" N LEU h 433 " --> pdb=" O GLY h 429 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) Processing helix chain 'h' and resid 443 through 454 Processing helix chain 'h' and resid 456 through 471 removed outlier: 3.501A pdb=" N ILE h 460 " --> pdb=" O ASP h 456 " (cutoff:3.500A) Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'q' and resid 10 through 15 Processing helix chain 'q' and resid 24 through 45 removed outlier: 4.158A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.540A 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 97 Processing helix chain 'q' and resid 100 through 122 Processing helix chain 'q' and resid 124 through 143 Processing helix chain 'q' and resid 144 through 147 Processing helix chain 'q' and resid 157 through 168 removed outlier: 4.156A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 190 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 261 through 285 removed outlier: 4.758A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) Processing helix chain 'q' and resid 298 through 308 Processing helix chain 'q' and resid 317 through 329 Processing helix chain 'q' and resid 340 through 344 Processing helix chain 'q' and resid 381 through 405 Processing helix chain 'q' and resid 413 through 429 removed outlier: 3.696A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 445 removed outlier: 4.268A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE q 445 " --> pdb=" O PHE q 441 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 457 Processing helix chain 'q' and resid 459 through 474 removed outlier: 3.517A pdb=" N VAL q 463 " --> pdb=" O LYS q 459 " (cutoff:3.500A) Processing helix chain 'q' and resid 492 through 496 Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 2 through 8 removed outlier: 3.557A pdb=" N THR z 6 " --> pdb=" O ALA z 2 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU z 7 " --> pdb=" O ALA z 3 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 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 88 Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.627A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.726A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 3.987A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 removed outlier: 3.660A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) 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 263 Processing helix chain 'z' and resid 264 through 282 removed outlier: 3.687A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 307 Processing helix chain 'z' and resid 318 through 329 removed outlier: 4.208A pdb=" N GLU z 322 " --> pdb=" O ARG z 318 " (cutoff:3.500A) Processing helix chain 'z' and resid 340 through 344 Processing helix chain 'z' and resid 380 through 404 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 432 through 445 removed outlier: 4.091A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.631A pdb=" N LYS z 449 " --> pdb=" O LEU z 445 " (cutoff:3.500A) Processing helix chain 'z' and resid 458 through 474 Processing helix chain 'z' and resid 489 through 493 Processing helix chain 'z' and resid 497 through 517 Processing helix chain 'P' and resid 62 through 88 removed outlier: 3.817A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU P 85 " --> pdb=" O CYS P 81 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ARG P 86 " --> pdb=" O ARG P 82 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU P 87 " --> pdb=" O GLU P 83 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE P 88 " --> pdb=" O MET P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 139 Processing helix chain 'P' and resid 140 through 151 removed outlier: 4.035A pdb=" N ARG P 144 " --> pdb=" O TYR P 140 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N MET P 145 " --> pdb=" O ARG P 141 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN P 151 " --> pdb=" O GLU P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 176 removed outlier: 3.617A pdb=" N ILE P 174 " --> pdb=" O PHE P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 209 Processing helix chain 'P' and resid 227 through 231 Processing helix chain 'P' and resid 260 through 270 removed outlier: 3.521A pdb=" N LEU P 264 " --> pdb=" O PHE P 260 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 198 through 203 removed outlier: 6.721A pdb=" N ALA N 213 " --> pdb=" O SER N 199 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N CYS N 201 " --> pdb=" O LEU N 211 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU N 211 " --> pdb=" O CYS N 201 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE N 203 " --> pdb=" O GLN N 209 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLN N 209 " --> pdb=" O PHE N 203 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP N 223 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU N 229 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 240 through 245 Processing sheet with id=AA3, first strand: chain 'N' and resid 284 through 289 removed outlier: 6.556A pdb=" N GLY N 299 " --> pdb=" O ASN N 285 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL N 287 " --> pdb=" O ALA N 297 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA N 297 " --> pdb=" O VAL N 287 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TYR N 289 " --> pdb=" O ALA N 295 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA N 295 " --> pdb=" O TYR N 289 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N CYS N 305 " --> pdb=" O ILE N 318 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE N 318 " --> pdb=" O CYS N 305 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU N 307 " --> pdb=" O VAL N 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 328 through 333 removed outlier: 3.976A pdb=" N THR N 348 " --> pdb=" O TYR N 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 9 through 13 removed outlier: 4.950A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 52 through 55 removed outlier: 6.015A pdb=" N MET A 44 " --> pdb=" O VAL G 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA8, first strand: chain 'A' and resid 181 through 182 removed outlier: 3.537A pdb=" N TYR A 181 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 189 " --> pdb=" O TYR A 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.333A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 213 through 216 removed outlier: 3.502A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 213 through 216 removed outlier: 3.502A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 254 through 256 removed outlier: 9.073A pdb=" N ASP G 255 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL A 252 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 255 " --> pdb=" O VAL E 268 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.504A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.453A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE B 521 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 61 through 64 removed outlier: 6.794A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU B 53 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB8, first strand: chain 'B' and resid 199 through 205 removed outlier: 3.817A pdb=" N GLY B 377 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.479A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 346 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU B 348 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU B 233 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE B 290 " --> pdb=" O ILE B 312 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 476 through 479 removed outlier: 3.507A pdb=" N THR B 484 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.382A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LYS D 213 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 227 through 229 Processing sheet with id=AC4, first strand: chain 'D' and resid 323 through 328 removed outlier: 5.747A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE D 249 " --> pdb=" O GLN D 301 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 421 through 423 Processing sheet with id=AC6, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.613A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 28 through 29 removed outlier: 4.594A pdb=" N ILE E 530 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU H 48 " --> pdb=" O ILE E 530 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP E 532 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL H 50 " --> pdb=" O ASP E 532 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG E 534 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC9, first strand: chain 'E' and resid 209 through 215 removed outlier: 3.862A pdb=" N GLY E 389 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 228 through 230 removed outlier: 3.554A pdb=" N LEU E 358 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 321 through 322 removed outlier: 8.741A pdb=" N VAL E 342 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE E 250 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 57 through 60 removed outlier: 6.445A pdb=" N MET G 47 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU Z 520 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AD5, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.773A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD7, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AD8, first strand: chain 'G' and resid 407 through 409 Processing sheet with id=AD9, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=AE1, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.398A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AE3, first strand: chain 'H' and resid 195 through 201 removed outlier: 3.969A pdb=" N GLY H 376 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AE5, first strand: chain 'H' and resid 309 through 311 Processing sheet with id=AE6, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AE7, first strand: chain 'Q' and resid 20 through 23 removed outlier: 4.909A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 149 through 150 removed outlier: 3.969A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.490A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS Q 205 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id=AF2, first strand: chain 'Q' and resid 240 through 242 Processing sheet with id=AF3, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AF4, first strand: chain 'Z' and resid 139 through 140 Processing sheet with id=AF5, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.501A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id=AF7, first strand: chain 'Z' and resid 311 through 313 removed outlier: 6.626A pdb=" N ASP Z 227 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU Z 231 " --> pdb=" O ILE Z 292 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.636A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 9 through 13 removed outlier: 4.555A pdb=" N ILE a 527 " --> pdb=" O ASP d 58 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N MET d 60 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE a 531 " --> pdb=" O GLN d 62 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.446A pdb=" N ASP a 42 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP g 521 " --> pdb=" O ASP a 42 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 138 through 139 Processing sheet with id=AG3, first strand: chain 'a' and resid 181 through 182 Processing sheet with id=AG4, first strand: chain 'a' and resid 196 through 201 removed outlier: 6.292A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N GLY a 379 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA a 200 " --> pdb=" O GLY a 379 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.482A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.482A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE a 286 " --> pdb=" O VAL a 308 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'g' and resid 254 through 256 removed outlier: 9.243A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'a' and resid 486 through 489 removed outlier: 3.526A pdb=" N LYS a 494 " --> pdb=" O ASP a 489 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 17 through 19 removed outlier: 4.486A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE b 521 " --> pdb=" O VAL e 62 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 61 through 64 removed outlier: 5.918A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AH3, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.594A pdb=" N HIS b 200 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU b 375 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE b 202 " --> pdb=" O LEU b 375 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLY b 377 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LYS b 204 " --> pdb=" O GLY b 377 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.422A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER b 345 " --> pdb=" O LYS b 236 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS b 236 " --> pdb=" O SER b 345 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS b 347 " --> pdb=" O ASN b 234 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AH6, first strand: chain 'd' and resid 153 through 154 Processing sheet with id=AH7, first strand: chain 'd' and resid 208 through 214 removed outlier: 4.071A pdb=" N GLY d 392 " --> pdb=" O LYS d 213 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 227 through 229 removed outlier: 6.488A pdb=" N CYS d 379 " --> pdb=" O ALA d 359 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA d 359 " --> pdb=" O CYS d 379 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU d 361 " --> pdb=" O GLU d 242 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLU d 242 " --> pdb=" O LEU d 361 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL d 297 " --> pdb=" O LYS d 243 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LYS d 245 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU d 299 " --> pdb=" O LYS d 245 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N GLN d 301 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE d 249 " --> pdb=" O GLN d 301 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AI1, first strand: chain 'e' and resid 26 through 29 removed outlier: 6.141A pdb=" N ASP h 46 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP e 532 " --> pdb=" O ASP h 46 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'e' and resid 153 through 154 Processing sheet with id=AI3, first strand: chain 'e' and resid 209 through 215 removed outlier: 3.851A pdb=" N GLY e 389 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'e' and resid 228 through 230 removed outlier: 6.471A pdb=" N CYS e 377 " --> pdb=" O ALA e 356 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA e 356 " --> pdb=" O CYS e 377 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE e 355 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS e 247 " --> pdb=" O PHE e 355 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLY e 357 " --> pdb=" O ASP e 245 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'g' and resid 57 through 60 removed outlier: 6.222A pdb=" N MET g 47 " --> pdb=" O VAL z 518 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU z 520 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'g' and resid 142 through 143 Processing sheet with id=AI7, first strand: chain 'g' and resid 185 through 187 Processing sheet with id=AI8, first strand: chain 'g' and resid 200 through 205 removed outlier: 6.885A pdb=" N ARG g 200 " --> pdb=" O ILE g 374 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU g 376 " --> pdb=" O ARG g 200 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLU g 202 " --> pdb=" O LEU g 376 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N GLY g 378 " --> pdb=" O GLU g 202 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE g 204 " --> pdb=" O GLY g 378 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'g' and resid 218 through 220 Processing sheet with id=AJ1, first strand: chain 'g' and resid 310 through 312 removed outlier: 9.003A pdb=" N VAL g 332 " --> pdb=" O ILE g 238 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU g 240 " --> pdb=" O VAL g 332 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'g' and resid 478 through 480 removed outlier: 3.582A pdb=" N VAL g 488 " --> pdb=" O GLY g 479 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'h' and resid 14 through 17 removed outlier: 4.360A pdb=" N VAL h 516 " --> pdb=" O ASN q 53 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N MET q 55 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU h 518 " --> pdb=" O MET q 55 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE q 57 " --> pdb=" O GLU h 518 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE h 520 " --> pdb=" O ILE q 57 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'h' and resid 195 through 201 removed outlier: 4.286A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AJ6, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ7, first strand: chain 'h' and resid 405 through 407 Processing sheet with id=AJ8, first strand: chain 'h' and resid 475 through 478 Processing sheet with id=AJ9, first strand: chain 'q' and resid 20 through 23 removed outlier: 5.105A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'q' and resid 149 through 150 removed outlier: 3.719A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'q' and resid 202 through 206 removed outlier: 6.514A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'q' and resid 220 through 223 Processing sheet with id=AK4, first strand: chain 'q' and resid 240 through 242 Processing sheet with id=AK5, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AK6, first strand: chain 'z' and resid 139 through 140 Processing sheet with id=AK7, first strand: chain 'z' and resid 191 through 196 Processing sheet with id=AK8, first strand: chain 'z' and resid 210 through 212 Processing sheet with id=AK9, first strand: chain 'z' and resid 310 through 313 removed outlier: 6.440A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE z 292 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU z 231 " --> pdb=" O ILE z 292 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'z' and resid 477 through 479 Processing sheet with id=AL2, first strand: chain 'P' and resid 162 through 164 removed outlier: 6.254A pdb=" N PHE P 162 " --> pdb=" O LYS P 216 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LYS P 218 " --> pdb=" O PHE P 162 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ILE P 164 " --> pdb=" O LYS P 218 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N CYS P 215 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N MET P 184 " --> pdb=" O CYS P 215 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL P 217 " --> pdb=" O MET P 184 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N HIS P 186 " --> pdb=" O VAL P 217 " (cutoff:3.500A) 4093 hydrogen bonds defined for protein. 11700 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: 37.81 Time building geometry restraints manager: 15.91 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: 22928 1.34 - 1.46: 12788 1.46 - 1.58: 32317 1.58 - 1.70: 48 1.70 - 1.82: 745 Bond restraints: 68826 Sorted by residual: bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.43e+01 bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.36e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" F2 AF3 A 603 " pdb="AL AF3 A 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.33e+01 ... (remaining 68821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 91289 1.63 - 3.26: 1230 3.26 - 4.89: 234 4.89 - 6.51: 160 6.51 - 8.14: 8 Bond angle restraints: 92921 Sorted by residual: angle pdb=" N ILE P 245 " pdb=" CA ILE P 245 " pdb=" C ILE P 245 " ideal model delta sigma weight residual 113.42 108.57 4.85 1.17e+00 7.31e-01 1.72e+01 angle pdb=" CG MET h 497 " pdb=" SD MET h 497 " pdb=" CE MET h 497 " ideal model delta sigma weight residual 100.90 93.41 7.49 2.20e+00 2.07e-01 1.16e+01 angle pdb=" N ILE h 168 " pdb=" CA ILE h 168 " pdb=" C ILE h 168 " ideal model delta sigma weight residual 111.91 109.08 2.83 8.90e-01 1.26e+00 1.01e+01 angle pdb=" N GLU d 93 " pdb=" CA GLU d 93 " pdb=" CB GLU d 93 " ideal model delta sigma weight residual 110.39 115.58 -5.19 1.66e+00 3.63e-01 9.76e+00 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 120.45 -7.27 2.37e+00 1.78e-01 9.41e+00 ... (remaining 92916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 41831 35.25 - 70.50: 616 70.50 - 105.75: 55 105.75 - 141.00: 11 141.00 - 176.25: 5 Dihedral angle restraints: 42518 sinusoidal: 17106 harmonic: 25412 Sorted by residual: dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 123.75 176.25 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 109.63 -169.63 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual -60.00 109.53 -169.53 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 42515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 7500 0.035 - 0.069: 2417 0.069 - 0.104: 793 0.104 - 0.139: 331 0.139 - 0.174: 11 Chirality restraints: 11052 Sorted by residual: chirality pdb=" CB ILE G 460 " pdb=" CA ILE G 460 " pdb=" CG1 ILE G 460 " pdb=" CG2 ILE G 460 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA ILE g 363 " pdb=" N ILE g 363 " pdb=" C ILE g 363 " pdb=" CB ILE g 363 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CB VAL h 36 " pdb=" CA VAL h 36 " pdb=" CG1 VAL h 36 " pdb=" CG2 VAL h 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 11049 not shown) Planarity restraints: 11863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO e 441 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 52 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO G 53 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU P 274 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO P 275 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO P 275 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO P 275 " 0.028 5.00e-02 4.00e+02 ... (remaining 11860 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 541 2.50 - 3.10: 50311 3.10 - 3.70: 104887 3.70 - 4.30: 151684 4.30 - 4.90: 259255 Nonbonded interactions: 566678 Sorted by model distance: nonbonded pdb="MG MG b 602 " pdb=" F1 AF3 b 603 " model vdw 1.905 2.120 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.915 2.120 nonbonded pdb=" O1A ADP z 601 " pdb="MG MG z 602 " model vdw 1.919 2.170 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.928 2.120 nonbonded pdb="MG MG z 602 " pdb=" F1 AF3 z 603 " model vdw 1.934 2.120 ... (remaining 566673 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = (chain 'G' and (resid 5 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 5 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 2.170 Check model and map are aligned: 0.400 Set scattering table: 0.520 Process input model: 140.390 Find NCS groups from input model: 5.940 Set up NCS constraints: 0.490 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:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.161 68826 Z= 0.323 Angle : 0.548 8.143 92921 Z= 0.270 Chirality : 0.042 0.174 11052 Planarity : 0.003 0.052 11863 Dihedral : 14.051 176.251 26060 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 1.58 (0.09), residues: 8784 helix: 2.35 (0.08), residues: 4417 sheet: 0.05 (0.16), residues: 1221 loop : -0.42 (0.11), residues: 3146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 304 HIS 0.012 0.001 HIS Z 161 PHE 0.026 0.001 PHE E 386 TYR 0.018 0.001 TYR G 437 ARG 0.005 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 584 time to evaluate : 6.123 Fit side-chains revert: symmetry clash REVERT: N 333 PHE cc_start: 0.7069 (m-80) cc_final: 0.6724 (m-80) REVERT: N 352 TRP cc_start: 0.7299 (m100) cc_final: 0.6529 (m100) REVERT: A 51 ASP cc_start: 0.8356 (m-30) cc_final: 0.8119 (m-30) REVERT: D 355 MET cc_start: 0.9298 (mmt) cc_final: 0.9078 (mpp) REVERT: E 493 CYS cc_start: 0.8463 (m) cc_final: 0.8004 (m) REVERT: G 15 LYS cc_start: 0.9008 (mptt) cc_final: 0.8779 (mmtt) REVERT: H 14 ASP cc_start: 0.8168 (t70) cc_final: 0.7911 (t0) REVERT: H 308 MET cc_start: 0.8875 (mtt) cc_final: 0.8648 (mtt) REVERT: Q 61 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8592 (mt-10) REVERT: Z 196 MET cc_start: 0.8193 (mtt) cc_final: 0.7980 (mtm) REVERT: Z 430 LYS cc_start: 0.9051 (tmmt) cc_final: 0.8827 (tppt) REVERT: a 430 MET cc_start: 0.8208 (mmt) cc_final: 0.8001 (mpt) REVERT: d 93 GLU cc_start: 0.8423 (mp0) cc_final: 0.8011 (mp0) REVERT: d 279 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8369 (tm-30) REVERT: e 58 ASP cc_start: 0.8071 (m-30) cc_final: 0.7797 (m-30) REVERT: h 324 MET cc_start: 0.9205 (mmm) cc_final: 0.8936 (mmm) REVERT: z 66 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8323 (mm-30) REVERT: z 358 GLU cc_start: 0.7611 (pm20) cc_final: 0.7228 (pm20) REVERT: P 63 ILE cc_start: 0.9167 (tp) cc_final: 0.8861 (tp) REVERT: P 66 TRP cc_start: 0.7169 (t-100) cc_final: 0.6300 (t-100) REVERT: P 67 ARG cc_start: 0.8442 (mmp80) cc_final: 0.8017 (mmp80) REVERT: P 68 ARG cc_start: 0.7296 (tpm170) cc_final: 0.7086 (tpm170) REVERT: P 201 CYS cc_start: 0.8433 (m) cc_final: 0.8210 (m) outliers start: 0 outliers final: 3 residues processed: 584 average time/residue: 1.6667 time to fit residues: 1249.6225 Evaluate side-chains 475 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 472 time to evaluate : 6.