Starting phenix.real_space_refine on Mon Oct 14 02:10:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sht_40494/10_2024/8sht_40494.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sht_40494/10_2024/8sht_40494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sht_40494/10_2024/8sht_40494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sht_40494/10_2024/8sht_40494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sht_40494/10_2024/8sht_40494.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sht_40494/10_2024/8sht_40494.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.052 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 422 5.16 5 C 42658 2.51 5 N 11873 2.21 5 O 13207 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 55 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 68272 Number of models: 1 Model: "" Number of chains: 50 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: "P" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1507 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 9 Chain: "N" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 210} Chain breaks: 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: 34.28, per 1000 atoms: 0.50 Number of scatterers: 68272 At special positions: 0 Unit cell: (181.976, 176.686, 179.86, 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 422 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13207 8.00 N 11873 7.00 C 42658 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 "HETATM68179 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM68051 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67923 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67795 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.44 Conformation dependent library (CDL) restraints added in 7.4 seconds 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16508 Finding SS restraints... Secondary structure from input PDB file: 359 helices and 100 sheets defined 55.4% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.12 Creating SS restraints... Processing helix chain 'A' and resid 14 through 34 removed outlier: 3.653A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 86 removed outlier: 3.635A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 removed outlier: 3.620A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.635A 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 140 through 144 Processing helix chain 'A' and resid 144 through 157 removed outlier: 4.164A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.236A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 259 through 281 removed outlier: 3.965A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 5.214A 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 433 through 445 Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.604A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 484 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 98 through 119 Processing helix chain 'B' and resid 122 through 144 Processing helix chain 'B' and resid 151 through 168 Processing helix chain 'B' and resid 169 through 174 removed outlier: 6.447A pdb=" N LEU B 172 " --> pdb=" O SER B 169 " (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: 3.520A pdb=" N VAL B 341 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 Processing helix chain 'B' and resid 411 through 427 removed outlier: 3.769A pdb=" N ARG B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 454 removed outlier: 4.059A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.744A 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: 4.385A 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: 4.122A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 Processing helix chain 'D' and resid 159 through 173 removed outlier: 3.798A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 Proline residue: D 185 - end of helix removed outlier: 3.693A 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: 3.965A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.984A 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 removed outlier: 3.558A pdb=" N LEU D 356 " --> pdb=" O ALA D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 443 Processing helix chain 'D' and resid 446 through 459 removed outlier: 4.120A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 4.074A pdb=" N SER D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 486 Processing helix chain 'D' and resid 504 through 507 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 21 through 25 removed outlier: 3.750A pdb=" N LYS E 25 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 49 removed outlier: 3.649A pdb=" N LEU E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 85 through 102 Processing helix chain 'E' and resid 107 through 126 removed outlier: 3.631A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.633A 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: 6.380A pdb=" N VAL E 178 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.947A 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: 3.939A 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: 3.864A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 456 removed outlier: 3.777A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.886A 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: 3.738A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 69 Processing helix chain 'G' and resid 74 through 91 Processing helix chain 'G' and resid 94 through 114 removed outlier: 3.773A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 141 removed outlier: 3.567A 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: 3.885A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 194 through 198 Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 262 through 285 removed outlier: 4.260A pdb=" N LEU G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 306 Processing helix chain 'G' and resid 316 through 328 Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 380 through 404 Processing helix chain 'G' and resid 412 through 427 removed outlier: 3.593A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 444 Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'G' and resid 459 through 471 Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 18 through 35 Processing helix chain 'H' and resid 36 through 40 Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.715A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 4.141A 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: 3.679A 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 171 through 185 removed outlier: 3.858A pdb=" N MET H 185 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 259 through 284 removed outlier: 3.581A 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 342 removed outlier: 3.679A 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: 3.605A pdb=" N LEU H 433 " --> pdb=" O GLY H 429 " (cutoff:3.500A) removed outlier: 4.052A 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: 3.573A pdb=" N ILE H 460 " --> pdb=" O ASP H 456 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 10 through 15 Processing helix chain 'Q' and resid 24 through 45 removed outlier: 5.079A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.455A 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 156 through 168 removed outlier: 4.148A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 190 removed outlier: 3.507A pdb=" N ILE Q 190 " --> pdb=" O ALA Q 186 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 261 through 285 removed outlier: 4.833A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.666A 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 430 removed outlier: 3.925A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS Q 430 " --> pdb=" O TYR Q 426 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 445 removed outlier: 4.261A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 457 Processing helix chain 'Q' and resid 459 through 474 removed outlier: 3.611A pdb=" N VAL Q 463 " --> pdb=" O LYS Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Q' and resid 535 through 539 removed outlier: 4.027A pdb=" N GLY Q 538 " --> pdb=" O PRO Q 535 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS Q 539 " --> pdb=" O PRO Q 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 535 through 539' Processing helix chain 'Z' and resid 3 through 8 Processing helix chain 'Z' and resid 16 through 35 Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 59 through 66 Processing helix chain 'Z' and resid 71 through 88 Processing helix chain 'Z' and resid 91 through 111 removed outlier: 3.564A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.773A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 4.295A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.635A 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: 3.809A pdb=" N THR Z 204 " --> pdb=" O GLU Z 201 " (cutoff:3.500A) Processing helix chain 'Z' and resid 252 through 264 removed outlier: 4.055A pdb=" N ARG Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) Processing helix chain 'Z' and resid 264 through 282 removed outlier: 3.603A 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 329 removed outlier: 3.670A pdb=" N MET Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) removed outlier: 4.295A 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: 4.146A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 