Starting phenix.real_space_refine on Sun Oct 13 10:07:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg9_40453/10_2024/8sg9_40453.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg9_40453/10_2024/8sg9_40453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg9_40453/10_2024/8sg9_40453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg9_40453/10_2024/8sg9_40453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg9_40453/10_2024/8sg9_40453.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg9_40453/10_2024/8sg9_40453.cif" } resolution = 2.9 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= 0.043 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 405 5.16 5 C 40970 2.51 5 N 11406 2.21 5 O 12690 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 49 residue(s): 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 65583 Number of models: 1 Model: "" Number of chains: 49 Chain: "N" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 474 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain breaks: 4 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: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4063 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 16, 'TRANS': 506} 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: "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: 50.30, per 1000 atoms: 0.77 Number of scatterers: 65583 At special positions: 0 Unit cell: (180.918, 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 405 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12690 8.00 N 11406 7.00 C 40970 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 "HETATM65490 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65170 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65362 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.19 Conformation dependent library (CDL) restraints added in 9.3 seconds 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15882 Finding SS restraints... Secondary structure from input PDB file: 360 helices and 99 sheets defined 56.8% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.21 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.506A pdb=" N ARG A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 3.609A 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: 3.819A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 removed outlier: 3.640A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.532A 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 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.686A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.276A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.540A 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 258 through 281 removed outlier: 4.542A pdb=" N GLN A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 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 removed outlier: 3.741A pdb=" N LEU A 463 " --> pdb=" O ASP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.878A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 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 removed outlier: 3.557A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 145 Processing helix chain 'B' and resid 151 through 169 removed outlier: 4.493A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.539A 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: 3.523A 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 426 Processing helix chain 'B' and resid 430 through 454 removed outlier: 4.141A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.582A 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 50 removed outlier: 4.350A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 105 through 126 removed outlier: 4.143A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.781A 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 172 removed outlier: 3.568A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 Proline residue: D 185 - end of helix removed outlier: 3.639A 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 293 removed outlier: 3.949A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.848A 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 418 Processing helix chain 'D' and resid 426 through 441 Processing helix chain 'D' and resid 446 through 459 removed outlier: 4.209A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.561A pdb=" N SER D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 487 removed outlier: 3.529A pdb=" N GLY D 487 " --> pdb=" O ARG D 483 " (cutoff:3.500A) 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: 3.637A pdb=" N LYS E 25 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 49 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 107 through 126 removed outlier: 3.612A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.636A 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: 6.670A pdb=" N VAL E 178 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.896A 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: 3.818A 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 440 removed outlier: 4.021A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 456 removed outlier: 3.885A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.830A 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: 3.640A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.834A 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: 3.606A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 141 removed outlier: 3.597A 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: 3.698A pdb=" N SER G 166 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 163 through 167' 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: 3.618A 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 339 through 343 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 470 removed outlier: 3.789A pdb=" N LEU G 462 " --> pdb=" O SER G 458 " (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 Processing helix chain 'H' and resid 36 through 40 removed outlier: 4.007A 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: 3.720A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 4.077A 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: 3.869A 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 185 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 Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 338 through 342 removed outlier: 3.654A pdb=" N LEU H 342 " --> pdb=" O ALA H 339 " (cutoff:3.500A) 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: 4.055A 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 470 removed outlier: 3.519A 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 28 Processing helix chain 'Q' and resid 28 through 45 removed outlier: 4.400A 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 156 through 168 removed outlier: 3.520A pdb=" N VAL Q 160 " --> pdb=" O ASP Q 156 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.260A 