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain G residue 519 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 738 optimal weight: 0.9990 chunk 663 optimal weight: 4.9990 chunk 368 optimal weight: 10.0000 chunk 226 optimal weight: 0.7980 chunk 447 optimal weight: 10.0000 chunk 354 optimal weight: 0.9990 chunk 685 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 417 optimal weight: 9.9990 chunk 510 optimal weight: 0.7980 chunk 794 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 169 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN D 235 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 GLN Z 161 HIS Z 198 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 450 ASN b 122 HIS ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 468 ASN q 53 ASN z 95 ASN z 161 HIS ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 68826 Z= 0.195 Angle : 0.565 9.049 92921 Z= 0.282 Chirality : 0.042 0.167 11052 Planarity : 0.003 0.052 11863 Dihedral : 7.647 174.959 9557 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.58 % Allowed : 6.02 % Favored : 93.39 % 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: 1.59 (0.09), residues: 8784 helix: 2.37 (0.08), residues: 4477 sheet: 0.03 (0.15), residues: 1179 loop : -0.48 (0.11), residues: 3128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 222 HIS 0.011 0.001 HIS z 161 PHE 0.017 0.001 PHE E 386 TYR 0.023 0.001 TYR N 290 ARG 0.008 0.000 ARG P 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 525 time to evaluate : 6.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 350 ASN cc_start: 0.6836 (p0) cc_final: 0.5316 (p0) REVERT: A 47 ASP cc_start: 0.7774 (t0) cc_final: 0.7507 (OUTLIER) REVERT: A 51 ASP cc_start: 0.8345 (m-30) cc_final: 0.7930 (m-30) REVERT: A 433 ARG cc_start: 0.8075 (mtt-85) cc_final: 0.7759 (mtt180) REVERT: E 48 MET cc_start: 0.9118 (tpp) cc_final: 0.8870 (mmm) REVERT: E 58 ASP cc_start: 0.8222 (m-30) cc_final: 0.7984 (m-30) REVERT: E 231 ASP cc_start: 0.8427 (t0) cc_final: 0.8134 (t0) REVERT: E 474 MET cc_start: 0.8318 (tmm) cc_final: 0.8026 (tmt) REVERT: E 493 CYS cc_start: 0.8555 (m) cc_final: 0.8070 (m) REVERT: G 15 LYS cc_start: 0.8834 (mptt) cc_final: 0.8622 (mmtt) REVERT: H 14 ASP cc_start: 0.8156 (t70) cc_final: 0.7908 (t0) REVERT: H 308 MET cc_start: 0.8797 (mtt) cc_final: 0.8590 (mtt) REVERT: H 524 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7145 (ttp80) REVERT: Z 196 MET cc_start: 0.8377 (mtt) cc_final: 0.8148 (mtm) REVERT: Z 286 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7836 (t0) REVERT: a 354 GLU cc_start: 0.7878 (tp30) cc_final: 0.7575 (tm-30) REVERT: a 430 MET cc_start: 0.8175 (mmt) cc_final: 0.7969 (mpt) REVERT: b 415 MET cc_start: 0.9367 (mmm) cc_final: 0.9092 (mmp) REVERT: d 93 GLU cc_start: 0.8376 (mp0) cc_final: 0.7993 (mp0) REVERT: d 279 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8277 (tm-30) REVERT: d 446 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7717 (mmm) REVERT: e 4 MET cc_start: 0.6828 (mpt) cc_final: 0.6549 (mpp) REVERT: e 58 ASP cc_start: 0.8143 (m-30) cc_final: 0.7723 (m-30) REVERT: g 110 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: h 7 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8315 (pp) REVERT: h 53 ARG cc_start: 0.8849 (mpp80) cc_final: 0.8646 (mmm160) REVERT: h 324 MET cc_start: 0.9210 (mmm) cc_final: 0.8917 (mmm) REVERT: z 66 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8186 (mm-30) REVERT: z 244 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8778 (t) REVERT: z 358 GLU cc_start: 0.7502 (pm20) cc_final: 0.7189 (pm20) REVERT: P 66 TRP cc_start: 0.7407 (t-100) cc_final: 0.6208 (t-100) REVERT: P 67 ARG cc_start: 0.8549 (mmp80) cc_final: 0.8235 (mmp80) outliers start: 43 outliers final: 20 residues processed: 543 average time/residue: 1.6222 time to fit residues: 1145.6874 Evaluate side-chains 494 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 469 time to evaluate : 6.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 169 ASN Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain H residue 524 ARG Chi-restraints excluded: chain Q residue 318 LYS Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 118 ASP Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 233 HIS Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain z residue 143 MET Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 441 optimal weight: 0.0270 chunk 246 optimal weight: 10.0000 chunk 661 optimal weight: 5.9990 chunk 541 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 796 optimal weight: 7.9990 chunk 859 optimal weight: 20.0000 chunk 708 optimal weight: 5.9990 chunk 789 optimal weight: 8.9990 chunk 271 optimal weight: 0.9990 chunk 638 optimal weight: 5.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 468 ASN ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 274 ASN z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 68826 Z= 0.327 Angle : 0.589 10.020 92921 Z= 0.293 Chirality : 0.043 0.165 11052 Planarity : 0.003 0.055 11863 Dihedral : 7.380 177.796 9552 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.91 % Allowed : 7.80 % Favored : 91.29 % 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: 1.52 (0.09), residues: 8784 helix: 2.33 (0.08), residues: 4492 sheet: -0.06 (0.15), residues: 1174 loop : -0.53 (0.11), residues: 3118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.015 0.001 HIS z 161 PHE 0.032 0.001 PHE P 136 TYR 0.015 0.001 TYR Z 498 ARG 0.006 0.000 ARG P 230 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 486 time to evaluate : 6.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 182 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7958 (tm-30) REVERT: A 47 ASP cc_start: 0.7931 (t0) cc_final: 0.7598 (OUTLIER) REVERT: A 51 ASP cc_start: 0.8377 (m-30) cc_final: 0.7926 (m-30) REVERT: A 230 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7768 (t) REVERT: A 433 ARG cc_start: 0.8044 (mtt-85) cc_final: 0.7742 (mtt180) REVERT: B 20 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7915 (mmt-90) REVERT: E 48 MET cc_start: 0.9135 (tpp) cc_final: 0.8878 (mmm) REVERT: E 58 ASP cc_start: 0.8254 (m-30) cc_final: 0.8012 (m-30) REVERT: E 474 MET cc_start: 0.8391 (tmm) cc_final: 0.8055 (tmt) REVERT: E 493 CYS cc_start: 0.8513 (m) cc_final: 0.8035 (m) REVERT: G 15 LYS cc_start: 0.8849 (mptt) cc_final: 0.8645 (mmtt) REVERT: H 14 ASP cc_start: 0.8173 (t70) cc_final: 0.7940 (t0) REVERT: H 524 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7056 (ttp80) REVERT: Z 196 MET cc_start: 0.8466 (mtt) cc_final: 0.8252 (mtm) REVERT: Z 286 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7902 (t0) REVERT: Z 357 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8038 (tp30) REVERT: a 354 GLU cc_start: 0.7906 (tp30) cc_final: 0.7544 (tm-30) REVERT: b 415 MET cc_start: 0.9503 (mmm) cc_final: 0.9122 (mmp) REVERT: d 48 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8644 (pp) REVERT: d 60 MET cc_start: 0.9216 (ttp) cc_final: 0.8988 (ttp) REVERT: d 93 GLU cc_start: 0.8412 (mp0) cc_final: 0.8004 (mp0) REVERT: d 279 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8312 (tm-30) REVERT: d 513 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8715 (tm) REVERT: e 58 ASP cc_start: 0.8176 (m-30) cc_final: 0.7758 (m-30) REVERT: e 118 GLU cc_start: 0.8506 (tt0) cc_final: 0.8166 (tm-30) REVERT: e 526 MET cc_start: 0.9357 (ttp) cc_final: 0.9137 (ttt) REVERT: g 110 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: h 7 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8366 (pp) REVERT: h 324 MET cc_start: 0.9200 (mmm) cc_final: 0.8920 (mmm) REVERT: h 524 ARG cc_start: 0.8108 (mmm-85) cc_final: 0.7841 (mmm160) REVERT: z 66 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8328 (mm-30) REVERT: z 358 GLU cc_start: 0.7503 (pm20) cc_final: 0.7194 (pm20) REVERT: P 66 TRP cc_start: 0.7372 (t-100) cc_final: 0.6780 (t-100) REVERT: P 84 MET cc_start: 0.6066 (tmm) cc_final: 0.5793 (tmm) outliers start: 67 outliers final: 31 residues processed: 516 average time/residue: 1.5599 time to fit residues: 1045.9303 Evaluate side-chains 503 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 464 time to evaluate : 6.