removed outlier: 3.565A 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 498 through 517 Processing helix chain 'a' and resid 14 through 33 removed outlier: 3.689A 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: 3.988A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 110 removed outlier: 3.620A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN a 110 " --> pdb=" O GLU a 106 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 136 Processing helix chain 'a' and resid 144 through 157 removed outlier: 4.234A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.274A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE a 179 " --> pdb=" O ALA a 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 204 through 208 Processing helix chain 'a' and resid 256 through 258 No H-bonds generated for 'chain 'a' and resid 256 through 258' Processing helix chain 'a' and resid 259 through 281 removed outlier: 3.838A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 5.023A 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 432 through 445 removed outlier: 3.935A pdb=" N LEU a 436 " --> pdb=" O SER a 432 " (cutoff:3.500A) Processing helix chain 'a' and resid 446 through 456 removed outlier: 3.548A pdb=" N ALA a 456 " --> pdb=" O LEU a 452 " (cutoff:3.500A) Processing helix chain 'a' and resid 459 through 477 Processing helix chain 'a' and resid 480 through 484 Processing helix chain 'a' and resid 498 through 502 Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 20 through 40 Processing helix chain 'b' and resid 66 through 73 Processing helix chain 'b' and resid 78 through 95 Processing helix chain 'b' and resid 98 through 119 Processing helix chain 'b' and resid 122 through 145 Processing helix chain 'b' and resid 151 through 168 Processing helix chain 'b' and resid 170 through 174 removed outlier: 3.633A 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 removed outlier: 3.600A pdb=" N VAL b 264 " --> pdb=" O SER b 260 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 308 Processing helix chain 'b' and resid 316 through 328 Processing helix chain 'b' and resid 337 through 341 Processing helix chain 'b' and resid 379 through 403 Processing helix chain 'b' and resid 411 through 427 Processing helix chain 'b' and resid 430 through 454 removed outlier: 4.065A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) Proline residue: b 447 - end of helix removed outlier: 3.849A 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: 3.659A pdb=" N GLN d 32 " --> pdb=" O ASP d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 81 removed outlier: 3.543A pdb=" N MET d 81 " --> pdb=" O ILE d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 102 Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.737A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.894A 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: 3.576A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 178 removed outlier: 4.196A 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: 3.661A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.915A 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 441 Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.787A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 removed outlier: 3.745A 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 504 through 507 Processing helix chain 'd' and resid 512 through 531 removed outlier: 4.969A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 50 removed outlier: 3.567A pdb=" N LEU e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) Processing helix chain 'e' and resid 73 through 80 Processing helix chain 'e' and resid 85 through 102 Processing helix chain 'e' and resid 107 through 125 Processing helix chain 'e' and resid 129 through 152 Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'e' and resid 175 through 180 removed outlier: 6.607A pdb=" N VAL e 178 " --> pdb=" O SER e 175 " (cutoff:3.500A) removed outlier: 4.098A 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: 4.009A pdb=" N THR e 295 " --> pdb=" O GLN e 291 " (cutoff:3.500A) Processing helix chain 'e' and resid 307 through 317 Processing helix chain 'e' and resid 326 through 338 Processing helix chain 'e' and resid 344 through 348 Processing helix chain 'e' and resid 391 through 415 Processing helix chain 'e' and resid 423 through 438 Processing helix chain 'e' and resid 441 through 456 removed outlier: 3.877A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 466 Processing helix chain 'e' and resid 469 through 484 Processing helix chain 'e' and resid 510 through 529 Processing helix chain 'g' and resid 19 through 38 removed outlier: 3.708A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 69 Processing helix chain 'g' and resid 74 through 91 Processing helix chain 'g' and resid 94 through 114 removed outlier: 3.780A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.581A 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: 3.831A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 removed outlier: 3.588A 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 306 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 442 Processing helix chain 'g' and resid 445 through 456 Processing helix chain 'g' and resid 458 through 471 removed outlier: 3.503A 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 removed outlier: 3.548A pdb=" N LEU h 22 " --> pdb=" O GLY h 18 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 69 Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.636A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 114 removed outlier: 4.191A 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: 3.630A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 147 through 164 Processing helix chain 'h' and resid 168 through 170 No H-bonds generated for 'chain 'h' and resid 168 through 170' Processing helix chain 'h' and resid 171 through 186 removed outlier: 3.748A pdb=" N MET h 185 " --> pdb=" O ASP h 181 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU h 186 " --> pdb=" O ALA h 182 " (cutoff:3.500A) Processing helix chain 'h' and resid 191 through 193 No H-bonds generated for 'chain 'h' and resid 191 through 193' Processing helix chain 'h' and resid 204 through 208 Processing helix chain 'h' and resid 224 through 228 Processing helix chain 'h' and resid 259 through 284 removed outlier: 3.561A 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 342 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: 3.793A pdb=" N LEU h 433 " --> pdb=" O GLY h 429 " (cutoff:3.500A) removed outlier: 4.024A 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: 4.175A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.550A 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: 3.801A pdb=" N VAL q 160 " --> pdb=" O ASP q 156 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 190 Processing helix chain 'q' and resid 198 through 200 No H-bonds generated for 'chain 'q' and resid 198 through 200' Processing helix chain 'q' and resid 211 through 215 Processing helix chain 'q' and resid 261 through 285 removed outlier: 4.730A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) Processing helix chain 'q' and resid 298 through 308 Processing helix chain 'q' and resid 317 through 329 Processing helix chain 'q' and resid 340 through 344 removed outlier: 3.502A 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 430 removed outlier: 3.536A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 445 removed outlier: 4.455A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) removed outlier: 3.767A 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 473 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 7 Processing helix chain 'z' and resid 16 through 35 Processing helix chain 'z' and resid 36 through 38 No H-bonds generated for 'chain 'z' and resid 36 through 38' Processing helix chain 'z' and resid 59 through 67 Processing helix chain 'z' and resid 71 through 88 Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.595A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.820A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 4.080A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 removed outlier: 3.630A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE z 179 " --> pdb=" O SER z 175 " (cutoff:3.500A) Processing helix chain 'z' and resid 187 through 189 No H-bonds generated for 'chain 'z' and resid 187 through 189' Processing helix chain 'z' and resid 200 through 204 removed outlier: 3.876A 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: 3.623A 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 329 removed outlier: 3.889A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) removed outlier: 4.431A 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 removed outlier: 3.513A pdb=" N ASP z 404 " --> pdb=" O ASN z 400 " (cutoff:3.500A) Processing helix chain 'z' and resid 412 through 426 Processing helix chain 'z' and resid 427 through 429 No H-bonds generated for 'chain 'z' and resid 427 through 429' Processing helix chain 'z' and resid 432 through 445 removed outlier: 4.176A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.588A 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 498 through 517 Processing helix chain 'P' and resid 57 through 62 Processing helix chain 'P' and resid 62 through 85 removed outlier: 3.604A pdb=" N PHE P 69 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 