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 286 removed outlier: 4.823A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.794A 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 340 through 344 removed outlier: 3.693A pdb=" N MET Q 344 " --> pdb=" O LEU Q 341 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 405 Processing helix chain 'Q' and resid 413 through 429 removed outlier: 3.760A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 445 removed outlier: 4.184A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.791A 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 Processing helix chain 'Q' and resid 492 through 496 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Z' and resid 3 through 8 Processing helix chain 'Z' and resid 16 through 35 removed outlier: 3.712A pdb=" N LEU Z 20 " --> pdb=" O ALA Z 16 " (cutoff:3.500A) 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: 3.608A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.680A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 4.277A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.638A 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 200 through 204 removed outlier: 3.539A pdb=" N THR Z 204 " --> pdb=" O GLU Z 201 " (cutoff:3.500A) Processing helix chain 'Z' and resid 252 through 263 Processing helix chain 'Z' and resid 264 through 282 removed outlier: 3.610A 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: 3.784A pdb=" N MET Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) removed outlier: 4.399A 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: 4.144A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 removed outlier: 3.812A pdb=" N LYS Z 449 " --> pdb=" O LEU Z 445 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 474 removed outlier: 3.540A 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 497 through 517 Processing helix chain 'a' and resid 14 through 33 removed outlier: 3.754A pdb=" N ARG a 18 " --> pdb=" O GLY a 14 " (cutoff:3.500A) removed outlier: 3.660A 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 91 through 110 Processing helix chain 'a' and resid 113 through 136 Processing helix chain 'a' and resid 144 through 157 removed outlier: 3.816A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.283A 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 280 removed outlier: 3.858A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 4.938A 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 removed outlier: 3.754A pdb=" N ALA a 437 " --> pdb=" O ARG a 433 " (cutoff:3.500A) Processing helix chain 'a' and resid 446 through 456 Processing helix chain 'a' and resid 459 through 477 removed outlier: 3.650A pdb=" N LEU a 463 " --> pdb=" O ASP a 459 " (cutoff:3.500A) Processing helix chain 'a' and resid 478 through 484 removed outlier: 3.803A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) 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: 4.434A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 174 removed outlier: 3.640A 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 Processing helix chain 'b' and resid 379 through 403 Processing helix chain 'b' and resid 411 through 426 Processing helix chain 'b' and resid 430 through 454 removed outlier: 4.095A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) Proline residue: b 447 - end of helix removed outlier: 3.758A 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 removed outlier: 3.512A pdb=" N GLN d 32 " --> pdb=" O ASP d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 81 Processing helix chain 'd' and resid 85 through 102 Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.957A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.793A 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: 3.604A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 178 removed outlier: 6.836A pdb=" N VAL d 176 " --> pdb=" O SER d 173 " (cutoff:3.500A) removed outlier: 4.325A 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: 3.891A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.862A 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: 3.530A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.767A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 removed outlier: 3.889A 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: 4.924A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 49 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 107 through 126 removed outlier: 3.702A 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: 6.597A pdb=" N VAL e 178 " --> pdb=" O SER e 175 " (cutoff:3.500A) removed outlier: 4.117A 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: 3.831A 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 440 removed outlier: 3.905A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 441 through 456 removed outlier: 3.995A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 466 removed outlier: 3.523A 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 37 removed outlier: 3.645A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 38 through 41 removed outlier: 3.822A pdb=" N LEU g 41 " --> pdb=" O ARG g 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 38 through 41' Processing helix chain 'g' and resid 62 through 69 removed outlier: 3.816A pdb=" N GLU g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 74 through 91 Processing helix chain 'g' and resid 94 through 115 removed outlier: 3.625A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN g 115 " --> pdb=" O HIS g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.631A 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: 3.891A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 removed outlier: 3.610A 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: 3.581A 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 339 through 343 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 removed outlier: 3.533A pdb=" N THR g 471 " --> pdb=" O ARG g 467 " (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: 3.553A pdb=" N LEU h 22 " --> pdb=" O GLY h 18 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 40 removed outlier: 3.577A 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: 3.729A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 114 removed outlier: 4.097A 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: 3.656A 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 185 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: 3.554A 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 338 through 340 No H-bonds generated for 'chain 'h' and resid 338 through 340' 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: 3.706A pdb=" N LEU h 433 " --> pdb=" O GLY h 429 " (cutoff:3.500A) removed outlier: 4.191A 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: 4.181A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.632A 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 