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain H residue 524 ARG Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 318 LYS Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 7 VAL Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 118 ASP Chi-restraints excluded: chain d residue 320 MET Chi-restraints excluded: chain d residue 355 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 233 HIS Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 473 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 786 optimal weight: 10.0000 chunk 598 optimal weight: 2.9990 chunk 413 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 379 optimal weight: 9.9990 chunk 534 optimal weight: 3.9990 chunk 798 optimal weight: 0.9990 chunk 845 optimal weight: 8.9990 chunk 417 optimal weight: 8.9990 chunk 757 optimal weight: 8.9990 chunk 227 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 194 HIS A 56 ASN A 170 ASN D 235 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 170 ASN ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 68826 Z= 0.254 Angle : 0.565 10.798 92921 Z= 0.280 Chirality : 0.042 0.168 11052 Planarity : 0.003 0.055 11863 Dihedral : 7.226 176.909 9552 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.66 % Favored : 96.33 % Rotamer: Outliers : 1.23 % Allowed : 9.00 % Favored : 89.77 % 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: 1.53 (0.09), residues: 8784 helix: 2.37 (0.08), residues: 4485 sheet: -0.14 (0.15), residues: 1185 loop : -0.53 (0.11), residues: 3114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 222 HIS 0.016 0.001 HIS z 161 PHE 0.017 0.001 PHE E 386 TYR 0.026 0.001 TYR N 290 ARG 0.007 0.000 ARG h 398 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 487 time to evaluate : 6.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 182 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7946 (tm-30) REVERT: N 262 LYS cc_start: 0.7565 (mmmt) cc_final: 0.7213 (mmmt) REVERT: N 264 MET cc_start: 0.8006 (mtp) cc_final: 0.7526 (mtp) REVERT: A 47 ASP cc_start: 0.7944 (t0) cc_final: 0.7554 (OUTLIER) REVERT: A 51 ASP cc_start: 0.8383 (m-30) cc_final: 0.7926 (m-30) REVERT: A 230 VAL cc_start: 0.7931 (OUTLIER) cc_final: 0.7646 (t) REVERT: A 314 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8454 (ptt90) REVERT: A 358 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8281 (m-30) REVERT: A 433 ARG cc_start: 0.8006 (mtt-85) cc_final: 0.7801 (mtt180) REVERT: B 20 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7903 (mmt-90) REVERT: E 58 ASP cc_start: 0.8235 (m-30) cc_final: 0.8020 (m-30) REVERT: E 474 MET cc_start: 0.8351 (tmm) cc_final: 0.8039 (tmt) REVERT: E 493 CYS cc_start: 0.8435 (m) cc_final: 0.7971 (m) REVERT: G 15 LYS cc_start: 0.8864 (mptt) cc_final: 0.8650 (mmtt) REVERT: H 14 ASP cc_start: 0.8180 (t70) cc_final: 0.7942 (t0) REVERT: H 308 MET cc_start: 0.8731 (mtt) cc_final: 0.8496 (mtt) REVERT: H 524 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7116 (ttp80) REVERT: Z 196 MET cc_start: 0.8433 (mtt) cc_final: 0.8227 (mtm) REVERT: Z 286 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7891 (t0) REVERT: Z 357 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8041 (tp30) REVERT: a 354 GLU cc_start: 0.7898 (tp30) cc_final: 0.7500 (tm-30) REVERT: b 415 MET cc_start: 0.9522 (mmm) cc_final: 0.9147 (mmp) REVERT: d 90 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8749 (mmt) REVERT: d 279 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8277 (tm-30) REVERT: d 446 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7708 (mmm) REVERT: d 513 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8668 (tm) REVERT: e 4 MET cc_start: 0.6285 (mpt) cc_final: 0.5989 (mpp) REVERT: e 58 ASP cc_start: 0.8174 (m-30) cc_final: 0.7705 (m-30) REVERT: e 526 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.9109 (ttt) REVERT: g 110 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: h 7 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8325 (pp) REVERT: h 324 MET cc_start: 0.9203 (mmm) cc_final: 0.8914 (mmm) REVERT: q 473 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: z 66 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8312 (mm-30) REVERT: z 244 VAL cc_start: 0.9008 (OUTLIER) cc_final: 0.8756 (t) REVERT: z 358 GLU cc_start: 0.7487 (pm20) cc_final: 0.7169 (pm20) REVERT: P 66 TRP cc_start: 0.7405 (t-100) cc_final: 0.6811 (t-100) REVERT: P 77 ARG cc_start: 0.6969 (tmm160) cc_final: 0.5550 (ppt170) REVERT: P 144 ARG cc_start: 0.7353 (mpp-170) cc_final: 0.7129 (mpp-170) outliers start: 91 outliers final: 32 residues processed: 536 average time/residue: 1.6040 time to fit residues: 1120.1446 Evaluate side-chains 512 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 466 time to evaluate : 6.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain H residue 524 ARG Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 318 LYS Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 118 ASP Chi-restraints excluded: chain d residue 320 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 526 MET Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 473 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 704 optimal weight: 9.9990 chunk 480 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 629 optimal weight: 7.9990 chunk 348 optimal weight: 6.9990 chunk 721 optimal weight: 7.9990 chunk 584 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 431 optimal weight: 4.9990 chunk 759 optimal weight: 0.7980 chunk 213 optimal weight: 10.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 HIS D 235 ASN D 502 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 68826 Z= 0.456 Angle : 0.649 10.051 92921 Z= 0.323 Chirality : 0.045 0.179 11052 Planarity : 0.004 0.056 11863 Dihedral : 7.349 178.565 9550 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.09 % Favored : 95.89 % Rotamer: Outliers : 1.44 % Allowed : 10.15 % Favored : 88.41 % 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: 1.36 (0.09), residues: 8784 helix: 2.22 (0.08), residues: 4486 sheet: -0.27 (0.15), residues: 1165 loop : -0.58 (0.11), residues: 3133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 222 HIS 0.016 0.001 HIS z 161 PHE 0.037 0.002 PHE P 136 TYR 0.018 0.002 TYR Q 304 ARG 0.008 0.000 ARG h 524 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 479 time to evaluate : 6.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 182 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8062 (tm-30) REVERT: N 262 LYS cc_start: 0.7636 (mmmt) cc_final: 0.7272 (mmmt) REVERT: N 264 MET cc_start: 0.8004 (mtp) cc_final: 0.7705 (mtp) REVERT: A 47 ASP cc_start: 0.8003 (t0) cc_final: 0.7583 (OUTLIER) REVERT: A 51 ASP cc_start: 0.8457 (m-30) cc_final: 0.7997 (m-30) REVERT: A 80 ASP cc_start: 0.8591 (t0) cc_final: 0.8275 (t0) REVERT: A 230 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7786 (t) REVERT: A 358 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8302 (m-30) REVERT: A 433 ARG cc_start: 0.8099 (mtt-85) cc_final: 0.7825 (mtt180) REVERT: B 20 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7827 (mmt-90) REVERT: D 50 THR cc_start: 0.9517 (OUTLIER) cc_final: 0.9292 (p) REVERT: E 48 MET cc_start: 0.9161 (tpp) cc_final: 0.8920 (mmm) REVERT: E 58 ASP cc_start: 0.8286 (m-30) cc_final: 0.8045 (m-30) REVERT: E 474 MET cc_start: 0.8500 (tmm) cc_final: 0.8101 (tmt) REVERT: E 493 CYS cc_start: 0.8479 (m) cc_final: 0.7974 (m) REVERT: H 14 ASP cc_start: 0.8256 (t70) cc_final: 0.8028 (t0) REVERT: H 524 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7018 (ttp80) REVERT: Q 61 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8732 (mt-10) REVERT: Z 286 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.7974 (t0) REVERT: Z 357 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8017 (tp30) REVERT: a 354 GLU cc_start: 0.7923 (tp30) cc_final: 0.7514 (tm-30) REVERT: b 415 MET cc_start: 0.9535 (mmm) cc_final: 0.9063 (mmp) REVERT: d 279 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8348 (tm-30) REVERT: d 446 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7765 (mmm) REVERT: d 513 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8771 (tm) REVERT: e 58 ASP cc_start: 0.8180 (m-30) cc_final: 0.7723 (m-30) REVERT: e 118 GLU cc_start: 0.8499 (tt0) cc_final: 0.8150 (tm-30) REVERT: g 110 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: g 229 MET cc_start: 0.9351 (ptp) cc_final: 0.9149 (mtm) REVERT: h 7 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8351 (pp) REVERT: h 324 MET cc_start: 0.9178 (mmm) cc_final: 0.8889 (mmm) REVERT: q 473 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: z 66 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8473 (mm-30) REVERT: z 244 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8767 (t) REVERT: z 358 GLU cc_start: 0.7524 (pm20) cc_final: 0.7187 (pm20) REVERT: z 415 GLU cc_start: 0.8672 (mp0) cc_final: 0.8406 (OUTLIER) REVERT: P 66 TRP cc_start: 0.7479 (t-100) cc_final: 0.6855 (t-100) REVERT: P 298 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7066 (OUTLIER) outliers start: 106 outliers final: 53 residues processed: 538 average time/residue: 1.5614 time to fit residues: 1097.7421 Evaluate side-chains 526 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 461 time to evaluate : 6.