140 Processing helix chain 'P' and resid 141 through 152 removed outlier: 4.666A pdb=" N MET P 145 " --> pdb=" O ARG P 141 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU P 152 " --> pdb=" O MET P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 176 removed outlier: 3.518A pdb=" N ILE P 174 " --> pdb=" O PHE P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 209 removed outlier: 3.719A pdb=" N ALA P 207 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU P 208 " --> pdb=" O CYS P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 227 through 231 Processing helix chain 'P' and resid 260 through 270 removed outlier: 3.611A pdb=" N LEU P 264 " --> pdb=" O PHE P 260 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 4.422A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR D 71 " --> pdb=" O LYS D 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55 removed outlier: 5.988A pdb=" N MET A 44 " --> pdb=" O VAL G 523 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 182 removed outlier: 3.537A pdb=" N TYR A 181 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 196 through 199 Processing sheet with id=AA6, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.535A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.535A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 254 through 256 removed outlier: 9.287A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG B 255 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU H 254 " --> pdb=" O ILE Q 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.520A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.396A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE B 521 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 64 removed outlier: 6.684A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU B 53 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB4, first strand: chain 'B' and resid 199 through 205 removed outlier: 3.839A pdb=" N GLY B 377 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.368A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS B 346 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 348 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU B 233 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.368A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS B 346 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 348 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU B 233 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N ALA B 332 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE B 239 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB8, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AB9, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.485A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LYS D 213 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.453A pdb=" N CYS D 379 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA D 359 " --> pdb=" O CYS D 379 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU D 361 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLU D 242 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU D 363 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG D 240 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL D 297 " --> pdb=" O LYS D 243 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE D 249 " --> pdb=" O GLN D 301 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.578A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 28 through 29 removed outlier: 3.602A pdb=" N ILE E 533 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU H 48 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE E 533 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL H 50 " --> pdb=" O ILE E 533 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC5, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.426A pdb=" N LYS E 210 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE E 387 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU E 212 " --> pdb=" O ILE E 387 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLY E 389 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LYS E 214 " --> pdb=" O GLY E 389 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.666A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU E 299 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LYS E 247 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE E 301 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA E 249 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA E 300 " --> pdb=" O VAL E 322 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 57 through 60 removed outlier: 6.493A pdb=" N MET G 47 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU Z 520 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AC9, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AD1, first strand: chain 'G' and resid 199 through 203 removed outlier: 6.645A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD3, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=AD5, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.494A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AD7, first strand: chain 'H' and resid 195 through 201 removed outlier: 3.564A pdb=" N GLY H 376 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AD9, first strand: chain 'H' and resid 309 through 311 Processing sheet with id=AE1, first strand: chain 'H' and resid 475 through 478 removed outlier: 3.532A pdb=" N ALA H 485 " --> pdb=" O GLY H 476 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 20 through 23 removed outlier: 5.108A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 149 through 150 removed outlier: 3.954A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.566A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS Q 205 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id=AE6, first strand: chain 'Q' and resid 240 through 242 Processing sheet with id=AE7, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AE8, first strand: chain 'Z' and resid 139 through 140 Processing sheet with id=AE9, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.353A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id=AF2, first strand: chain 'Z' and resid 310 through 313 removed outlier: 6.578A pdb=" N PHE Z 289 " --> pdb=" O VAL Z 311 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU Z 313 " --> pdb=" O PHE Z 289 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL Z 291 " --> pdb=" O LEU Z 313 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU Z 231 " --> pdb=" O ILE Z 292 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.519A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 9 through 13 removed outlier: 4.454A pdb=" N ILE a 527 " --> pdb=" O ASP d 58 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N MET d 60 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE a 531 " --> pdb=" O GLN d 62 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.361A pdb=" N ASP a 42 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP g 521 " --> pdb=" O ASP a 42 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 138 through 139 Processing sheet with id=AF7, first strand: chain 'a' and resid 181 through 182 Processing sheet with id=AF8, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.840A pdb=" N ASN a 196 " --> pdb=" O ALA a 373 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY a 379 " --> pdb=" O ALA a 200 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N SER a 212 " --> pdb=" O ASN a 366 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.840A pdb=" N ASN a 196 " --> pdb=" O ALA a 373 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY a 379 " --> pdb=" O ALA a 200 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N SER a 212 " --> pdb=" O ASN a 366 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA a 348 " --> pdb=" O ALA a 232 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE a 286 " --> pdb=" O VAL a 308 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 254 through 256 removed outlier: 9.009A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG b 255 " --> pdb=" O VAL e 268 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 486 through 489 Processing sheet with id=AG3, first strand: chain 'b' and resid 17 through 19 removed outlier: 6.291A pdb=" N ASP e 58 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN b 519 " --> pdb=" O ASP e 58 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'b' and resid 61 through 64 removed outlier: 6.915A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR d 538 " --> pdb=" O ILE b 51 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU b 53 " --> pdb=" O THR d 538 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AG6, first strand: chain 'b' and resid 199 through 205 removed outlier: 3.729A pdb=" N GLY b 377 " --> pdb=" O LYS b 204 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.431A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER b 345 " --> pdb=" O LYS b 236 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS b 236 " --> pdb=" O SER b 345 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS b 347 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS b 289 " --> pdb=" O LYS b 236 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AG9, first strand: chain 'd' and resid 153 through 154 Processing sheet with id=AH1, first strand: chain 'd' and resid 208 through 214 removed