76 Processing helix chain 'q' and resid 80 through 97 Processing helix chain 'q' and resid 100 through 121 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 166 removed outlier: 4.426A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (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: 4.842A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.673A 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 381 through 405 Processing helix chain 'q' and resid 413 through 428 Processing helix chain 'q' and resid 433 through 444 removed outlier: 4.297A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 457 Processing helix chain 'q' and resid 459 through 474 Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 2 through 8 removed outlier: 3.585A pdb=" N LEU z 7 " --> pdb=" O ALA z 3 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 35 removed outlier: 3.589A pdb=" N LEU z 20 " --> pdb=" O ALA z 16 " (cutoff:3.500A) 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: 3.599A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.755A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 4.230A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 removed outlier: 3.721A 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 200 through 204 removed outlier: 3.819A pdb=" N THR z 204 " --> pdb=" O GLU z 201 " (cutoff:3.500A) Processing helix chain 'z' and resid 252 through 263 Processing helix chain 'z' and resid 264 through 282 removed outlier: 3.638A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 308 removed outlier: 3.723A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 328 removed outlier: 4.249A 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: 4.182A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.577A 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 sheet with id=AA1, first strand: chain 'N' and resid 209 through 212 removed outlier: 6.480A pdb=" N CYS N 219 " --> pdb=" O SER N 232 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER N 232 " --> pdb=" O CYS N 219 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU N 221 " --> pdb=" O LEU N 230 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 244 through 245 removed outlier: 6.654A pdb=" N VAL N 265 " --> pdb=" O VAL N 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 13 removed outlier: 4.623A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 46 Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA7, 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: 7.600A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.609A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.609A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 286 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 254 through 256 removed outlier: 9.212A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AB3, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.454A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE B 521 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 61 through 64 removed outlier: 6.914A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 53 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB6, first strand: chain 'B' and resid 199 through 205 removed outlier: 3.807A pdb=" N GLY B 377 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.464A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 346 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU B 348 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU B 233 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB9, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC1, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.390A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LYS D 213 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.655A pdb=" N SER D 358 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS D 245 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU D 360 " --> pdb=" O LYS D 243 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL D 297 " --> pdb=" O LYS D 243 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE D 249 " --> pdb=" O GLN D 301 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.566A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 28 through 29 removed outlier: 3.568A pdb=" N ILE E 533 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU H 48 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE E 533 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL H 50 " --> pdb=" O ILE E 533 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC6, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.507A pdb=" N LYS E 210 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE E 387 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU E 212 " --> pdb=" O ILE E 387 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLY E 389 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LYS E 214 " --> pdb=" O GLY E 389 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.684A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 321 through 322 removed outlier: 6.651A pdb=" N ALA E 300 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N VAL E 342 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE E 250 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 15 through 17 Processing sheet with id=AD1, first strand: chain 'G' and resid 57 through 60 removed outlier: 7.239A pdb=" N MET G 47 " --> pdb=" O GLU Z 520 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N MET Z 522 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N MET G 49 " --> pdb=" O MET Z 522 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AD3, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AD4, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.754A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD6, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AD7, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=AD8, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.349A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AE1, first strand: chain 'H' and resid 195 through 201 removed outlier: 3.812A pdb=" N GLY H 376 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AE3, first strand: chain 'H' and resid 309 through 311 Processing sheet with id=AE4, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AE5, first strand: chain 'Q' and resid 20 through 23 removed outlier: 5.020A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 149 through 150 removed outlier: 3.948A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.478A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS Q 205 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N GLY Q 379 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE Q 207 " --> pdb=" O GLY Q 379 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 220 through 223 removed outlier: 3.755A pdb=" N VAL Q 350 " --> pdb=" O VAL Q 234 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 240 through 242 