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 169 ASN Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain N residue 352 TRP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain H residue 524 ARG Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 221 MET Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 318 LYS Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 7 VAL Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 118 ASP Chi-restraints excluded: chain d residue 320 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 214 VAL Chi-restraints excluded: chain g residue 480 VAL Chi-restraints excluded: chain g residue 483 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 473 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 285 VAL Chi-restraints excluded: chain P residue 298 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 284 optimal weight: 4.9990 chunk 761 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 496 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 846 optimal weight: 10.0000 chunk 702 optimal weight: 0.9980 chunk 391 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 444 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 235 ASN E 445 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 ASN ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 68826 Z= 0.196 Angle : 0.561 11.073 92921 Z= 0.278 Chirality : 0.042 0.189 11052 Planarity : 0.003 0.054 11863 Dihedral : 7.139 175.757 9550 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.44 % Favored : 96.54 % Rotamer: Outliers : 1.36 % Allowed : 10.95 % Favored : 87.69 % 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: 1.51 (0.09), residues: 8784 helix: 2.38 (0.08), residues: 4484 sheet: -0.19 (0.15), residues: 1180 loop : -0.55 (0.11), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 222 HIS 0.016 0.001 HIS z 161 PHE 0.013 0.001 PHE a 167 TYR 0.027 0.001 TYR N 290 ARG 0.008 0.000 ARG P 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 502 time to evaluate : 6.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 182 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8015 (tm-30) REVERT: N 264 MET cc_start: 0.7935 (mtp) cc_final: 0.7735 (mtp) REVERT: A 47 ASP cc_start: 0.7950 (t0) cc_final: 0.7524 (OUTLIER) REVERT: A 51 ASP cc_start: 0.8422 (m-30) cc_final: 0.8000 (m-30) REVERT: A 230 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7783 (t) REVERT: A 433 ARG cc_start: 0.8027 (mtt-85) cc_final: 0.7826 (mtt180) REVERT: B 20 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7896 (mmt-90) REVERT: B 62 MET cc_start: 0.7968 (ttm) cc_final: 0.7713 (ttp) REVERT: E 48 MET cc_start: 0.9160 (tpp) cc_final: 0.8902 (mmm) REVERT: E 58 ASP cc_start: 0.8261 (m-30) cc_final: 0.8041 (m-30) REVERT: E 199 MET cc_start: 0.7123 (mmm) cc_final: 0.6830 (mmp) REVERT: E 474 MET cc_start: 0.8345 (tmm) cc_final: 0.8102 (tmt) REVERT: E 493 CYS cc_start: 0.8402 (m) cc_final: 0.7937 (m) REVERT: H 14 ASP cc_start: 0.8149 (t70) cc_final: 0.7931 (t0) REVERT: H 524 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7136 (ttp80) REVERT: Q 200 ASP cc_start: 0.8706 (m-30) cc_final: 0.8351 (t0) REVERT: Z 286 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7892 (t0) REVERT: Z 357 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.8012 (tp30) REVERT: a 354 GLU cc_start: 0.7877 (tp30) cc_final: 0.7474 (tm-30) REVERT: a 416 GLU cc_start: 0.8448 (mp0) cc_final: 0.8200 (mp0) REVERT: b 415 MET cc_start: 0.9510 (mmm) cc_final: 0.9063 (mmp) REVERT: d 90 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8675 (mmt) REVERT: d 279 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8311 (tm-30) REVERT: d 513 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8651 (tm) REVERT: e 58 ASP cc_start: 0.8189 (m-30) cc_final: 0.7719 (m-30) REVERT: g 110 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8062 (tm-30) REVERT: h 7 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8318 (pp) REVERT: h 324 MET cc_start: 0.9164 (mmm) cc_final: 0.8856 (mmm) REVERT: h 524 ARG cc_start: 0.8264 (mmm160) cc_final: 0.8054 (mmm160) REVERT: q 253 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8669 (p) REVERT: q 311 MET cc_start: 0.9094 (ttp) cc_final: 0.8830 (ttp) REVERT: q 473 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: z 66 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8308 (mm-30) REVERT: z 244 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8709 (t) REVERT: z 358 GLU cc_start: 0.7499 (pm20) cc_final: 0.7160 (pm20) REVERT: P 66 TRP cc_start: 0.7480 (t-100) cc_final: 0.6892 (t-100) REVERT: P 68 ARG cc_start: 0.7180 (tpm170) cc_final: 0.6946 (tpm170) REVERT: P 168 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7343 (tp30) outliers start: 100 outliers final: 33 residues processed: 559 average time/residue: 1.6106 time to fit residues: 1178.2753 Evaluate side-chains 516 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 472 time to evaluate : 6.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain N residue 352 TRP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain H residue 524 ARG Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain a residue 464 VAL Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 480 VAL Chi-restraints excluded: chain g residue 483 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 473 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 285 VAL Chi-restraints excluded: chain P residue 298 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 816 optimal weight: 7.9990 chunk 95 optimal weight: 0.4980 chunk 482 optimal weight: 9.9990 chunk 618 optimal weight: 0.9990 chunk 479 optimal weight: 0.0470 chunk 712 optimal weight: 2.9990 chunk 472 optimal weight: 9.9990 chunk 843 optimal weight: 7.9990 chunk 527 optimal weight: 8.9990 chunk 514 optimal weight: 6.9990 chunk 389 optimal weight: 9.9990 overall best weight: 2.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 169 ASN D 235 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 68826 Z= 0.225 Angle : 0.565 10.673 92921 Z= 0.279 Chirality : 0.042 0.166 11052 Planarity : 0.003 0.053 11863 Dihedral : 7.054 174.455 9550 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Rotamer: Outliers : 1.10 % Allowed : 11.78 % Favored : 87.12 % 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: 1.54 (0.09), residues: 8784 helix: 2.40 (0.08), residues: 4481 sheet: -0.16 (0.15), residues: 1173 loop : -0.54 (0.11), residues: 3130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.017 0.001 HIS z 161 PHE 0.036 0.001 PHE P 136 TYR 0.012 0.001 TYR G 274 ARG 0.009 0.000 ARG P 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 482 time to evaluate : 6.168 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: N 182 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8099 (tm-30) REVERT: A 47 ASP cc_start: 0.7965 (t0) cc_final: 0.7562 (t0) REVERT: A 51 ASP cc_start: 0.8420 (m-30) cc_final: 0.7990 (m-30) REVERT: A 230 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7851 (t) REVERT: B 20 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7881 (mmt-90) REVERT: B 62 MET cc_start: 0.8032 (ttm) cc_final: 0.7793 (ttp) REVERT: B 488 MET cc_start: 0.9372 (mmp) cc_final: 0.9168 (mmp) REVERT: D 50 THR cc_start: 0.9485 (OUTLIER) cc_final: 0.9280 (p) REVERT: D 192 MET cc_start: 0.8789 (tpp) cc_final: 0.8570 (mmp) REVERT: E 48 MET cc_start: 0.9169 (tpp) cc_final: 0.8910 (mmm) REVERT: E 58 ASP cc_start: 0.8268 (m-30) cc_final: 0.8064 (m-30) REVERT: E 474 MET cc_start: 0.8367 (tmm) cc_final: 0.8108 (tmt) REVERT: E 493 CYS cc_start: 0.8426 (m) cc_final: 0.7959 (m) REVERT: H 14 ASP cc_start: 0.8101 (t70) cc_final: 0.7879 (t0) REVERT: H 524 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6818 (ttp80) REVERT: Q 61 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8690 (mp0) REVERT: Z 286 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7894 (t0) REVERT: Z 357 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8010 (tp30) REVERT: a 354 GLU cc_start: 0.7869 (tp30) cc_final: 0.7334 (tm-30) REVERT: a 416 GLU cc_start: 0.8449 (mp0) cc_final: 0.8181 (mp0) REVERT: b 415 MET cc_start: 0.9511 (mmm) cc_final: 0.9032 (mmp) REVERT: d 90 MET cc_start: 0.9243 (OUTLIER) cc_final: 0.8720 (mmt) REVERT: d 279 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8318 (tm-30) REVERT: d 446 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7503 (mmm) REVERT: d 513 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8713 (tm) REVERT: e 58 ASP cc_start: 0.8194 (m-30) cc_final: 0.7728 (m-30) REVERT: e 118 GLU cc_start: 0.8536 (tt0) cc_final: 0.8178 (tm-30) REVERT: g 110 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: h 7 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8297 (pp) REVERT: h 324 MET cc_start: 0.9146 (mmm) cc_final: 0.8829 (mmm) REVERT: h 524 ARG cc_start: 0.8287 (mmm160) cc_final: 0.8061 (mmm160) REVERT: q 253 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8654 (p) REVERT: q 311 MET cc_start: 0.9084 (ttp) cc_final: 0.8878 (ttp) REVERT: q 473 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: z 66 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8315 (mm-30) REVERT: z 244 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8708 (t) REVERT: z 358 GLU cc_start: 0.7485 (pm20) cc_final: 0.7140 (pm20) REVERT: P 66 TRP cc_start: 0.7499 (t-100) cc_final: 0.6885 (t-100) REVERT: P 168 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7355 (tp30) REVERT: P 199 ASN cc_start: 0.8563 (t0) cc_final: 0.8150 (m110) outliers start: 81 outliers final: 38 residues processed: 534 average time/residue: 1.5612 time to fit residues: 1093.9354 Evaluate side-chains 525 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 473 time to evaluate : 6.