outlier: 4.050A pdb=" N GLY d 392 " --> pdb=" O LYS d 213 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'd' and resid 227 through 229 removed outlier: 6.562A pdb=" N LEU d 361 " --> pdb=" O GLU d 242 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU d 242 " --> pdb=" O LEU d 361 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL d 297 " --> pdb=" O LYS d 245 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AH4, first strand: chain 'e' and resid 26 through 29 removed outlier: 4.421A pdb=" N ILE e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU h 48 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP e 532 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL h 50 " --> pdb=" O ASP e 532 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ARG e 534 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'e' and resid 153 through 154 Processing sheet with id=AH6, first strand: chain 'e' and resid 209 through 215 removed outlier: 3.862A pdb=" N GLY e 389 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'e' and resid 228 through 230 removed outlier: 6.466A pdb=" N PHE e 355 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS e 247 " --> pdb=" O PHE e 355 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY e 357 " --> pdb=" O ASP e 245 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU e 299 " --> pdb=" O ASP e 245 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS e 247 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE e 301 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA e 249 " --> pdb=" O ILE e 301 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA e 300 " --> pdb=" O VAL e 322 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'g' and resid 57 through 60 removed outlier: 7.260A pdb=" N MET g 47 " --> pdb=" O GLU z 520 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N MET z 522 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET g 49 " --> pdb=" O MET z 522 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'g' and resid 142 through 143 Processing sheet with id=AI1, first strand: chain 'g' and resid 185 through 187 Processing sheet with id=AI2, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.877A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'g' and resid 218 through 220 Processing sheet with id=AI4, first strand: chain 'g' and resid 310 through 312 removed outlier: 6.352A pdb=" N VAL g 239 " --> pdb=" O ILE g 291 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N VAL g 332 " --> pdb=" O ILE g 238 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU g 240 " --> pdb=" O VAL g 332 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'g' and resid 478 through 480 Processing sheet with id=AI6, first strand: chain 'h' and resid 14 through 17 removed outlier: 6.300A pdb=" N ASN q 53 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU h 518 " --> pdb=" O ASN q 53 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.457A pdb=" N GLY h 196 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU h 374 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LYS h 198 " --> pdb=" O LEU h 374 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY h 376 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL h 200 " --> pdb=" O GLY h 376 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AI9, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ1, first strand: chain 'h' and resid 405 through 407 Processing sheet with id=AJ2, first strand: chain 'h' and resid 475 through 478 Processing sheet with id=AJ3, first strand: chain 'q' and resid 20 through 23 removed outlier: 4.984A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'q' and resid 149 through 150 removed outlier: 3.855A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.538A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLY q 379 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE q 207 " --> pdb=" O GLY q 379 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'q' and resid 220 through 223 Processing sheet with id=AJ7, first strand: chain 'q' and resid 240 through 242 Processing sheet with id=AJ8, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AJ9, first strand: chain 'z' and resid 139 through 140 Processing sheet with id=AK1, first strand: chain 'z' and resid 191 through 196 Processing sheet with id=AK2, first strand: chain 'z' and resid 210 through 212 removed outlier: 6.440A pdb=" N CYS z 366 " --> pdb=" O ALA z 347 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ALA z 347 " --> pdb=" O CYS z 366 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'z' and resid 210 through 212 removed outlier: 6.440A pdb=" N CYS z 366 " --> pdb=" O ALA z 347 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ALA z 347 " --> pdb=" O CYS z 366 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASP z 227 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL z 290 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE z 292 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU z 231 " --> pdb=" O ILE z 292 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N VAL z 311 " --> pdb=" O LYS z 287 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'z' and resid 477 through 479 Processing sheet with id=AK5, first strand: chain 'P' and resid 162 through 163 removed outlier: 6.398A pdb=" N PHE P 162 " --> pdb=" O LYS P 216 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LYS P 218 " --> pdb=" O PHE P 162 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL P 182 " --> pdb=" O LYS P 213 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N CYS P 215 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET P 184 " --> pdb=" O CYS P 215 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL P 217 " --> pdb=" O MET P 184 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N HIS P 186 " --> pdb=" O VAL P 217 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE P 238 " --> pdb=" O ILE P 245 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU P 243 " --> pdb=" O LYS P 240 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'N' and resid 97 through 99 removed outlier: 7.202A pdb=" N VAL N 393 " --> pdb=" O ARG N 98 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP N 394 " --> pdb=" O PHE N 382 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE N 382 " --> pdb=" O TRP N 394 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'N' and resid 198 through 203 removed outlier: 6.808A pdb=" N ALA N 213 " --> pdb=" O SER N 199 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N CYS N 201 " --> pdb=" O LEU N 211 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU N 211 " --> pdb=" O CYS N 201 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE N 203 " --> pdb=" O GLN N 209 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLN N 209 " --> pdb=" O PHE N 203 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N CYS N 219 " --> pdb=" O SER N 232 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER N 232 " --> pdb=" O CYS N 219 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU N 221 " --> pdb=" O LEU N 230 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'N' and resid 242 through 243 Processing sheet with id=AK9, first strand: chain 'N' and resid 284 through 289 removed outlier: 4.042A pdb=" N SER N 286 " --> pdb=" O GLY N 299 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG N 306 " --> pdb=" O SER N 298 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA N 317 " --> pdb=" O LEU N 307 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP N 309 " --> pdb=" O GLU N 315 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU N 315 " --> pdb=" O ASP N 309 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'N' and resid 330 through 331 removed outlier: 3.630A pdb=" N SER N 330 " --> pdb=" O GLY N 343 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER N 361 " --> pdb=" O VAL N 351 " (cutoff:3.500A) 4115 hydrogen bonds defined for protein. 11742 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: 30.57 Time building geometry restraints manager: 14.