Processing sheet with id=AF1, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AF2, first strand: chain 'Z' and resid 139 through 140 Processing sheet with id=AF3, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.301A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id=AF5, first strand: chain 'Z' and resid 311 through 313 removed outlier: 9.156A pdb=" N VAL Z 311 " --> pdb=" O LYS Z 287 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE Z 289 " --> pdb=" O VAL Z 311 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU Z 313 " --> pdb=" O PHE Z 289 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL Z 291 " --> pdb=" O LEU Z 313 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP Z 227 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU Z 231 " --> pdb=" O ILE Z 292 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.572A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'a' and resid 9 through 13 removed outlier: 4.412A pdb=" N ILE a 527 " --> pdb=" O ASP d 58 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET d 60 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE a 531 " --> pdb=" O GLN d 62 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.305A pdb=" N ASP a 42 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP g 521 " --> pdb=" O ASP a 42 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 138 through 139 Processing sheet with id=AG1, first strand: chain 'a' and resid 181 through 182 Processing sheet with id=AG2, first strand: chain 'a' and resid 196 through 201 removed outlier: 6.273A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLY a 379 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA a 200 " --> pdb=" O GLY a 379 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.512A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.512A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'g' and resid 254 through 256 removed outlier: 9.065A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG b 255 " --> pdb=" O VAL e 268 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS e 263 " --> pdb=" O ALA h 253 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 486 through 489 Processing sheet with id=AG7, first strand: chain 'b' and resid 17 through 19 removed outlier: 4.449A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE b 521 " --> pdb=" O VAL e 62 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 61 through 64 removed outlier: 7.088A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AH1, first strand: chain 'b' and resid 199 through 205 removed outlier: 3.822A pdb=" N GLY b 377 " --> pdb=" O LYS b 204 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.398A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER b 345 " --> pdb=" O LYS b 236 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS b 236 " --> pdb=" O SER b 345 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS b 347 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS b 289 " --> pdb=" O LYS b 236 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AH4, first strand: chain 'd' and resid 153 through 154 Processing sheet with id=AH5, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.584A pdb=" N LYS d 209 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL d 390 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL d 211 " --> pdb=" O VAL d 390 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLY d 392 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYS d 213 " --> pdb=" O GLY d 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.595A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS d 379 " --> pdb=" O ALA d 359 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA d 359 " --> pdb=" O CYS d 379 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.595A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS d 379 " --> pdb=" O ALA d 359 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA d 359 " --> pdb=" O CYS d 379 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LYS d 245 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU d 299 " --> pdb=" O LYS d 245 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLN d 301 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE d 249 " --> pdb=" O GLN d 301 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU d 298 " --> pdb=" O ILE d 325 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASP d 327 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE d 300 " --> pdb=" O ASP d 327 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 491 through 493 removed outlier: 3.558A pdb=" N SER d 501 " --> pdb=" O GLY d 492 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'e' and resid 26 through 29 removed outlier: 7.242A pdb=" N LEU h 48 " --> pdb=" O ASP e 531 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE e 533 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL h 50 " --> pdb=" O ILE e 533 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS e 535 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'e' and resid 153 through 154 Processing sheet with id=AI2, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.400A pdb=" N LYS e 210 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE e 387 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU e 212 " --> pdb=" O ILE e 387 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLY e 389 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS e 214 " --> pdb=" O GLY e 389 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'e' and resid 228 through 230 removed outlier: 6.506A pdb=" N LEU e 358 " --> pdb=" O GLU e 244 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU e 244 " --> pdb=" O LEU e 358 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN e 360 " --> pdb=" O LYS e 242 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS e 242 " --> pdb=" O GLN e 360 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'g' and resid 57 through 60 removed outlier: 6.457A pdb=" N MET g 47 " --> pdb=" O VAL z 518 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU z 520 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'g' and resid 142 through 143 Processing sheet with id=AI6, first strand: chain 'g' and resid 185 through 187 Processing sheet with id=AI7, first strand: chain 'g' and resid 200 through 205 removed outlier: 4.066A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR g 373 " --> pdb=" O LEU g 215 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'g' and resid 218 through 220 Processing sheet with id=AI9, first strand: chain 'g' and resid 310 through 312 removed outlier: 6.361A pdb=" N VAL g 290 " --> pdb=" O ILE g 312 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N VAL g 332 " --> pdb=" O ILE g 238 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU g 240 " --> pdb=" O VAL g 332 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'g' and resid 478 through 480 Processing sheet with id=AJ2, first strand: chain 'h' and resid 14 