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain N residue 352 TRP Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain H residue 524 ARG Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain a residue 464 VAL Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 320 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 480 VAL Chi-restraints excluded: chain g residue 483 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 473 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 285 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 521 optimal weight: 10.0000 chunk 336 optimal weight: 7.9990 chunk 503 optimal weight: 0.8980 chunk 254 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 536 optimal weight: 4.9990 chunk 574 optimal weight: 9.9990 chunk 416 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 662 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 235 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 68826 Z= 0.338 Angle : 0.606 14.353 92921 Z= 0.299 Chirality : 0.043 0.168 11052 Planarity : 0.003 0.054 11863 Dihedral : 7.095 174.899 9550 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.82 % Favored : 96.16 % Rotamer: Outliers : 1.26 % Allowed : 11.78 % Favored : 86.96 % 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: 1.47 (0.09), residues: 8784 helix: 2.36 (0.08), residues: 4481 sheet: -0.25 (0.15), residues: 1167 loop : -0.57 (0.11), residues: 3136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 304 HIS 0.016 0.001 HIS z 161 PHE 0.018 0.001 PHE N 296 TYR 0.022 0.001 TYR N 290 ARG 0.009 0.000 ARG P 230 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 476 time to evaluate : 6.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 182 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8078 (tm-30) REVERT: A 47 ASP cc_start: 0.7989 (t0) cc_final: 0.7590 (t0) REVERT: A 51 ASP cc_start: 0.8437 (m-30) cc_final: 0.8004 (m-30) REVERT: A 156 MET cc_start: 0.8762 (mtm) cc_final: 0.8549 (mtp) REVERT: A 230 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7819 (t) REVERT: B 20 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7891 (mmt-90) REVERT: B 62 MET cc_start: 0.8082 (ttm) cc_final: 0.7840 (ttp) REVERT: D 334 GLU cc_start: 0.8456 (tp30) cc_final: 0.8190 (tp30) REVERT: E 48 MET cc_start: 0.9181 (tpp) cc_final: 0.8920 (mmm) REVERT: E 199 MET cc_start: 0.7026 (mmm) cc_final: 0.6705 (mmp) REVERT: E 493 CYS cc_start: 0.8460 (m) cc_final: 0.7977 (m) REVERT: G 337 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8823 (mt-10) REVERT: H 14 ASP cc_start: 0.8231 (t70) cc_final: 0.7999 (t0) REVERT: H 524 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6676 (ttp80) REVERT: Q 61 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8698 (mp0) REVERT: Q 200 ASP cc_start: 0.8720 (m-30) cc_final: 0.8364 (t0) REVERT: Z 286 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7936 (t0) REVERT: Z 357 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.8017 (tp30) REVERT: a 15 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: a 354 GLU cc_start: 0.7895 (tp30) cc_final: 0.7195 (tm-30) REVERT: b 415 MET cc_start: 0.9513 (mmm) cc_final: 0.9057 (mmp) REVERT: d 279 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8324 (tm-30) REVERT: d 446 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7533 (mmm) REVERT: d 513 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8680 (tm) REVERT: e 58 ASP cc_start: 0.8189 (m-30) cc_final: 0.7702 (m-30) REVERT: g 110 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: h 7 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8312 (pp) REVERT: h 324 MET cc_start: 0.9145 (mmm) cc_final: 0.8839 (mmm) REVERT: h 524 ARG cc_start: 0.8354 (mmm160) cc_final: 0.8115 (mmm160) REVERT: q 253 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8749 (p) REVERT: q 473 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: z 66 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8349 (mm-30) REVERT: z 244 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8727 (t) REVERT: z 358 GLU cc_start: 0.7507 (pm20) cc_final: 0.7192 (pm20) REVERT: P 168 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7313 (tm-30) REVERT: P 184 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7257 (mpp) REVERT: P 213 LYS cc_start: 0.8938 (tttm) cc_final: 0.8630 (tttt) outliers start: 93 outliers final: 43 residues processed: 533 average time/residue: 1.5821 time to fit residues: 1108.9081 Evaluate side-chains 528 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 470 time to evaluate : 6.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain N residue 352 TRP Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain H residue 524 ARG Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 15 GLU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain a residue 464 VAL Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 320 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 214 VAL Chi-restraints excluded: chain g residue 480 VAL Chi-restraints excluded: chain g residue 483 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 473 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 184 MET Chi-restraints excluded: chain P residue 285 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 767 optimal weight: 10.0000 chunk 807 optimal weight: 4.9990 chunk 737 optimal weight: 6.9990 chunk 785 optimal weight: 0.8980 chunk 473 optimal weight: 2.9990 chunk 342 optimal weight: 5.9990 chunk 617 optimal weight: 4.9990 chunk 241 optimal weight: 0.9990 chunk 710 optimal weight: 0.9980 chunk 743 optimal weight: 6.9990 chunk 783 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 235 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN z 161 HIS P 199 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 68826 Z= 0.218 Angle : 0.576 12.399 92921 Z= 0.284 Chirality : 0.042 0.197 11052 Planarity : 0.003 0.053 11863 Dihedral : 6.978 172.594 9550 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 1.07 % Allowed : 12.13 % Favored : 86.80 % 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: 1.52 (0.09), residues: 8784 helix: 2.40 (0.08), residues: 4482 sheet: -0.22 (0.15), residues: 1180 loop : -0.55 (0.11), residues: 3122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 222 HIS 0.018 0.001 HIS z 161 PHE 0.039 0.001 PHE P 136 TYR 0.013 0.001 TYR G 274 ARG 0.009 0.000 ARG P 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 484 time to evaluate : 6.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 182 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8094 (tm-30) REVERT: A 47 ASP cc_start: 0.7967 (t0) cc_final: 0.7518 (t0) REVERT: A 51 ASP cc_start: 0.8409 (m-30) cc_final: 0.7984 (m-30) REVERT: A 230 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7802 (t) REVERT: B 20 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7916 (mmt-90) REVERT: B 62 MET cc_start: 0.8040 (ttm) cc_final: 0.7811 (ttp) REVERT: D 334 GLU cc_start: 0.8431 (tp30) cc_final: 0.8209 (tp30) REVERT: E 48 MET cc_start: 0.9164 (tpp) cc_final: 0.8900 (mmm) REVERT: E 199 MET cc_start: 0.7087 (mmm) cc_final: 0.6797 (mmp) REVERT: E 493 CYS cc_start: 0.8413 (m) cc_final: 0.7944 (m) REVERT: G 337 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8562 (mt-10) REVERT: H 14 ASP cc_start: 0.8100 (t70) cc_final: 0.7878 (t0) REVERT: H 220 PHE cc_start: 0.8853 (t80) cc_final: 0.8552 (t80) REVERT: H 524 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.6692 (ttp80) REVERT: Q 61 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8734 (mp0) REVERT: Q 200 ASP cc_start: 0.8711 (m-30) cc_final: 0.8362 (t0) REVERT: Z 286 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7888 (t0) REVERT: Z 357 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8021 (tp30) REVERT: a 15 