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 23029 1.35 - 1.46: 13251 1.46 - 1.58: 31982 1.58 - 1.70: 48 1.70 - 1.82: 744 Bond restraints: 69054 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.52e+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 6.39e+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 6.36e+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 6.36e+01 bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.34e+01 ... (remaining 69049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 91898 1.76 - 3.52: 987 3.52 - 5.28: 226 5.28 - 7.04: 108 7.04 - 8.80: 6 Bond angle restraints: 93225 Sorted by residual: angle pdb=" CA MET N 193 " pdb=" CB MET N 193 " pdb=" CG MET N 193 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 120.96 -7.78 2.37e+00 1.78e-01 1.08e+01 angle pdb=" CB LYS z 430 " pdb=" CG LYS z 430 " pdb=" CD LYS z 430 " ideal model delta sigma weight residual 111.30 118.65 -7.35 2.30e+00 1.89e-01 1.02e+01 angle pdb=" C ALA q 151 " pdb=" N LYS q 152 " pdb=" CA LYS q 152 " ideal model delta sigma weight residual 121.54 127.52 -5.98 1.91e+00 2.74e-01 9.80e+00 angle pdb=" N GLU P 78 " pdb=" CA GLU P 78 " pdb=" CB GLU P 78 " ideal model delta sigma weight residual 110.16 114.59 -4.43 1.48e+00 4.57e-01 8.97e+00 ... (remaining 93220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 41914 35.98 - 71.96: 664 71.96 - 107.94: 53 107.94 - 143.92: 10 143.92 - 179.90: 6 Dihedral angle restraints: 42647 sinusoidal: 17162 harmonic: 25485 Sorted by residual: dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual -60.00 119.90 -179.90 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual -60.00 117.00 -177.00 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP q 601 " pdb=" O5' ADP q 601 " pdb=" PA ADP q 601 " pdb=" O2A ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 132.01 167.99 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 42644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 8171 0.040 - 0.079: 2034 0.079 - 0.119: 799 0.119 - 0.158: 78 0.158 - 0.198: 3 Chirality restraints: 11085 Sorted by residual: chirality pdb=" CB VAL h 36 " pdb=" CA VAL h 36 " pdb=" CG1 VAL h 36 " pdb=" CG2 VAL h 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CB VAL H 36 " pdb=" CA VAL H 36 " pdb=" CG1 VAL H 36 " pdb=" CG2 VAL H 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA ILE g 363 " pdb=" N ILE g 363 " pdb=" C ILE g 363 " pdb=" CB ILE g 363 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 11082 not shown) Planarity restraints: 11897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO e 441 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE b 11 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C ILE b 11 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE b 11 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE b 12 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS z 161 " -0.011 2.00e-02 2.50e+03 1.45e-02 3.17e+00 pdb=" CG HIS z 161 " 0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS z 161 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS z 161 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS z 161 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS z 161 " -0.001 2.00e-02 2.50e+03 ... (remaining 11894 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 615 2.55 - 3.14: 53502 3.14 - 3.72: 107540 3.72 - 4.31: 149413 4.31 - 4.90: 256542 Nonbonded interactions: 567612 Sorted by model distance: nonbonded pdb=" O1A ADP q 601 " pdb="MG MG q 602 " model vdw 1.962 2.170 nonbonded pdb="MG MG D 602 " pdb=" F2 AF3 D 603 " model vdw 1.963 2.120 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.970 2.120 nonbonded pdb=" O3A ADP h 601 " pdb="MG MG h 602 " model vdw 1.988 2.170 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.990 2.120 ... (remaining 567607 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: 1.870 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: 0.080 Extract box with map and model: 1.970 Check model and map are aligned: 0.390 Set scattering table: 0.480 Process input model: 126.510 Find NCS groups from input model: 5.900 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 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 0.161 69054 Z= 0.272 Angle : 0.531 8.795 93225 Z= 0.259 Chirality : 0.041 0.198 11085 Planarity : 0.003 0.049 11897 Dihedral : 14.546 179.902 26139 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.01 % Allowed : 0.20 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.09), residues: 8805 helix: 2.32 (0.08), residues: 4428 sheet: 0.30 (0.16), residues: 1166 loop : -0.54 (0.11), residues: 3211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 168 HIS 0.018 0.001 HIS z 161 PHE 0.021 0.001 PHE P 136 TYR 0.019 0.001 TYR G 437 ARG 0.009 0.000 ARG z 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 594 time to evaluate : 5.921 Fit side-chains REVERT: A 171 MET cc_start: 0.8778 (ttp) cc_final: 0.8346 (ttm) REVERT: A 359 ASP cc_start: 0.7698 (t0) cc_final: 0.7370 (t0) REVERT: B 49 ASP cc_start: 0.8023 (m-30) cc_final: 0.7810 (m-30) REVERT: D 257 LYS cc_start: 0.9126 (tttt) cc_final: 0.8922 (ttmt) REVERT: E 4 MET cc_start: 0.2976 (ptt) cc_final: 0.2295 (tmm) REVERT: G 527 LYS cc_start: 0.8910 (tppt) cc_final: 0.8588 (tttm) REVERT: H 293 LEU cc_start: 0.9118 (mt) cc_final: 0.8797 (mt) REVERT: Z 496 ASP cc_start: 0.7726 (t70) cc_final: 0.7331 (t0) REVERT: a 51 ASP cc_start: 0.8090 (m-30) cc_final: 0.7839 (m-30) REVERT: e 39 MET cc_start: 0.8439 (ttp) cc_final: 0.8212 (ttm) REVERT: e 93 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8010 (mm-30) REVERT: g 46 MET cc_start: 0.9079 (mmm) cc_final: 0.8857 (mmm) REVERT: h 524 ARG cc_start: 0.7767 (mtp-110) cc_final: 0.7229 (mmm160) REVERT: q 319 TRP cc_start: 0.7930 (m-90) cc_final: 0.7642 (m-90) REVERT: P 260 PHE cc_start: 0.6029 (p90) cc_final: 0.5372 (p90) outliers start: 1 outliers final: 3 residues processed: 595 average time/residue: 1.4626 time to fit residues: 1141.2018 Evaluate side-chains 490 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 487 time to evaluate : 5.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain d residue 503 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 741 optimal weight: 4.9990 chunk 665 optimal weight: 10.0000 chunk 369 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 448 optimal weight: 2.9990 chunk 355 optimal weight: 8.9990 chunk 688 optimal weight: 1.9990 chunk 266 optimal weight: 6.9990 chunk 418 optimal weight: 3.9990 chunk 512 optimal weight: 7.9990 chunk 797 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 GLN G 390 ASN H 25 ASN Z 23 ASN ** Z 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN d 129 HIS g 390 ASN ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 95 ASN z 161 HIS N 275 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 69054 Z= 0.357 Angle : 0.604 8.499 93225 Z= 0.303 Chirality : 0.044 0.180 11085 Planarity : 0.004 0.055 11897 Dihedral : 7.578 177.507 9585 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.74 % Allowed : 6.34 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.09), residues: 8805 helix: 2.18 (0.08), residues: 4494 sheet: 0.24 (0.16), residues: 1123 loop : -0.62 (0.11), residues: 3188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP z 495 HIS 0.010 0.001 HIS z 161 PHE 0.020 0.001 PHE e 306 TYR 0.017 0.001 TYR G 437 ARG 0.011 0.000 ARG z 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 519 time to evaluate : 5.981 Fit side-chains REVERT: A 47 ASP cc_start: 0.7727 (t70) cc_final: 0.7302 (t0) REVERT: A 171 MET cc_start: 0.8791 (ttp) cc_final: 0.8355 (ttm) REVERT: A 358 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7748 (m-30) REVERT: A 359 ASP cc_start: 0.7749 (t0) cc_final: 0.7438 (t0) REVERT: A 382 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8286 (m-30) REVERT: D 93 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: D 257 LYS cc_start: 0.9150 (tttt) cc_final: 0.8946 (ttmt) REVERT: E 4 MET cc_start: 0.3092 (ptt) cc_final: 0.2370 (tmm) REVERT: G 527 LYS cc_start: 0.8946 (tppt) cc_final: 0.8572 (tttm) REVERT: H 293 LEU cc_start: 0.9215 (mt) cc_final: 0.8906 (mt) REVERT: Z 244 VAL cc_start: 0.9147 (OUTLIER) cc_final: 0.8876 (t) REVERT: Z 496 ASP cc_start: 0.7851 (t70) cc_final: 0.7418 (t0) REVERT: a 51 ASP cc_start: 0.8082 (m-30) cc_final: 0.7807 (m-30) REVERT: e 93 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8089 (mm-30) REVERT: h 7 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8468 (pp) REVERT: h 383 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7395 (mm-30) REVERT: h 401 LYS cc_start: 0.8660 (tppt) cc_final: 0.8211 (pptt) REVERT: q 319 TRP cc_start: 0.7986 (m-90) cc_final: 0.7696 (m-90) REVERT: P 202 MET cc_start: 0.8753 (ptp) cc_final: 0.8444 (ptp) REVERT: P 260 PHE cc_start: 0.6150 (p90) cc_final: 0.5483 (p90) REVERT: N 307 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8149 (tp) outliers start: 55 outliers final: 16 residues processed: 539 average time/residue: 1.5060 time to fit residues: 1061.5373 Evaluate side-chains 508 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 486 time to evaluate : 6.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain G residue 455 CYS Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain N residue 307 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 443 optimal weight: 10.0000 chunk 247 optimal weight: 7.9990 chunk 663 optimal weight: 10.0000 chunk 542 optimal weight: 9.9990 chunk 219 optimal weight: 1.9990 chunk 798 optimal weight: 0.7980 chunk 862 optimal weight: 2.9990 chunk 711 optimal weight: 1.9990 chunk 792 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 640 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS P 199 ASN N 275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 69054 Z= 0.256 Angle : 0.560 8.214 93225 Z= 0.279 Chirality : 0.042 0.169 11085 Planarity : 0.003 0.058 11897 Dihedral : 7.333 174.322 9578 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.97 % Allowed : 8.49 % Favored : 90.53 % 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: 1.40 (0.09), residues: 8805 helix: 2.20 (0.08), residues: 4506 sheet: 0.10 (0.16), residues: 1133 loop : -0.62 (0.11), residues: 3166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 496 HIS 0.014 0.001 HIS z 161 PHE 0.020 0.001 PHE a 167 TYR 0.015 0.001 TYR G 437 ARG 0.009 0.000 ARG E 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 524 time to evaluate : 6.046 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7836 (t70) cc_final: 0.7336 (t0) REVERT: A 171 MET cc_start: 0.8757 (ttp) cc_final: 0.8250 (ttm) REVERT: A 246 MET cc_start: 0.9070 (mmm) cc_final: 0.8754 (mmp) REVERT: A 359 ASP cc_start: 0.7711 (t0) cc_final: 0.7417 (t0) REVERT: B 316 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7673 (m-30) REVERT: D 63 