through 17 removed outlier: 4.300A pdb=" N VAL h 516 " --> pdb=" O ASN q 53 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N MET q 55 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU h 518 " --> pdb=" O MET q 55 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ILE q 57 " --> pdb=" O GLU h 518 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE h 520 " --> pdb=" O ILE q 57 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'h' and resid 195 through 201 removed outlier: 3.889A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AJ5, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ6, first strand: chain 'h' and resid 405 through 407 Processing sheet with id=AJ7, first strand: chain 'h' and resid 475 through 478 Processing sheet with id=AJ8, first strand: chain 'q' and resid 20 through 22 removed outlier: 5.013A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'q' and resid 149 through 150 removed outlier: 3.816A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'q' and resid 202 through 206 removed outlier: 6.622A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'q' and resid 220 through 223 Processing sheet with id=AK3, first strand: chain 'q' and resid 239 through 242 Processing sheet with id=AK4, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AK5, first strand: chain 'z' and resid 139 through 140 Processing sheet with id=AK6, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.369A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'z' and resid 210 through 212 Processing sheet with id=AK8, first strand: chain 'z' and resid 310 through 313 removed outlier: 9.125A pdb=" N VAL z 311 " --> pdb=" O LYS z 287 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP z 227 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL z 290 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE z 292 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU z 231 " --> pdb=" O ILE z 292 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'z' and resid 477 through 479 3998 hydrogen bonds defined for protein. 11430 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: 36.21 Time building geometry restraints manager: 19.75 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: 22054 1.34 - 1.46: 9457 1.46 - 1.58: 34046 1.58 - 1.69: 48 1.69 - 1.81: 718 Bond restraints: 66323 Sorted by residual: 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 6.42e+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 6.41e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" F2 AF3 d 603 " pdb="AL AF3 d 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.34e+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 66318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 88576 2.09 - 4.18: 742 4.18 - 6.27: 231 6.27 - 8.36: 13 8.36 - 10.45: 1 Bond angle restraints: 89563 Sorted by residual: angle pdb=" N ILE a 49 " pdb=" CA ILE a 49 " pdb=" C ILE a 49 " ideal model delta sigma weight residual 113.20 107.26 5.94 9.60e-01 1.09e+00 3.82e+01 angle pdb=" C ALA q 530 " pdb=" CA ALA q 530 " pdb=" CB ALA q 530 " ideal model delta sigma weight residual 117.23 110.29 6.94 1.36e+00 5.41e-01 2.60e+01 angle pdb=" CA ALA q 530 " pdb=" C ALA q 530 " pdb=" N GLY q 531 " ideal model delta sigma weight residual 119.98 116.86 3.12 8.50e-01 1.38e+00 1.35e+01 angle pdb=" C ALA q 151 " pdb=" N LYS q 152 " pdb=" CA LYS q 152 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 121.06 -7.88 2.37e+00 1.78e-01 1.11e+01 ... (remaining 89558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 40343 34.93 - 69.87: 596 69.87 - 104.80: 58 104.80 - 139.74: 9 139.74 - 174.67: 6 Dihedral angle restraints: 41012 sinusoidal: 16493 harmonic: 24519 Sorted by residual: 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 300.00 125.33 174.67 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 -60.00 113.28 -173.28 1 2.00e+01 2.50e-03 4.78e+01 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 300.00 129.27 170.73 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 41009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 9515 0.067 - 0.134: 1153 0.134 - 0.201: 19 0.201 - 0.268: 0 0.268 - 0.334: 1 Chirality restraints: 10688 Sorted by residual: chirality pdb=" CB ILE b 11 " pdb=" CA ILE b 11 " pdb=" CG1 ILE b 11 " pdb=" CG2 ILE b 11 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA GLU a 77 " pdb=" N GLU a 77 " pdb=" C GLU a 77 " pdb=" CB GLU a 77 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CB ILE G 363 " pdb=" CA ILE G 363 " pdb=" CG1 ILE G 363 " pdb=" CG2 ILE G 363 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.65e-01 ... (remaining 10685 not shown) Planarity restraints: 11425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP a 47 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C ASP a 47 " 0.040 2.00e-02 2.50e+03 pdb=" O ASP a 47 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP a 48 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO e 441 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 404 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO G 405 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 405 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 405 " 0.027 5.00e-02 4.00e+02 ... (remaining 11422 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 513 2.52 - 3.12: 49330 3.12 - 3.71: 103015 3.71 - 4.31: 144827 4.31 - 4.90: 250018 Nonbonded interactions: 547703 Sorted by model distance: nonbonded pdb="MG MG b 602 " pdb=" F1 AF3 b 603 " model vdw 1.928 2.120 nonbonded pdb=" O1A ADP q 601 " pdb="MG MG q 602 " model vdw 1.946 2.170 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.951 2.120 nonbonded pdb="MG MG z 602 " pdb=" F1 AF3 z 603 " model vdw 1.969 2.120 nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.972 2.120 ... (remaining 547698 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 8 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 8 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: 3.470 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: 0.000 Extract box with map and model: 2.510 Check model and map are aligned: 0.540 Set scattering table: 0.630 Process input model: 165.290 Find NCS groups from input model: 7.000 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 193.