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7640 (mt-10) REVERT: a 354 GLU cc_start: 0.7864 (tp30) cc_final: 0.7318 (tm-30) REVERT: a 416 GLU cc_start: 0.8464 (mp0) cc_final: 0.8182 (mp0) REVERT: b 415 MET cc_start: 0.9501 (mmm) cc_final: 0.9039 (mmp) REVERT: d 90 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8727 (mmt) REVERT: d 279 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8301 (tm-30) REVERT: d 446 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7473 (mmm) REVERT: d 513 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8703 (tm) REVERT: e 58 ASP cc_start: 0.8191 (m-30) cc_final: 0.7722 (m-30) REVERT: e 118 GLU cc_start: 0.8534 (tt0) cc_final: 0.8176 (tm-30) REVERT: g 110 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: h 7 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8305 (pp) REVERT: h 324 MET cc_start: 0.9134 (mmm) cc_final: 0.8826 (mmm) REVERT: q 253 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8635 (p) REVERT: q 473 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: z 66 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8369 (mm-30) REVERT: z 244 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8694 (t) REVERT: z 358 GLU cc_start: 0.7472 (pm20) cc_final: 0.7173 (pm20) REVERT: P 168 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7289 (tm-30) REVERT: P 184 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7254 (mpp) outliers start: 79 outliers final: 37 residues processed: 529 average time/residue: 1.5810 time to fit residues: 1105.1634 Evaluate side-chains 516 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 463 time to evaluate : 6.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain N residue 352 TRP Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain H residue 524 ARG Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 15 GLU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain a residue 464 VAL Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 320 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 214 VAL Chi-restraints excluded: chain g residue 483 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 473 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 184 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 516 optimal weight: 10.0000 chunk 831 optimal weight: 10.0000 chunk 507 optimal weight: 9.9990 chunk 394 optimal weight: 0.9980 chunk 577 optimal weight: 10.0000 chunk 871 optimal weight: 0.4980 chunk 802 optimal weight: 2.9990 chunk 694 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 536 optimal weight: 4.9990 chunk 425 optimal weight: 0.0030 overall best weight: 1.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 235 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 217 ASN ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN z 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 68826 Z= 0.201 Angle : 0.573 12.594 92921 Z= 0.281 Chirality : 0.042 0.185 11052 Planarity : 0.003 0.080 11863 Dihedral : 6.874 169.953 9550 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.60 % Favored : 96.38 % Rotamer: Outliers : 0.91 % Allowed : 12.48 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.57 (0.09), residues: 8784 helix: 2.44 (0.08), residues: 4477 sheet: -0.18 (0.15), residues: 1188 loop : -0.54 (0.11), residues: 3119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 66 HIS 0.017 0.001 HIS z 161 PHE 0.020 0.001 PHE N 296 TYR 0.015 0.001 TYR N 290 ARG 0.013 0.000 ARG P 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 469 time to evaluate : 6.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 182 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8098 (tm-30) REVERT: A 47 ASP cc_start: 0.7936 (t0) cc_final: 0.7566 (t0) REVERT: A 51 ASP cc_start: 0.8412 (m-30) cc_final: 0.7955 (m-30) REVERT: A 230 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7803 (t) REVERT: B 20 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7924 (mmt-90) REVERT: B 62 MET cc_start: 0.8065 (ttm) cc_final: 0.7849 (ttp) REVERT: D 334 GLU cc_start: 0.8422 (tp30) cc_final: 0.8202 (tp30) REVERT: E 48 MET cc_start: 0.9154 (tpp) cc_final: 0.8882 (mmm) REVERT: E 199 MET cc_start: 0.7231 (mmm) cc_final: 0.6987 (mmp) REVERT: E 493 CYS cc_start: 0.8419 (m) cc_final: 0.7964 (m) REVERT: G 337 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8565 (mt-10) REVERT: H 14 ASP cc_start: 0.8097 (t70) cc_final: 0.7871 (t0) REVERT: H 46 ASP cc_start: 0.8221 (m-30) cc_final: 0.7723 (m-30) REVERT: H 220 PHE cc_start: 0.8780 (t80) cc_final: 0.8496 (t80) REVERT: H 524 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6710 (ttp80) REVERT: Q 61 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8721 (mp0) REVERT: Q 200 ASP cc_start: 0.8711 (m-30) cc_final: 0.8361 (t0) REVERT: Z 286 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7876 (t0) REVERT: Z 357 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7988 (tp30) REVERT: a 15 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: a 354 GLU cc_start: 0.7866 (tp30) cc_final: 0.7176 (tm-30) REVERT: a 416 GLU cc_start: 0.8484 (mp0) cc_final: 0.8203 (mp0) REVERT: b 415 MET cc_start: 0.9496 (mmm) cc_final: 0.9025 (mmp) REVERT: d 90 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8678 (mmt) REVERT: d 279 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8243 (tm-30) REVERT: d 446 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7432 (mmm) REVERT: d 513 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8678 (tm) REVERT: e 58 ASP cc_start: 0.8191 (m-30) cc_final: 0.7701 (m-30) REVERT: g 110 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: h 7 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8311 (pp) REVERT: h 324 MET cc_start: 0.9123 (mmm) cc_final: 0.8806 (mmm) REVERT: q 253 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8575 (p) REVERT: q 473 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: z 66 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8354 (mm-30) REVERT: z 244 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8691 (t) REVERT: z 358 GLU cc_start: 0.7445 (pm20) cc_final: 0.7155 (pm20) REVERT: P 63 ILE cc_start: 0.9095 (tp) cc_final: 0.8879 (tp) REVERT: P 168 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7384 (tm-30) REVERT: P 184 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7195 (mpp) REVERT: P 213 LYS cc_start: 0.8640 (tttm) cc_final: 0.8386 (tttt) outliers start: 67 outliers final: 37 residues processed: 509 average time/residue: 1.5449 time to fit residues: 1041.3735 Evaluate side-chains 517 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 464 time to evaluate : 6.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 169 ASN Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain N residue 352 TRP Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 524 ARG Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 15 GLU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain a residue 430 MET Chi-restraints excluded: chain a residue 464 VAL Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 483 GLU Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 473 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 184 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 551 optimal weight: 0.8980 chunk 739 optimal weight: 2.9990 chunk 212 optimal weight: 9.9990 chunk 640 optimal weight: 0.0040 chunk 102 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 695 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 chunk 713 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 235 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS P 199 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.069942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.057031 restraints weight = 196194.819| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.01 r_work: 0.2586 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.114 68826 Z= 0.162 Angle : 0.561 19.318 92921 Z= 0.274 Chirality : 0.041 0.178 11052 Planarity : 0.003 0.070 11863 Dihedral : 6.727 166.461 9550 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.42 % Favored : 96.56 % Rotamer: Outliers : 0.76 % Allowed : 12.74 % Favored : 86.50 % 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: 1.65 (0.09), residues: 8784 helix: 2.52 (0.08), residues: 4475 sheet: -0.15 (0.15), residues: 1212 loop : -0.52 (0.11), residues: 3097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 66 HIS 0.019 0.001 HIS z 161 PHE 0.046 0.001 PHE P 136 TYR 0.016 0.001 TYR G 437 ARG 0.019 0.000 ARG h 524 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18403.16 seconds wall clock time: 319 minutes 12.00 seconds (19152.00 seconds total)