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8161 (t0) REVERT: D 93 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: D 257 LYS cc_start: 0.9148 (tttt) cc_final: 0.8941 (ttmt) REVERT: E 4 MET cc_start: 0.3258 (ptt) cc_final: 0.2527 (tmm) REVERT: E 446 TYR cc_start: 0.9116 (m-80) cc_final: 0.8902 (m-80) REVERT: G 527 LYS cc_start: 0.8915 (tppt) cc_final: 0.8541 (tttm) REVERT: H 7 ILE cc_start: 0.9017 (tp) cc_final: 0.8744 (tt) REVERT: H 293 LEU cc_start: 0.9217 (mt) cc_final: 0.8917 (mt) REVERT: Q 61 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8366 (mp0) REVERT: Z 244 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8844 (t) REVERT: Z 496 ASP cc_start: 0.7773 (t70) cc_final: 0.7331 (t0) REVERT: a 51 ASP cc_start: 0.8072 (m-30) cc_final: 0.7847 (m-30) REVERT: e 93 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8086 (mm-30) REVERT: h 7 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8461 (pp) REVERT: q 92 MET cc_start: 0.9270 (tpp) cc_final: 0.9009 (tpt) REVERT: q 319 TRP cc_start: 0.7962 (m-90) cc_final: 0.7675 (m-90) REVERT: z 522 MET cc_start: 0.8126 (mtm) cc_final: 0.7670 (mtm) REVERT: P 183 ILE cc_start: 0.6809 (mm) cc_final: 0.6571 (mp) REVERT: P 184 MET cc_start: 0.6405 (mpp) cc_final: 0.6091 (mmt) REVERT: P 202 MET cc_start: 0.8714 (ptp) cc_final: 0.8459 (ptp) REVERT: N 225 GLU cc_start: 0.8581 (tp30) cc_final: 0.8121 (mm-30) REVERT: N 307 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8021 (tp) REVERT: N 333 PHE cc_start: 0.8294 (m-10) cc_final: 0.8042 (m-10) outliers start: 72 outliers final: 21 residues processed: 555 average time/residue: 1.4953 time to fit residues: 1090.9800 Evaluate side-chains 526 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 498 time to evaluate : 6.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain G residue 455 CYS Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 151 GLN Chi-restraints excluded: chain N residue 307 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 789 optimal weight: 2.9990 chunk 600 optimal weight: 10.0000 chunk 414 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 381 optimal weight: 0.9980 chunk 536 optimal weight: 5.9990 chunk 801 optimal weight: 5.9990 chunk 848 optimal weight: 30.0000 chunk 418 optimal weight: 4.9990 chunk 759 optimal weight: 0.9990 chunk 228 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS P 199 ASN P 287 ASN N 231 GLN N 350 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 69054 Z= 0.220 Angle : 0.545 9.927 93225 Z= 0.269 Chirality : 0.042 0.206 11085 Planarity : 0.003 0.062 11897 Dihedral : 7.115 176.543 9578 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.92 % Allowed : 10.04 % Favored : 89.05 % 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: 1.44 (0.09), residues: 8805 helix: 2.25 (0.08), residues: 4505 sheet: 0.05 (0.16), residues: 1120 loop : -0.60 (0.11), residues: 3180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 496 HIS 0.013 0.001 HIS z 161 PHE 0.035 0.001 PHE P 158 TYR 0.020 0.001 TYR z 351 ARG 0.011 0.000 ARG z 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 520 time to evaluate : 6.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7689 (t70) cc_final: 0.7121 (t0) REVERT: A 171 MET cc_start: 0.8753 (ttp) cc_final: 0.8284 (ttm) REVERT: A 359 ASP cc_start: 0.7665 (t0) cc_final: 0.7383 (t0) REVERT: B 49 ASP cc_start: 0.7787 (m-30) cc_final: 0.7587 (m-30) REVERT: D 257 LYS cc_start: 0.9148 (tttt) cc_final: 0.8945 (ttmt) REVERT: E 4 MET cc_start: 0.3104 (ptt) cc_final: 0.2398 (tmm) REVERT: G 527 LYS cc_start: 0.8901 (tppt) cc_final: 0.8540 (tttm) REVERT: H 7 ILE cc_start: 0.9073 (tp) cc_final: 0.8799 (tt) REVERT: H 293 LEU cc_start: 0.9204 (mt) cc_final: 0.8897 (mt) REVERT: Q 61 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8309 (mp0) REVERT: Z 244 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8849 (t) REVERT: Z 496 ASP cc_start: 0.7769 (t70) cc_final: 0.7319 (t0) REVERT: a 51 ASP cc_start: 0.8073 (m-30) cc_final: 0.7858 (m-30) REVERT: e 93 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8101 (mm-30) REVERT: h 7 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8463 (pp) REVERT: q 92 MET cc_start: 0.9265 (tpp) cc_final: 0.8995 (tpt) REVERT: q 319 TRP cc_start: 0.7952 (m-90) cc_final: 0.7666 (m-90) REVERT: P 184 MET cc_start: 0.6564 (mpp) cc_final: 0.6105 (mmt) REVERT: P 202 MET cc_start: 0.8634 (ptp) cc_final: 0.8316 (ptt) REVERT: P 260 PHE cc_start: 0.6284 (p90) cc_final: 0.5820 (p90) REVERT: N 225 GLU cc_start: 0.8562 (tp30) cc_final: 0.8156 (mm-30) REVERT: N 307 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7959 (tp) REVERT: N 333 PHE cc_start: 0.8334 (m-10) cc_final: 0.8071 (m-10) outliers start: 68 outliers final: 29 residues processed: 553 average time/residue: 1.4574 time to fit residues: 1061.5963 Evaluate side-chains 521 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 488 time to evaluate : 5.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 70 GLN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 69 PHE Chi-restraints excluded: chain N residue 307 LEU Chi-restraints excluded: chain N residue 340 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 706 optimal weight: 3.9990 chunk 481 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 631 optimal weight: 6.9990 chunk 350 optimal weight: 9.9990 chunk 724 optimal weight: 6.9990 chunk 586 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 433 optimal weight: 10.0000 chunk 761 optimal weight: 9.9990 chunk 214 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 301 GLN g 74 HIS ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN z 161 HIS P 151 GLN P 199 ASN P 287 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 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 : 0.005 0.048 69054 Z= 0.319 Angle : 0.581 9.564 93225 Z= 0.287 Chirality : 0.043 0.170 11085 Planarity : 0.003 0.057 11897 Dihedral : 7.120 174.783 9578 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.19 % Allowed : 10.89 % Favored : 87.92 % 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: 1.37 (0.09), residues: 8805 helix: 2.21 (0.08), residues: 4503 sheet: -0.04 (0.16), residues: 1118 loop : -0.63 (0.11), residues: 3184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP z 495 HIS 0.008 0.001 HIS z 161 PHE 0.020 0.001 PHE a 167 TYR 0.016 0.001 TYR E 446 ARG 0.007 0.000 ARG E 201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 508 time to evaluate : 6.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7732 (t70) cc_final: 0.7160 (t0) REVERT: A 171 MET cc_start: 0.8752 (ttp) cc_final: 0.8273 (ttm) REVERT: A 246 MET cc_start: 0.9059 (mmm) cc_final: 0.8752 (mmp) REVERT: A 359 ASP cc_start: 0.7694 (t0) cc_final: 0.7412 (t0) REVERT: D 257 LYS cc_start: 0.9156 (tttt) cc_final: 0.8955 (ttmt) REVERT: E 4 MET cc_start: 0.2968 (ptt) cc_final: 0.2333 (tmm) REVERT: G 527 LYS cc_start: 0.8915 (tppt) cc_final: 0.8549 (tttm) REVERT: H 7 ILE cc_start: 0.9063 (tp) cc_final: 0.8776 (tt) REVERT: H 293 LEU cc_start: 0.9211 (mt) cc_final: 0.8907 (mt) REVERT: Q 55 MET cc_start: 0.8540 (mtt) cc_final: 0.8265 (mtt) REVERT: Q 61 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8316 (mp0) REVERT: Z 244 VAL cc_start: 0.9147 (OUTLIER) cc_final: 0.8882 (t) REVERT: Z 496 ASP cc_start: 0.7807 (t70) cc_final: 0.7351 (t0) REVERT: e 93 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8077 (mm-30) REVERT: h 7 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8497 (pp) REVERT: q 319 TRP cc_start: 0.7967 (m-90) cc_final: 0.7671 (m-90) REVERT: P 184 MET cc_start: 0.6250 (tpp) cc_final: 0.5988 (mmm) REVERT: P 202 MET cc_start: 0.8589 (ptp) cc_final: 0.8326 (ptt) REVERT: P 260 PHE cc_start: 0.6247 (p90) cc_final: 0.5712 (p90) REVERT: N 225 GLU cc_start: 0.8573 (tp30) cc_final: 0.8183 (mm-30) REVERT: N 307 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8006 (tp) REVERT: N 333 PHE cc_start: 0.8380 (m-10) cc_final: 0.8143 (m-10) outliers start: 88 outliers final: 45 residues processed: 559 average time/residue: 1.4553 time to fit residues: 1076.6465 Evaluate side-chains 545 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 496 time to evaluate : 6.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 455 CYS Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Q residue 473 GLU Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 80 MET Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 160 MET Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 69 PHE Chi-restraints excluded: chain N residue 245 LEU Chi-restraints excluded: chain N residue 305 CYS Chi-restraints excluded: chain N residue 307 LEU Chi-restraints excluded: chain N residue 340 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 285 optimal weight: 5.9990 chunk 764 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 chunk 498 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 849 optimal weight: 6.9990 chunk 705 optimal weight: 5.9990 chunk 393 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 281 optimal weight: 8.9990 chunk 445 optimal weight: 3.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS P 199 ASN P 287 ASN N 275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 69054 Z= 0.298 Angle : 0.574 9.296 93225 Z= 0.284 Chirality : 0.043 0.168 11085 Planarity : 0.003 0.079 11897 Dihedral : 7.072 172.256 9578 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.33 % Allowed : 11.50 % Favored : 87.18 % 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: 1.35 (0.09), residues: 8805 helix: 2.20 (0.08), residues: 4501 sheet: -0.07 (0.16), residues: 1117 loop : -0.64 (0.11), residues: 3187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP z 495 HIS 0.008 0.001 HIS z 161 PHE 0.037 0.001 PHE P 158 TYR 0.025 0.001 TYR z 351 ARG 0.016 0.000 ARG z 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 502 time to evaluate : 5.