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 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 : 0.004 0.160 66323 Z= 0.292 Angle : 0.535 10.450 89563 Z= 0.264 Chirality : 0.041 0.334 10688 Planarity : 0.003 0.055 11425 Dihedral : 13.773 174.674 25130 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.67 (0.09), residues: 8486 helix: 2.39 (0.08), residues: 4349 sheet: 0.19 (0.16), residues: 1129 loop : -0.43 (0.11), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 168 HIS 0.013 0.001 HIS z 161 PHE 0.022 0.001 PHE H 174 TYR 0.012 0.001 TYR q 468 ARG 0.006 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 561 time to evaluate : 8.002 Fit side-chains REVERT: A 47 ASP cc_start: 0.7861 (t0) cc_final: 0.7655 (t0) REVERT: A 344 MET cc_start: 0.8893 (mpp) cc_final: 0.8522 (mmm) REVERT: A 508 ILE cc_start: 0.9091 (tp) cc_final: 0.8886 (tp) REVERT: B 17 ASP cc_start: 0.8219 (t0) cc_final: 0.7795 (t70) REVERT: E 29 MET cc_start: 0.7945 (mmm) cc_final: 0.7739 (mmm) REVERT: E 464 GLU cc_start: 0.8732 (tt0) cc_final: 0.8445 (tp30) REVERT: E 501 MET cc_start: 0.9317 (mmp) cc_final: 0.8983 (mmp) REVERT: G 113 LEU cc_start: 0.9064 (mt) cc_final: 0.8796 (mp) REVERT: H 14 ASP cc_start: 0.8485 (t70) cc_final: 0.8271 (t0) REVERT: H 81 ASP cc_start: 0.8499 (m-30) cc_final: 0.8147 (m-30) REVERT: Q 41 GLN cc_start: 0.8791 (tp40) cc_final: 0.8302 (tp40) REVERT: Q 249 MET cc_start: 0.8389 (pmm) cc_final: 0.8081 (pmm) REVERT: Q 296 LYS cc_start: 0.8555 (tmmt) cc_final: 0.8308 (ttpp) REVERT: a 209 MET cc_start: 0.8383 (mtm) cc_final: 0.8099 (mtp) REVERT: a 416 GLU cc_start: 0.8237 (mp0) cc_final: 0.7933 (mp0) REVERT: b 139 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7778 (tm-30) REVERT: b 353 MET cc_start: 0.9036 (tpt) cc_final: 0.8753 (tpp) REVERT: e 4 MET cc_start: 0.4429 (mmt) cc_final: 0.4156 (tmm) REVERT: e 464 GLU cc_start: 0.8539 (tp30) cc_final: 0.8213 (tp30) REVERT: g 52 ASP cc_start: 0.8019 (t0) cc_final: 0.7790 (t0) REVERT: h 524 ARG cc_start: 0.7636 (tmt170) cc_final: 0.7036 (tmm160) REVERT: q 41 GLN cc_start: 0.8818 (tp-100) cc_final: 0.8476 (tm-30) REVERT: z 44 MET cc_start: 0.8798 (mmm) cc_final: 0.8486 (mmm) outliers start: 0 outliers final: 0 residues processed: 561 average time/residue: 1.9777 time to fit residues: 1413.6135 Evaluate side-chains 432 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 5.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 713 optimal weight: 9.9990 chunk 640 optimal weight: 6.9990 chunk 355 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 432 optimal weight: 8.9990 chunk 342 optimal weight: 2.9990 chunk 662 optimal weight: 8.9990 chunk 256 optimal weight: 0.9990 chunk 402 optimal weight: 8.9990 chunk 492 optimal weight: 0.3980 chunk 767 optimal weight: 6.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 73 GLN H 283 HIS Z 84 GLN ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 423 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN z 161 HIS ** z 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 346 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 66323 Z= 0.333 Angle : 0.605 10.778 89563 Z= 0.301 Chirality : 0.044 0.171 10688 Planarity : 0.003 0.062 11425 Dihedral : 7.445 176.998 9216 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.69 % Allowed : 6.00 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.60 (0.09), residues: 8486 helix: 2.35 (0.08), residues: 4392 sheet: 0.10 (0.16), residues: 1095 loop : -0.51 (0.11), residues: 2999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 168 HIS 0.012 0.001 HIS z 161 PHE 0.025 0.001 PHE H 174 TYR 0.018 0.001 TYR E 446 ARG 0.007 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 457 time to evaluate : 6.265 Fit side-chains REVERT: A 344 MET cc_start: 0.9059 (mpp) cc_final: 0.8722 (mmm) REVERT: A 508 ILE cc_start: 0.9124 (tp) cc_final: 0.8912 (tp) REVERT: B 62 MET cc_start: 0.8522 (ttm) cc_final: 0.8248 (ttm) REVERT: D 57 MET cc_start: 0.9043 (mmm) cc_final: 0.8768 (mmm) REVERT: D 67 ASP cc_start: 0.8374 (m-30) cc_final: 0.8169 (m-30) REVERT: E 464 GLU cc_start: 0.8771 (tt0) cc_final: 0.8439 (tp30) REVERT: E 532 ASP cc_start: 0.7748 (m-30) cc_final: 0.7416 (m-30) REVERT: G 47 MET cc_start: 0.9173 (mtp) cc_final: 0.8829 (mtp) REVERT: G 59 MET cc_start: 0.8955 (ttp) cc_final: 0.8616 (ttp) REVERT: G 521 ASP cc_start: 0.7663 (t70) cc_final: 0.7197 (t70) REVERT: H 14 ASP cc_start: 0.8518 (t70) cc_final: 0.8291 (t0) REVERT: H 81 ASP cc_start: 0.8558 (m-30) cc_final: 0.8177 (m-30) REVERT: Q 41 GLN cc_start: 0.8857 (tp40) cc_final: 0.8356 (tp40) REVERT: Q 249 MET cc_start: 0.8431 (pmm) cc_final: 0.8152 (pmm) REVERT: Z 69 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.9019 (mp) REVERT: Z 415 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: a 209 MET cc_start: 0.8462 (mtm) cc_final: 0.8198 (mtp) REVERT: a 299 TYR cc_start: 0.8533 (m-80) cc_final: 0.8328 (m-80) REVERT: a 416 GLU cc_start: 0.8107 (mp0) cc_final: 0.7870 (mp0) REVERT: b 139 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7788 (tm-30) REVERT: e 4 MET cc_start: 0.4367 (mmt) cc_final: 0.4042 (tmm) REVERT: e 464 GLU cc_start: 0.8581 (tp30) cc_final: 0.8264 (tp30) REVERT: g 47 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8470 (mtp) REVERT: g 528 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8362 (tmmt) REVERT: h 524 ARG cc_start: 0.7692 (tmt170) cc_final: 0.7283 (tmm160) REVERT: q 41 GLN cc_start: 0.8861 (tp-100) cc_final: 0.8554 (tm-30) REVERT: q 152 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8454 (ptmm) REVERT: z 190 MET cc_start: 0.9181 (mmp) cc_final: 0.8803 (mmp) REVERT: z 244 VAL cc_start: 0.8776 (OUTLIER) cc_final: 0.8431 (t) outliers start: 49 outliers final: 12 residues processed: 477 average time/residue: 1.5479 time to fit residues: 948.0001 Evaluate side-chains 438 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 420 time to evaluate : 5.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain b residue 11 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 426 optimal weight: 0.7980 chunk 238 optimal weight: 4.9990 chunk 638 optimal weight: 0.7980 chunk 522 optimal weight: 0.9990 chunk 211 optimal weight: 0.0060 chunk 768 optimal weight: 7.9990 chunk 830 optimal weight: 2.9990 chunk 684 optimal weight: 2.9990 chunk 762 optimal weight: 6.9990 chunk 262 optimal weight: 2.9990 chunk 616 optimal weight: 7.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 227 ASN ** d 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN z 161 HIS ** z 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 66323 Z= 0.156 Angle : 0.535 9.995 89563 Z= 0.264 Chirality : 0.041 0.172 10688 Planarity : 0.003 0.058 11425 Dihedral : 7.182 177.547 9216 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.63 % Allowed : 7.91 % Favored : 91.45 % 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: 1.70 (0.09), residues: 8486 helix: 2.45 (0.08), residues: 4401 sheet: 0.14 (0.16), residues: 1078 loop : -0.50 (0.11), residues: 3007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 168 HIS 0.011 0.001 HIS z 161 PHE 0.021 0.001 PHE H 174 TYR 0.016 0.001 TYR z 498 ARG 0.010 0.000 ARG G 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 471 time to evaluate : 6.290 Fit side-chains REVERT: B 62 MET cc_start: 0.8292 (ttm) cc_final: 0.8010 (ttm) REVERT: B 408 TYR cc_start: 0.9057 (m-80) cc_final: 0.8600 (m-80) REVERT: D 28 ASP cc_start: 0.8311 (t0) cc_final: 0.7692 (t0) REVERT: D 57 MET cc_start: 0.9041 (mmm) cc_final: 0.8806 (mmm) REVERT: E 464 GLU cc_start: 0.8710 (tt0) cc_final: 0.8395 (tp30) REVERT: G 47 MET cc_start: 0.9191 (mtp) cc_final: 0.8954 (mtm) REVERT: G 113 LEU cc_start: 0.9131 (mt) cc_final: 