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7785 (t70) cc_final: 0.7175 (t0) REVERT: A 171 MET cc_start: 0.8734 (ttp) cc_final: 0.8276 (ttm) REVERT: A 246 MET cc_start: 0.9095 (mmm) cc_final: 0.8741 (mmp) REVERT: A 359 ASP cc_start: 0.7684 (t0) cc_final: 0.7412 (t0) REVERT: B 197 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8405 (mm-30) REVERT: B 316 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7703 (m-30) REVERT: D 257 LYS cc_start: 0.9153 (tttt) cc_final: 0.8953 (ttmt) REVERT: E 4 MET cc_start: 0.2967 (ptt) cc_final: 0.2346 (tmm) REVERT: E 48 MET cc_start: 0.9093 (tpp) cc_final: 0.8871 (mmm) REVERT: E 443 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8624 (tp) REVERT: G 52 ASP cc_start: 0.8376 (t70) cc_final: 0.8119 (t0) REVERT: G 527 LYS cc_start: 0.8920 (tppt) cc_final: 0.8555 (tttm) REVERT: H 7 ILE cc_start: 0.9117 (tp) cc_final: 0.8841 (tt) REVERT: H 293 LEU cc_start: 0.9214 (mt) cc_final: 0.8915 (mt) REVERT: Q 61 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8313 (mp0) REVERT: Z 244 VAL cc_start: 0.9149 (OUTLIER) cc_final: 0.8876 (t) REVERT: Z 496 ASP cc_start: 0.7810 (t70) cc_final: 0.7350 (t0) REVERT: e 93 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8082 (mm-30) REVERT: e 426 GLU cc_start: 0.8520 (mp0) cc_final: 0.8316 (mp0) REVERT: h 53 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7900 (mpp-170) REVERT: q 319 TRP cc_start: 0.7964 (m-90) cc_final: 0.7669 (m-90) REVERT: z 359 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8502 (tppt) REVERT: P 184 MET cc_start: 0.6267 (tpp) cc_final: 0.5913 (mmt) REVERT: P 202 MET cc_start: 0.8540 (ptp) cc_final: 0.8289 (ptt) REVERT: P 260 PHE cc_start: 0.6345 (p90) cc_final: 0.5682 (p90) REVERT: N 225 GLU cc_start: 0.8571 (tp30) cc_final: 0.8181 (mm-30) REVERT: N 333 PHE cc_start: 0.8377 (m-10) cc_final: 0.8102 (m-10) outliers start: 98 outliers final: 43 residues processed: 558 average time/residue: 1.4695 time to fit residues: 1080.8098 Evaluate side-chains 543 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 494 time to evaluate : 5.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 455 CYS Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Q residue 473 GLU Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 80 MET Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain h residue 53 ARG Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 160 MET Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 341 VAL Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain P residue 69 PHE Chi-restraints excluded: chain P residue 136 PHE Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain N residue 245 LEU Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 305 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 819 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 484 optimal weight: 5.9990 chunk 620 optimal weight: 0.8980 chunk 480 optimal weight: 9.9990 chunk 715 optimal weight: 6.9990 chunk 474 optimal weight: 10.0000 chunk 846 optimal weight: 6.9990 chunk 529 optimal weight: 3.9990 chunk 515 optimal weight: 1.9990 chunk 390 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN Q 53 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS P 199 ASN P 287 ASN N 275 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 69054 Z= 0.273 Angle : 0.571 10.258 93225 Z= 0.282 Chirality : 0.042 0.166 11085 Planarity : 0.003 0.056 11897 Dihedral : 7.004 168.688 9578 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.90 % Favored : 96.09 % Rotamer: Outliers : 1.03 % Allowed : 12.19 % Favored : 86.79 % 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: 1.37 (0.09), residues: 8805 helix: 2.22 (0.08), residues: 4501 sheet: -0.07 (0.16), residues: 1116 loop : -0.63 (0.11), residues: 3188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP z 495 HIS 0.006 0.001 HIS z 161 PHE 0.020 0.001 PHE a 167 TYR 0.027 0.001 TYR z 351 ARG 0.010 0.000 ARG z 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 508 time to evaluate : 6.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7783 (t70) cc_final: 0.7183 (t0) REVERT: A 171 MET cc_start: 0.8753 (ttp) cc_final: 0.8385 (ttm) REVERT: A 359 ASP cc_start: 0.7688 (t0) cc_final: 0.7412 (t0) REVERT: B 197 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8398 (mm-30) REVERT: E 4 MET cc_start: 0.2964 (ptt) cc_final: 0.2347 (tmm) REVERT: E 443 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8616 (tp) REVERT: G 527 LYS cc_start: 0.8921 (tppt) cc_final: 0.8553 (tttm) REVERT: H 7 ILE cc_start: 0.9086 (tp) cc_final: 0.8821 (tt) REVERT: H 293 LEU cc_start: 0.9216 (mt) cc_final: 0.8915 (mt) REVERT: Q 61 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: Z 244 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8868 (t) REVERT: Z 496 ASP cc_start: 0.7801 (t70) cc_final: 0.7339 (t0) REVERT: a 288 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.8980 (t) REVERT: b 415 MET cc_start: 0.9201 (mmm) cc_final: 0.8990 (mmm) REVERT: e 93 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8081 (mm-30) REVERT: e 426 GLU cc_start: 0.8517 (mp0) cc_final: 0.8293 (mp0) REVERT: g 151 MET cc_start: 0.8433 (tpp) cc_final: 0.8212 (tpp) REVERT: h 53 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7907 (mpp-170) REVERT: q 319 TRP cc_start: 0.7959 (m-90) cc_final: 0.7663 (m-90) REVERT: z 359 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8338 (ttmp) REVERT: P 184 MET cc_start: 0.6094 (tpp) cc_final: 0.5823 (mmm) REVERT: P 202 MET cc_start: 0.8532 (ptp) cc_final: 0.8264 (ptt) REVERT: P 260 PHE cc_start: 0.6340 (p90) cc_final: 0.5671 (p90) REVERT: N 225 GLU cc_start: 0.8567 (tp30) cc_final: 0.8173 (mm-30) REVERT: N 307 LEU cc_start: 0.8461 (tp) cc_final: 0.8171 (tp) REVERT: N 333 PHE cc_start: 0.8383 (m-10) cc_final: 0.8065 (m-10) outliers start: 76 outliers final: 46 residues processed: 555 average time/residue: 1.5098 time to fit residues: 1106.7647 Evaluate side-chains 538 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 486 time to evaluate : 5.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 455 CYS Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Q residue 473 GLU Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 288 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 53 ARG Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 160 MET Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 341 VAL Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain P residue 69 PHE Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 305 CYS Chi-restraints excluded: chain N residue 340 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 523 optimal weight: 0.9990 chunk 337 optimal weight: 8.9990 chunk 505 optimal weight: 0.0670 chunk 254 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 538 optimal weight: 0.9980 chunk 576 optimal weight: 9.9990 chunk 418 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 665 optimal weight: 6.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN g 526 HIS ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS P 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 69054 Z= 0.153 Angle : 0.536 11.202 93225 Z= 0.263 Chirality : 0.041 0.172 11085 Planarity : 0.003 0.056 11897 Dihedral : 6.733 161.493 9578 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.77 % Allowed : 12.86 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.09), residues: 8805 helix: 2.36 (0.08), residues: 4504 sheet: 0.00 (0.16), residues: 1128 loop : -0.57 (0.11), residues: 3173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 266 HIS 0.010 0.001 HIS z 161 PHE 0.043 0.001 PHE P 158 TYR 0.025 0.001 TYR z 351 ARG 0.007 0.000 ARG z 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 544 time to evaluate : 6.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7723 (t70) cc_final: 0.7190 (t0) REVERT: A 171 MET cc_start: 0.8688 (ttp) cc_final: 0.8303 (ttm) REVERT: A 359 ASP cc_start: 0.7572 (t0) cc_final: 0.7350 (t0) REVERT: A 389 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: B 221 ASP cc_start: 0.8409 (t0) cc_final: 0.7811 (t0) REVERT: E 4 MET cc_start: 0.2947 (ptt) cc_final: 0.2347 (tmm) REVERT: E 443 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8576 (tp) REVERT: G 52 ASP cc_start: 0.8256 (t70) cc_final: 0.8004 (t0) REVERT: G 198 TYR cc_start: 0.9395 (m-80) cc_final: 0.9166 (m-80) REVERT: G 527 LYS cc_start: 0.8943 (tppt) cc_final: 0.8573 (tttm) REVERT: H 7 ILE cc_start: 0.9083 (tp) cc_final: 0.8825 (tt) REVERT: H 293 LEU cc_start: 0.9157 (mt) cc_final: 0.8829 (mt) REVERT: Q 61 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: Z 10 LYS cc_start: 0.8695 (ptmt) cc_final: 0.8131 (pttt) REVERT: Z 244 VAL cc_start: 0.9110 (OUTLIER) cc_final: 0.8853 (t) REVERT: Z 496 ASP cc_start: 0.7758 (t70) cc_final: 0.7304 (t0) REVERT: a 288 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8922 (t) REVERT: b 415 MET cc_start: 0.9147 (mmm) cc_final: 0.8907 (mmm) REVERT: e 93 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8079 (mm-30) REVERT: e 306 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8739 (p90) REVERT: g 28 ASN cc_start: 0.8658 (t0) cc_final: 0.8025 (t0) REVERT: q 319 TRP cc_start: 0.7927 (m-90) cc_final: 0.7638 (m-90) REVERT: z 270 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7297 (mtt180) REVERT: z 359 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8349 (ttmp) REVERT: P 173 MET cc_start: 0.6709 (tmt) cc_final: 0.6473 (ppp) REVERT: P 184 MET cc_start: 0.6380 (tpp) cc_final: 0.6084 (mmt) REVERT: P 202 MET cc_start: 0.8497 (ptp) cc_final: 0.8193 (ptt) REVERT: P 260 PHE cc_start: 0.6440 (p90) cc_final: 0.5750 (p90) REVERT: N 225 GLU cc_start: 0.8585 (tp30) cc_final: 0.8184 (mm-30) REVERT: N 307 LEU cc_start: 0.8298 (tp) cc_final: 0.8027 (tp) REVERT: N 333 PHE cc_start: 0.8317 (m-10) cc_final: 0.7968 (m-10) outliers start: 57 outliers final: 32 residues processed: 578 average time/residue: 1.4785 time to fit residues: 1133.7829 Evaluate side-chains 545 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 505 time to evaluate : 6.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 288 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 306 PHE Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 160 MET Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 341 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 270 ARG Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain P residue 183 ILE Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 340 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 769 optimal weight: 5.9990 chunk 810 optimal weight: 5.9990 chunk 739 optimal weight: 10.0000 chunk 788 optimal weight: 9.9990 chunk 474 optimal weight: 1.9990 chunk 343 optimal weight: 8.9990 chunk 619 optimal weight: 0.0070 chunk 242 optimal weight: 5.9990 chunk 712 optimal weight: 4.9990 chunk 745 optimal weight: 8.9990 chunk 785 optimal weight: 6.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 460 GLN ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS P 199 ASN N 275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 69054 Z= 0.335 Angle : 0.604 11.469 93225 Z= 0.297 Chirality : 0.043 0.170 11085 Planarity : 0.003 0.084 11897 Dihedral : 6.803 163.984 9578 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.80 % Allowed : 13.38 % Favored : 85.83 % 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: 1.40 (0.09), residues: 8805 helix: 2.25 (0.08), residues: 4504 sheet: -0.09 (0.16), residues: 1130 loop : -0.61 (0.11), residues: 3171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP z 495 HIS 0.006 0.001 HIS z 161 PHE 0.031 0.001 PHE b 252 TYR 0.028 0.001 TYR z 351 ARG 0.019 0.000 ARG z 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 495 time to evaluate : 6.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7835 (t70) cc_final: 0.7276 (OUTLIER) REVERT: A 171 MET cc_start: 0.8739 (ttp) cc_final: 0.8313 (ttm) REVERT: A 359 ASP cc_start: 0.7667 (t0) cc_final: 0.7395 (t0) REVERT: E 4 MET cc_start: 0.2912 (ptt) cc_final: 0.2313 (tmm) REVERT: E 48 MET cc_start: 0.9050 (tpp) cc_final: 0.8842 (mmm) REVERT: E 443 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8609 (tp) REVERT: G 527 LYS cc_start: 0.8966 (tppt) cc_final: 0.8587 (tttm) REVERT: H 53 ARG cc_start: 0.7822 (mtt180) cc_final: 0.7445 (mtt180) REVERT: H 293 LEU cc_start: 0.9207 (mt) cc_final: 0.8907 (mt) REVERT: Z 244 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8899 (t) REVERT: Z 496 ASP cc_start: 0.7818 (t70) cc_final: 0.7349 (t0) REVERT: a 288 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.9004 (t) REVERT: b 415 MET cc_start: 0.9234 (mmm) cc_final: 0.9002 (mmm) REVERT: e 93 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8092 (mm-30) REVERT: e 306 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8775 (p90) REVERT: q 319 TRP cc_start: 0.7958 (m-90) cc_final: 0.7658 (m-90) REVERT: z 124 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7607 (mm-30) REVERT: z 359 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8375 (ttmp) REVERT: P 184 MET cc_start: 0.6153 (tpp) cc_final: 0.5860 (mmm) REVERT: P 202 MET cc_start: 0.8443 (ptp) cc_final: 0.8141 (ptt) REVERT: P 260 PHE cc_start: 0.6433 (p90) cc_final: 0.5727 (p90) REVERT: N 225 GLU cc_start: 0.8569 (tp30) cc_final: 0.8192 (mm-30) REVERT: N 307 LEU cc_start: 0.8447 (tp) cc_final: 0.8153 (tp) REVERT: N 333 PHE cc_start: 0.8313 (m-10) cc_final: 0.8034 (m-10) outliers start: 59 outliers final: 38 residues processed: 535 average time/residue: 1.4545 time to fit residues: 1034.5350 Evaluate side-chains 526 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 484 time to evaluate : 5.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 288 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain e residue 80 MET Chi-restraints excluded: chain e residue 306 PHE Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 160 MET Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 341 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 517 optimal weight: 10.0000 chunk 833 optimal weight: 1.9990 chunk 508 optimal weight: 4.9990 chunk 395 optimal weight: 0.8980 chunk 579 optimal weight: 2.9990 chunk 874 optimal weight: 30.0000 chunk 805 optimal weight: 0.4980 chunk 696 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 538 optimal weight: 0.9990 chunk 427 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS P 199 ASN N 275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 69054 Z= 0.172 Angle : 0.557 13.537 93225 Z= 0.273 Chirality : 0.041 0.172 11085 Planarity : 0.003 0.056 11897 Dihedral : 6.599 157.935 9578 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.64 % Allowed : 13.65 % Favored : 85.72 % 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: 1.49 (0.09), residues: 8805 helix: 2.34 (0.08), residues: 4504 sheet: -0.07 (0.16), residues: 1117 loop : -0.58 (0.11), residues: 3184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 266 HIS 0.009 0.001 HIS z 161 PHE 0.044 0.001 PHE P 158 TYR 0.027 0.001 TYR z 351 ARG 0.006 0.000 ARG z 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 516 time to evaluate : 6.050 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7768 (t70) cc_final: 0.7238 (t0) REVERT: A 171 MET cc_start: 0.8689 (ttp) cc_final: 0.8354 (ttm) REVERT: A 359 ASP cc_start: 0.7598 (t0) cc_final: 0.7348 (t0) REVERT: B 221 ASP cc_start: 0.8415 (t0) cc_final: 0.7821 (t0) REVERT: E 4 MET cc_start: 0.2893 (ptt) cc_final: 0.2307 (tmm) REVERT: E 443 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8567 (tp) REVERT: G 52 ASP cc_start: 0.8261 (t70) cc_final: 0.8009 (t0) REVERT: G 527 LYS cc_start: 0.8939 (tppt) cc_final: 0.8547 (tttm) REVERT: H 293 LEU cc_start: 0.9168 (mt) cc_final: 0.8859 (mt) REVERT: Q 61 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: Z 244 VAL cc_start: 0.9128 (OUTLIER) cc_final: 0.8861 (t) REVERT: Z 496 ASP cc_start: 0.7756 (t70) cc_final: 0.7290 (t0) REVERT: a 288 THR cc_start: 0.9213 (OUTLIER) cc_final: 0.8949 (t) REVERT: b 415 MET cc_start: 0.9173 (mmm) cc_final: 0.8913 (mmm) REVERT: e 93 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8079 (mm-30) REVERT: q 92 MET cc_start: 0.9252 (tpp) cc_final: 0.8958 (tpt) REVERT: q 319 TRP cc_start: 0.7925 (m-90) cc_final: 0.7633 (m-90) REVERT: z 124 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7505 (mm-30) REVERT: z 359 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8361 (ttmp) REVERT: P 184 MET cc_start: 0.6081 (tpp) cc_final: 0.5666 (mmt) REVERT: P 202 MET cc_start: 0.8394 (ptp) cc_final: 0.8084 (ptt) REVERT: P 260 PHE cc_start: 0.6419 (p90) cc_final: 0.6078 (p90) REVERT: N 225 GLU cc_start: 0.8592 (tp30) cc_final: 0.8199 (mm-30) REVERT: N 307 LEU cc_start: 0.8335 (tp) cc_final: 0.8051 (tp) outliers start: 47 outliers final: 35 residues processed: 549 average time/residue: 1.4554 time to fit residues: 1061.0690 Evaluate side-chains 533 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 493 time to evaluate : 5.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 288 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 160 MET Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 341 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 553 optimal weight: 0.8980 chunk 741 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 642 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 697 optimal weight: 5.9990 chunk 291 optimal weight: 7.9990 chunk 716 optimal weight: 0.2980 chunk 88 optimal weight: 0.0030 chunk 128 optimal weight: 3.9990 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS P 199 ASN N 275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.082016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.066285 restraints weight = 172386.848| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.88 r_work: 0.2689 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 69054 Z= 0.167 Angle : 0.549 11.203 93225 Z= 0.268 Chirality : 0.041 0.175 11085 Planarity : 0.003 0.056 11897 Dihedral : 6.443 157.624 9578 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.57 % Allowed : 13.69 % Favored : 85.75 % 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: 1.55 (0.09), residues: 8805 helix: 2.38 (0.08), residues: 4507 sheet: -0.03 (0.16), residues: 1122 loop : -0.56 (0.11), residues: 3176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 222 HIS 0.009 0.001 HIS z 161 PHE 0.040 0.001 PHE P 158 TYR 0.026 0.001 TYR z 351 ARG 0.007 0.000 ARG z 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17133.66 seconds wall clock time: 300 minutes 29.40 seconds (18029.40 seconds total)