0.8823 (mp) REVERT: G 182 MET cc_start: 0.8004 (mtp) cc_final: 0.7783 (mtp) REVERT: H 14 ASP cc_start: 0.8517 (t70) cc_final: 0.8286 (t0) REVERT: H 81 ASP cc_start: 0.8495 (m-30) cc_final: 0.8135 (m-30) REVERT: Q 41 GLN cc_start: 0.8831 (tp40) cc_final: 0.8354 (tp40) REVERT: Q 249 MET cc_start: 0.8452 (pmm) cc_final: 0.8093 (pmm) REVERT: Z 15 ARG cc_start: 0.8497 (ttm110) cc_final: 0.8170 (ttp-110) REVERT: Z 69 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.9011 (mp) REVERT: Z 415 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: a 209 MET cc_start: 0.8457 (mtm) cc_final: 0.8187 (mtp) REVERT: d 120 CYS cc_start: 0.8875 (m) cc_final: 0.8546 (m) REVERT: d 222 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: e 4 MET cc_start: 0.4324 (mmt) cc_final: 0.3906 (tmm) REVERT: e 29 MET cc_start: 0.8068 (mtp) cc_final: 0.7768 (mtm) REVERT: e 464 GLU cc_start: 0.8583 (tp30) cc_final: 0.8253 (tp30) REVERT: g 47 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8070 (mtp) REVERT: g 151 MET cc_start: 0.8824 (tpp) cc_final: 0.8554 (tpt) REVERT: g 527 LYS cc_start: 0.8974 (mtmm) cc_final: 0.8717 (mtpp) REVERT: g 528 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8267 (tmmt) REVERT: h 524 ARG cc_start: 0.7658 (tmt170) cc_final: 0.7255 (tmm160) REVERT: q 41 GLN cc_start: 0.8772 (tp-100) cc_final: 0.8508 (tm-30) REVERT: q 152 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8328 (ptmm) REVERT: q 200 ASP cc_start: 0.8760 (t70) cc_final: 0.8518 (t0) REVERT: q 522 ASP cc_start: 0.8840 (t0) cc_final: 0.8516 (t0) REVERT: z 244 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8348 (t) outliers start: 45 outliers final: 12 residues processed: 494 average time/residue: 1.5018 time to fit residues: 963.2218 Evaluate side-chains 459 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 440 time to evaluate : 6.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 497 MET Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 387 ASP Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 759 optimal weight: 0.3980 chunk 577 optimal weight: 10.0000 chunk 398 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 366 optimal weight: 7.9990 chunk 516 optimal weight: 9.9990 chunk 771 optimal weight: 0.0670 chunk 816 optimal weight: 10.0000 chunk 403 optimal weight: 9.9990 chunk 731 optimal weight: 8.9990 chunk 220 optimal weight: 10.0000 overall best weight: 4.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 472 GLN H 117 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN h 501 ASN z 84 GLN z 161 HIS ** z 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 66323 Z= 0.391 Angle : 0.607 10.943 89563 Z= 0.300 Chirality : 0.044 0.167 10688 Planarity : 0.003 0.057 11425 Dihedral : 7.144 176.801 9216 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.89 % Allowed : 9.10 % Favored : 90.02 % 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: 1.60 (0.09), residues: 8486 helix: 2.39 (0.08), residues: 4392 sheet: 0.03 (0.16), residues: 1085 loop : -0.53 (0.11), residues: 3009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP e 304 HIS 0.012 0.001 HIS z 161 PHE 0.024 0.001 PHE H 455 TYR 0.021 0.001 TYR E 446 ARG 0.005 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 440 time to evaluate : 6.103 Fit side-chains REVERT: B 62 MET cc_start: 0.8366 (ttm) cc_final: 0.8111 (ttm) REVERT: B 415 MET cc_start: 0.9352 (mmm) cc_final: 0.8901 (mmp) REVERT: B 480 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8656 (mmp) REVERT: D 28 ASP cc_start: 0.8434 (t0) cc_final: 0.7815 (t0) REVERT: D 57 MET cc_start: 0.8963 (mmm) cc_final: 0.8745 (mmm) REVERT: E 464 GLU cc_start: 0.8759 (tt0) cc_final: 0.8432 (tp30) REVERT: G 47 MET cc_start: 0.9209 (mtp) cc_final: 0.8650 (mtp) REVERT: G 54 MET cc_start: 0.8563 (mmp) cc_final: 0.8187 (mpp) REVERT: G 182 MET cc_start: 0.8238 (mtp) cc_final: 0.8000 (mtp) REVERT: H 14 ASP cc_start: 0.8533 (t70) cc_final: 0.8297 (t0) REVERT: H 81 ASP cc_start: 0.8550 (m-30) cc_final: 0.8175 (m-30) REVERT: H 227 MET cc_start: 0.9279 (mpp) cc_final: 0.9061 (mmm) REVERT: Q 41 GLN cc_start: 0.8896 (tp40) cc_final: 0.8381 (tp40) REVERT: Q 249 MET cc_start: 0.8373 (pmm) cc_final: 0.7984 (pmm) REVERT: Z 15 ARG cc_start: 0.8473 (ttm110) cc_final: 0.8142 (ttp-110) REVERT: Z 69 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.9050 (mp) REVERT: Z 161 HIS cc_start: 0.6399 (OUTLIER) cc_final: 0.5865 (t70) REVERT: Z 415 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: a 209 MET cc_start: 0.8473 (mtm) cc_final: 0.8217 (mtp) REVERT: a 344 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8511 (mpm) REVERT: d 222 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7426 (tm-30) REVERT: e 4 MET cc_start: 0.4340 (mmt) cc_final: 0.3862 (tmm) REVERT: e 207 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8390 (mt-10) REVERT: e 464 GLU cc_start: 0.8624 (tp30) cc_final: 0.8300 (tp30) REVERT: g 47 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8390 (mtp) REVERT: g 151 MET cc_start: 0.8872 (tpp) cc_final: 0.8593 (tpt) REVERT: g 528 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8315 (tmmt) REVERT: h 524 ARG cc_start: 0.7701 (tmt170) cc_final: 0.7287 (tmm160) REVERT: q 41 GLN cc_start: 0.8837 (tp-100) cc_final: 0.8563 (tm-30) REVERT: q 152 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8568 (ptmm) REVERT: q 522 ASP cc_start: 0.8923 (t0) cc_final: 0.8542 (t0) REVERT: z 244 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8398 (t) outliers start: 63 outliers final: 21 residues processed: 475 average time/residue: 1.5236 time to fit residues: 941.3107 Evaluate side-chains 452 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 420 time to evaluate : 5.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 341 LEU Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 11 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 207 GLU Chi-restraints excluded: chain e residue 533 ILE Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 25 LEU Chi-restraints excluded: chain q residue 152 LYS 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: 845 random chunks: chunk 680 optimal weight: 0.7980 chunk 463 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 608 optimal weight: 6.9990 chunk 337 optimal weight: 4.9990 chunk 696 optimal weight: 10.0000 chunk 564 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 417 optimal weight: 0.9990 chunk 733 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN Q 397 ASN ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 301 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN g 526 HIS z 161 HIS z 218 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 66323 Z= 0.331 Angle : 0.588 10.279 89563 Z= 0.291 Chirality : 0.043 0.169 10688 Planarity : 0.003 0.057 11425 Dihedral : 7.099 178.189 9216 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.00 % Allowed : 10.05 % Favored : 88.95 % 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: 1.56 (0.09), residues: 8486 helix: 2.36 (0.08), residues: 4393 sheet: -0.02 (0.16), residues: 1099 loop : -0.55 (0.11), residues: 2994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 304 HIS 0.015 0.001 HIS z 161 PHE 0.025 0.001 PHE H 455 TYR 0.018 0.001 TYR E 446 ARG 0.009 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 439 time to evaluate : 6.060 Fit side-chains revert: symmetry clash REVERT: A 306 MET cc_start: 0.9020 (mtp) cc_final: 0.8546 (mtm) REVERT: B 62 MET cc_start: 0.8319 (ttm) cc_final: 0.8096 (ttm) REVERT: B 415 MET cc_start: 0.9342 (mmm) cc_final: 0.8908 (mmp) REVERT: B 480 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8608 (mmp) REVERT: D 28 ASP cc_start: 0.8412 (t0) cc_final: 0.7779 (t0) REVERT: D 57 MET cc_start: 0.8880 (mmm) cc_final: 0.8655 (mmm) REVERT: E 464 GLU cc_start: 0.8732 (tt0) cc_final: 0.8411 (tp30) REVERT: G 54 MET cc_start: 0.8566 (mmp) cc_final: 0.8231 (mpp) REVERT: H 14 ASP cc_start: 0.8530 (t70) cc_final: 0.8290 (t0) REVERT: H 81 ASP cc_start: 0.8561 (m-30) cc_final: 0.8194 (m-30) REVERT: Q 249 MET cc_start: 0.8372 (pmm) cc_final: 0.8015 (pmm) REVERT: Q 311 MET cc_start: 0.9001 (ttp) cc_final: 0.8655 (ttp) REVERT: Q 492 MET cc_start: 0.8335 (mmm) cc_final: 0.7380 (mtm) REVERT: Z 15 ARG cc_start: 0.8490 (ttm110) cc_final: 0.8165 (ttp-110) REVERT: Z 161 HIS cc_start: 0.6375 (OUTLIER) cc_final: 0.5835 (t70) REVERT: Z 415 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: a 209 MET cc_start: 0.8476 (mtm) cc_final: 0.8205 (mtp) REVERT: a 344 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8540 (mpm) REVERT: d 222 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: e 4 MET cc_start: 0.4353 (mmt) cc_final: 0.3856 (tmm) REVERT: e 21 ASP cc_start: 0.8342 (t0) cc_final: 0.7927 (t0) REVERT: e 29 MET cc_start: 0.7855 (mtm) cc_final: 0.7471 (ttm) REVERT: e 80 MET cc_start: 0.9232 (mmt) cc_final: 0.8879 (mtt) REVERT: e 464 GLU cc_start: 0.8643 (tp30) cc_final: 0.8323 (tp30) REVERT: g 47 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8372 (mtp) REVERT: g 151 MET cc_start: 0.8893 (tpp) cc_final: 0.8606 (tpt) REVERT: g 528 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8321 (tmmt) REVERT: q 41 GLN cc_start: 0.8840 (tp-100) cc_final: 0.8570 (tm-30) REVERT: q 152 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8422 (ptmm) REVERT: q 200 ASP cc_start: 0.8779 (t70) cc_final: 0.8531 (t0) REVERT: q 522 ASP cc_start: 0.8979 (t0) cc_final: 0.8736 (t0) REVERT: z 244 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8368 (t) outliers start: 71 outliers final: 27 residues processed: 481 average time/residue: 1.5184 time to fit residues: 949.3195 Evaluate side-chains 460 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 424 time to evaluate : 6.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 341 LEU Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 11 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 387 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 533 ILE Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 274 optimal weight: 2.9990 chunk 735 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 479 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 817 optimal weight: 8.9990 chunk 678 optimal weight: 0.7980 chunk 378 optimal weight: 0.0040 chunk 67 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 429 optimal weight: 0.4980 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN h 501 ASN z 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 66323 Z= 0.157 Angle : 0.539 11.009 89563 Z= 0.264 Chirality : 0.041 0.166 10688 Planarity : 0.003 0.058 11425 Dihedral : 6.911 177.639 9216 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.76 % Allowed : 10.80 % Favored : 88.44 % 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: 1.70 (0.09), residues: 8486 helix: 2.47 (0.08), residues: 4401 sheet: 0.07 (0.16), residues: 1090 loop : -0.50 (0.11), residues: 2995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.015 0.001 HIS z 161 PHE 0.019 0.001 PHE H 174 TYR 0.011 0.001 TYR E 420 ARG 0.007 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 456 time to evaluate : 6.373 Fit side-chains revert: symmetry clash REVERT: A 306 MET cc_start: 0.9031 (mtp) cc_final: 0.8621 (mtm) REVERT: B 480 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8417 (mmp) REVERT: D 28 ASP cc_start: 0.8269 (t0) cc_final: 0.7652 (t0) REVERT: D 57 MET cc_start: 0.8908 (mmm) cc_final: 0.8666 (mmm) REVERT: D 429 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: E 464 GLU cc_start: 0.8713 (tt0) cc_final: 0.8397 (tp30) REVERT: G 54 MET cc_start: 0.8571 (mmp) cc_final: 0.8183 (mpp) REVERT: H 14 ASP cc_start: 0.8524 (t70) cc_final: 0.8284 (t0) REVERT: H 81 ASP cc_start: 0.8518 (m-30) cc_final: 0.8159 (m-30) REVERT: Q 41 GLN cc_start: 0.8871 (tp40) cc_final: 0.8406 (tp40) REVERT: Q 249 MET cc_start: 0.8334 (pmm) cc_final: 0.7948 (pmm) REVERT: Z 15 ARG cc_start: 0.8507 (ttm110) cc_final: 0.8178 (ttp-110) REVERT: Z 415 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: a 209 MET cc_start: 0.8456 (mtm) cc_final: 0.8168 (mtp) REVERT: b 445 MET cc_start: 0.8700 (tpp) cc_final: 0.8462 (tpp) REVERT: d 222 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7444 (tm-30) REVERT: e 4 MET cc_start: 0.4456 (mmt) cc_final: 0.3835 (tmm) REVERT: e 21 ASP cc_start: 0.8330 (t0) cc_final: 0.7895 (t0) REVERT: e 464 GLU cc_start: 0.8631 (tp30) cc_final: 0.8293 (tp30) REVERT: g 47 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8269 (mtp) REVERT: g 151 MET cc_start: 0.8910 (tpp) cc_final: 0.8612 (tpt) REVERT: g 527 LYS cc_start: 0.8992 (mtpp) cc_final: 0.8627 (mtmm) REVERT: g 528 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8292 (tmmt) REVERT: h 524 ARG cc_start: 0.7670 (tmt170) cc_final: 0.7408 (tmm160) REVERT: q 41 GLN cc_start: 0.8777 (tp-100) cc_final: 0.8439 (tm-30) REVERT: q 200 ASP cc_start: 0.8759 (t70) cc_final: 0.8503 (t0) REVERT: q 522 ASP cc_start: 0.8968 (t0) cc_final: 0.8740 (t0) REVERT: z 244 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8293 (t) outliers start: 54 outliers final: 24 residues processed: 484 average time/residue: 1.5290 time to fit residues: 965.2171 Evaluate side-chains 469 residues out of total 7100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 438 time to evaluate : 6.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 429 GLU Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 341 LEU Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain a residue 185 ARG Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 533 ILE Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 788 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 465 optimal weight: 7.9990 chunk 597 optimal weight: 2.9990 chunk 462 optimal weight: 9.9990 chunk 688 optimal weight: 8.9990 chunk 456 optimal weight: 8.9990 chunk 814 optimal weight: 10.0000 chunk 509 optimal weight: 9.9990 chunk 496 optimal weight: 3.9990 chunk 376 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: