Starting phenix.real_space_refine on Mon Jan 20 21:12:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sg9_40453/01_2025/8sg9_40453.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sg9_40453/01_2025/8sg9_40453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sg9_40453/01_2025/8sg9_40453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sg9_40453/01_2025/8sg9_40453.map" model { file = "/net/cci-nas-00/data/ceres_data/8sg9_40453/01_2025/8sg9_40453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sg9_40453/01_2025/8sg9_40453.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 405 5.16 5 C 40970 2.51 5 N 11406 2.21 5 O 12690 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 65583 Number of models: 1 Model: "" Number of chains: 49 Chain: "N" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 474 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain breaks: 4 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4132 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Conformer: "C" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} bond proxies already assigned to first conformer: 4158 Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4063 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 16, 'TRANS': 506} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N BPHE E 9 " occ=0.38 ... (20 atoms not shown) pdb=" CZ CPHE E 9 " occ=0.62 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 35.82, per 1000 atoms: 0.55 Number of scatterers: 65583 At special positions: 0 Unit cell: (180.918, 176.686, 180.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 405 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12690 8.00 N 11406 7.00 C 40970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM65490 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65170 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65362 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.34 Conformation dependent library (CDL) restraints added in 7.6 seconds 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15882 Finding SS restraints... Secondary structure from input PDB file: 360 helices and 99 sheets defined 56.8% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.30 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.506A pdb=" N ARG A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 86 removed outlier: 3.819A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 removed outlier: 3.640A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.686A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.276A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 258 through 281 removed outlier: 4.542A pdb=" N GLN A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 381 through 405 Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 433 through 445 Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 459 through 477 removed outlier: 3.741A pdb=" N LEU A 463 " --> pdb=" O ASP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.878A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.557A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 145 Processing helix chain 'B' and resid 151 through 169 removed outlier: 4.493A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.539A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 260 through 284 Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.523A pdb=" N VAL B 341 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 Processing helix chain 'B' and resid 411 through 426 Processing helix chain 'B' and resid 430 through 454 removed outlier: 4.141A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.582A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 472 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'D' and resid 28 through 50 removed outlier: 4.350A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 105 through 126 removed outlier: 4.143A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 Processing helix chain 'D' and resid 159 through 172 removed outlier: 3.568A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 Proline residue: D 185 - end of helix removed outlier: 3.639A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 268 through 293 removed outlier: 3.949A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 341 Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 441 Processing helix chain 'D' and resid 446 through 459 removed outlier: 4.209A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.561A pdb=" N SER D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 487 removed outlier: 3.529A pdb=" N GLY D 487 " --> pdb=" O ARG D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 507 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 21 through 25 removed outlier: 3.637A pdb=" N LYS E 25 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 49 Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 85 through 102 Processing helix chain 'E' and resid 107 through 126 removed outlier: 3.612A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 151 Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'E' and resid 175 through 180 removed outlier: 6.670A pdb=" N VAL E 178 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 196 Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 218 through 222 Processing helix chain 'E' and resid 270 through 295 removed outlier: 3.818A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 391 through 415 Processing helix chain 'E' and resid 423 through 440 removed outlier: 4.021A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 456 removed outlier: 3.885A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.830A pdb=" N MET E 460 " --> pdb=" O GLU E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 484 Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 510 through 529 Processing helix chain 'G' and resid 19 through 38 removed outlier: 3.640A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 62 through 69 Processing helix chain 'G' and resid 74 through 91 Processing helix chain 'G' and resid 94 through 115 removed outlier: 3.606A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 141 removed outlier: 3.597A pdb=" N VAL G 122 " --> pdb=" O HIS G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 161 Processing helix chain 'G' and resid 163 through 167 removed outlier: 3.698A pdb=" N SER G 166 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 163 through 167' Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 194 through 198 Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 262 through 284 Processing helix chain 'G' and resid 297 through 307 removed outlier: 3.618A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 328 Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 339 through 343 Processing helix chain 'G' and resid 380 through 404 Processing helix chain 'G' and resid 412 through 427 Processing helix chain 'G' and resid 433 through 444 Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'G' and resid 458 through 470 removed outlier: 3.789A pdb=" N LEU G 462 " --> pdb=" O SER G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 18 through 35 Processing helix chain 'H' and resid 36 through 40 removed outlier: 4.007A pdb=" N LEU H 40 " --> pdb=" O ARG H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.720A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 4.077A pdb=" N THR H 98 " --> pdb=" O THR H 94 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 117 through 140 removed outlier: 3.869A pdb=" N ILE H 121 " --> pdb=" O HIS H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 164 Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'H' and resid 171 through 185 Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 259 through 284 Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 338 through 342 removed outlier: 3.654A pdb=" N LEU H 342 " --> pdb=" O ALA H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 378 through 402 Processing helix chain 'H' and resid 410 through 425 Processing helix chain 'H' and resid 429 through 442 removed outlier: 4.055A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 454 Processing helix chain 'H' and resid 456 through 470 removed outlier: 3.519A pdb=" N ILE H 460 " --> pdb=" O ASP H 456 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 10 through 15 Processing helix chain 'Q' and resid 24 through 28 Processing helix chain 'Q' and resid 28 through 45 removed outlier: 4.400A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 76 Processing helix chain 'Q' and resid 80 through 97 Processing helix chain 'Q' and resid 100 through 122 Processing helix chain 'Q' and resid 124 through 143 Processing helix chain 'Q' and resid 144 through 147 Processing helix chain 'Q' and resid 156 through 168 removed outlier: 3.520A pdb=" N VAL Q 160 " --> pdb=" O ASP Q 156 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 190 Processing helix chain 'Q' and resid 198 through 200 No H-bonds generated for 'chain 'Q' and resid 198 through 200' Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 261 through 286 removed outlier: 4.823A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 308 Processing helix chain 'Q' and resid 317 through 329 Processing helix chain 'Q' and resid 340 through 344 removed outlier: 3.693A pdb=" N MET Q 344 " --> pdb=" O LEU Q 341 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 405 Processing helix chain 'Q' and resid 413 through 429 removed outlier: 3.760A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 445 removed outlier: 4.184A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 457 Processing helix chain 'Q' and resid 459 through 474 Processing helix chain 'Q' and resid 492 through 496 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Z' and resid 3 through 8 Processing helix chain 'Z' and resid 16 through 35 removed outlier: 3.712A pdb=" N LEU Z 20 " --> pdb=" O ALA Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 59 through 67 Processing helix chain 'Z' and resid 71 through 88 Processing helix chain 'Z' and resid 91 through 111 removed outlier: 3.608A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.680A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 4.277A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.638A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 189 No H-bonds generated for 'chain 'Z' and resid 187 through 189' Processing helix chain 'Z' and resid 200 through 204 removed outlier: 3.539A pdb=" N THR Z 204 " --> pdb=" O GLU Z 201 " (cutoff:3.500A) Processing helix chain 'Z' and resid 252 through 263 Processing helix chain 'Z' and resid 264 through 282 removed outlier: 3.610A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 307 Processing helix chain 'Z' and resid 317 through 328 removed outlier: 3.784A pdb=" N MET Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 340 through 344 Processing helix chain 'Z' and resid 380 through 404 Processing helix chain 'Z' and resid 412 through 426 Processing helix chain 'Z' and resid 427 through 429 No H-bonds generated for 'chain 'Z' and resid 427 through 429' Processing helix chain 'Z' and resid 430 through 431 No H-bonds generated for 'chain 'Z' and resid 430 through 431' Processing helix chain 'Z' and resid 432 through 445 removed outlier: 4.144A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 removed outlier: 3.812A pdb=" N LYS Z 449 " --> pdb=" O LEU Z 445 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 474 removed outlier: 3.540A pdb=" N THR Z 462 " --> pdb=" O ASP Z 458 " (cutoff:3.500A) Processing helix chain 'Z' and resid 489 through 493 Processing helix chain 'Z' and resid 497 through 517 Processing helix chain 'a' and resid 14 through 33 removed outlier: 3.754A pdb=" N ARG a 18 " --> pdb=" O GLY a 14 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 57 through 65 Processing helix chain 'a' and resid 69 through 86 Processing helix chain 'a' and resid 91 through 110 Processing helix chain 'a' and resid 113 through 136 Processing helix chain 'a' and resid 144 through 157 removed outlier: 3.816A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.283A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 204 through 208 Processing helix chain 'a' and resid 256 through 258 No H-bonds generated for 'chain 'a' and resid 256 through 258' Processing helix chain 'a' and resid 259 through 280 removed outlier: 3.858A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 304 Processing helix chain 'a' and resid 312 through 324 Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'a' and resid 381 through 405 Processing helix chain 'a' and resid 413 through 427 Processing helix chain 'a' and resid 428 through 430 No H-bonds generated for 'chain 'a' and resid 428 through 430' Processing helix chain 'a' and resid 433 through 445 removed outlier: 3.754A pdb=" N ALA a 437 " --> pdb=" O ARG a 433 " (cutoff:3.500A) Processing helix chain 'a' and resid 446 through 456 Processing helix chain 'a' and resid 459 through 477 removed outlier: 3.650A pdb=" N LEU a 463 " --> pdb=" O ASP a 459 " (cutoff:3.500A) Processing helix chain 'a' and resid 478 through 484 removed outlier: 3.803A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 502 Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 20 through 40 Processing helix chain 'b' and resid 66 through 73 Processing helix chain 'b' and resid 78 through 95 Processing helix chain 'b' and resid 98 through 119 Processing helix chain 'b' and resid 122 through 145 Processing helix chain 'b' and resid 151 through 169 removed outlier: 4.434A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 174 removed outlier: 3.640A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 175 through 189 Processing helix chain 'b' and resid 195 through 197 No H-bonds generated for 'chain 'b' and resid 195 through 197' Processing helix chain 'b' and resid 208 through 212 Processing helix chain 'b' and resid 260 through 284 Processing helix chain 'b' and resid 297 through 307 Processing helix chain 'b' and resid 316 through 328 Processing helix chain 'b' and resid 337 through 341 Processing helix chain 'b' and resid 379 through 403 Processing helix chain 'b' and resid 411 through 426 Processing helix chain 'b' and resid 430 through 454 removed outlier: 4.095A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) Proline residue: b 447 - end of helix removed outlier: 3.758A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 457 through 472 Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 516 Processing helix chain 'd' and resid 28 through 48 removed outlier: 3.512A pdb=" N GLN d 32 " --> pdb=" O ASP d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 81 Processing helix chain 'd' and resid 85 through 102 Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.957A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 131 through 152 Processing helix chain 'd' and resid 159 through 172 removed outlier: 3.604A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 178 removed outlier: 6.836A pdb=" N VAL d 176 " --> pdb=" O SER d 173 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 193 Proline residue: d 185 - end of helix Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 217 through 221 Processing helix chain 'd' and resid 268 through 293 removed outlier: 3.891A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 310 through 320 Processing helix chain 'd' and resid 329 through 331 No H-bonds generated for 'chain 'd' and resid 329 through 331' Processing helix chain 'd' and resid 332 through 341 Processing helix chain 'd' and resid 347 through 351 Processing helix chain 'd' and resid 352 through 356 Processing helix chain 'd' and resid 394 through 417 Processing helix chain 'd' and resid 426 through 442 removed outlier: 3.530A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.767A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 removed outlier: 3.889A pdb=" N SER d 463 " --> pdb=" O GLU d 459 " (cutoff:3.500A) Processing helix chain 'd' and resid 472 through 487 Processing helix chain 'd' and resid 512 through 531 removed outlier: 4.924A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 49 Processing helix chain 'e' and resid 50 through 52 No H-bonds generated for 'chain 'e' and resid 50 through 52' Processing helix chain 'e' and resid 73 through 81 Processing helix chain 'e' and resid 85 through 102 Processing helix chain 'e' and resid 107 through 126 removed outlier: 3.702A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 151 Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'e' and resid 175 through 180 removed outlier: 6.597A pdb=" N VAL e 178 " --> pdb=" O SER e 175 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 181 through 196 Processing helix chain 'e' and resid 205 through 207 No H-bonds generated for 'chain 'e' and resid 205 through 207' Processing helix chain 'e' and resid 218 through 222 Processing helix chain 'e' and resid 270 through 295 removed outlier: 3.831A pdb=" N THR e 295 " --> pdb=" O GLN e 291 " (cutoff:3.500A) Processing helix chain 'e' and resid 307 through 317 Processing helix chain 'e' and resid 326 through 338 Processing helix chain 'e' and resid 344 through 348 Processing helix chain 'e' and resid 349 through 353 Processing helix chain 'e' and resid 391 through 415 Processing helix chain 'e' and resid 423 through 440 removed outlier: 3.905A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 441 through 456 removed outlier: 3.995A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 466 removed outlier: 3.523A pdb=" N MET e 460 " --> pdb=" O GLU e 456 " (cutoff:3.500A) Processing helix chain 'e' and resid 469 through 484 Processing helix chain 'e' and resid 500 through 505 Processing helix chain 'e' and resid 510 through 529 Processing helix chain 'g' and resid 19 through 37 removed outlier: 3.645A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 38 through 41 removed outlier: 3.822A pdb=" N LEU g 41 " --> pdb=" O ARG g 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 38 through 41' Processing helix chain 'g' and resid 62 through 69 removed outlier: 3.816A pdb=" N GLU g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 74 through 91 Processing helix chain 'g' and resid 94 through 115 removed outlier: 3.625A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN g 115 " --> pdb=" O HIS g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.631A pdb=" N VAL g 122 " --> pdb=" O HIS g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 161 Processing helix chain 'g' and resid 163 through 167 removed outlier: 3.891A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 removed outlier: 3.610A pdb=" N ALA g 172 " --> pdb=" O TRP g 168 " (cutoff:3.500A) Processing helix chain 'g' and resid 208 through 212 Processing helix chain 'g' and resid 262 through 284 Processing helix chain 'g' and resid 297 through 307 removed outlier: 3.581A pdb=" N ALA g 307 " --> pdb=" O TYR g 303 " (cutoff:3.500A) Processing helix chain 'g' and resid 316 through 328 Processing helix chain 'g' and resid 334 through 338 Processing helix chain 'g' and resid 339 through 343 Processing helix chain 'g' and resid 380 through 404 Processing helix chain 'g' and resid 412 through 426 Processing helix chain 'g' and resid 427 through 429 No H-bonds generated for 'chain 'g' and resid 427 through 429' Processing helix chain 'g' and resid 433 through 443 Processing helix chain 'g' and resid 445 through 456 Processing helix chain 'g' and resid 458 through 471 removed outlier: 3.533A pdb=" N THR g 471 " --> pdb=" O ARG g 467 " (cutoff:3.500A) Processing helix chain 'g' and resid 490 through 494 Processing helix chain 'g' and resid 499 through 518 Processing helix chain 'h' and resid 18 through 35 removed outlier: 3.553A pdb=" N LEU h 22 " --> pdb=" O GLY h 18 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 40 removed outlier: 3.577A pdb=" N LEU h 40 " --> pdb=" O ARG h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 69 Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.729A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 114 removed outlier: 4.097A pdb=" N THR h 98 " --> pdb=" O THR h 94 " (cutoff:3.500A) Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 117 through 140 removed outlier: 3.656A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 147 through 164 Processing helix chain 'h' and resid 168 through 170 No H-bonds generated for 'chain 'h' and resid 168 through 170' Processing helix chain 'h' and resid 171 through 185 Processing helix chain 'h' and resid 191 through 193 No H-bonds generated for 'chain 'h' and resid 191 through 193' Processing helix chain 'h' and resid 204 through 208 Processing helix chain 'h' and resid 224 through 228 Processing helix chain 'h' and resid 259 through 284 removed outlier: 3.554A pdb=" N SER h 284 " --> pdb=" O LYS h 280 " (cutoff:3.500A) Processing helix chain 'h' and resid 296 through 306 Processing helix chain 'h' and resid 315 through 327 Processing helix chain 'h' and resid 338 through 340 No H-bonds generated for 'chain 'h' and resid 338 through 340' Processing helix chain 'h' and resid 378 through 402 Processing helix chain 'h' and resid 410 through 425 Processing helix chain 'h' and resid 429 through 442 removed outlier: 3.706A pdb=" N LEU h 433 " --> pdb=" O GLY h 429 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) Processing helix chain 'h' and resid 443 through 454 Processing helix chain 'h' and resid 456 through 471 Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'q' and resid 10 through 15 Processing helix chain 'q' and resid 24 through 45 removed outlier: 4.181A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 76 Processing helix chain 'q' and resid 80 through 97 Processing helix chain 'q' and resid 100 through 121 Processing helix chain 'q' and resid 124 through 143 Processing helix chain 'q' and resid 144 through 147 Processing helix chain 'q' and resid 157 through 166 removed outlier: 4.426A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 190 Processing helix chain 'q' and resid 198 through 200 No H-bonds generated for 'chain 'q' and resid 198 through 200' Processing helix chain 'q' and resid 211 through 215 Processing helix chain 'q' and resid 261 through 285 removed outlier: 4.842A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) Processing helix chain 'q' and resid 298 through 308 Processing helix chain 'q' and resid 317 through 329 Processing helix chain 'q' and resid 381 through 405 Processing helix chain 'q' and resid 413 through 428 Processing helix chain 'q' and resid 433 through 444 removed outlier: 4.297A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 457 Processing helix chain 'q' and resid 459 through 474 Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 2 through 8 removed outlier: 3.585A pdb=" N LEU z 7 " --> pdb=" O ALA z 3 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 35 removed outlier: 3.589A pdb=" N LEU z 20 " --> pdb=" O ALA z 16 " (cutoff:3.500A) Processing helix chain 'z' and resid 36 through 38 No H-bonds generated for 'chain 'z' and resid 36 through 38' Processing helix chain 'z' and resid 59 through 67 Processing helix chain 'z' and resid 71 through 88 Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.599A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.755A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 4.230A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 removed outlier: 3.721A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) Processing helix chain 'z' and resid 187 through 189 No H-bonds generated for 'chain 'z' and resid 187 through 189' Processing helix chain 'z' and resid 200 through 204 removed outlier: 3.819A pdb=" N THR z 204 " --> pdb=" O GLU z 201 " (cutoff:3.500A) Processing helix chain 'z' and resid 252 through 263 Processing helix chain 'z' and resid 264 through 282 removed outlier: 3.638A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 308 removed outlier: 3.723A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 328 removed outlier: 4.249A pdb=" N GLU z 322 " --> pdb=" O ARG z 318 " (cutoff:3.500A) Processing helix chain 'z' and resid 340 through 344 Processing helix chain 'z' and resid 380 through 404 Processing helix chain 'z' and resid 412 through 426 Processing helix chain 'z' and resid 427 through 429 No H-bonds generated for 'chain 'z' and resid 427 through 429' Processing helix chain 'z' and resid 430 through 431 No H-bonds generated for 'chain 'z' and resid 430 through 431' Processing helix chain 'z' and resid 432 through 445 removed outlier: 4.182A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.577A pdb=" N LYS z 449 " --> pdb=" O LEU z 445 " (cutoff:3.500A) Processing helix chain 'z' and resid 458 through 474 Processing helix chain 'z' and resid 489 through 493 Processing helix chain 'z' and resid 497 through 517 Processing sheet with id=AA1, first strand: chain 'N' and resid 209 through 212 removed outlier: 6.480A pdb=" N CYS N 219 " --> pdb=" O SER N 232 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER N 232 " --> pdb=" O CYS N 219 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU N 221 " --> pdb=" O LEU N 230 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 244 through 245 removed outlier: 6.654A pdb=" N VAL N 265 " --> pdb=" O VAL N 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 13 removed outlier: 4.623A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 46 Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA7, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.333A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.609A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.609A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 286 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 254 through 256 removed outlier: 9.212A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AB3, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.454A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE B 521 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 61 through 64 removed outlier: 6.914A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 53 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB6, first strand: chain 'B' and resid 199 through 205 removed outlier: 3.807A pdb=" N GLY B 377 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.464A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 346 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU B 348 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU B 233 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB9, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC1, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.390A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LYS D 213 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.655A pdb=" N SER D 358 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS D 245 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU D 360 " --> pdb=" O LYS D 243 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL D 297 " --> pdb=" O LYS D 243 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE D 249 " --> pdb=" O GLN D 301 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.566A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 28 through 29 removed outlier: 3.568A pdb=" N ILE E 533 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU H 48 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE E 533 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL H 50 " --> pdb=" O ILE E 533 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC6, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.507A pdb=" N LYS E 210 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE E 387 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU E 212 " --> pdb=" O ILE E 387 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLY E 389 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LYS E 214 " --> pdb=" O GLY E 389 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.684A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 321 through 322 removed outlier: 6.651A pdb=" N ALA E 300 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N VAL E 342 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE E 250 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 15 through 17 Processing sheet with id=AD1, first strand: chain 'G' and resid 57 through 60 removed outlier: 7.239A pdb=" N MET G 47 " --> pdb=" O GLU Z 520 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N MET Z 522 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N MET G 49 " --> pdb=" O MET Z 522 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AD3, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AD4, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.754A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD6, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AD7, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=AD8, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.349A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AE1, first strand: chain 'H' and resid 195 through 201 removed outlier: 3.812A pdb=" N GLY H 376 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AE3, first strand: chain 'H' and resid 309 through 311 Processing sheet with id=AE4, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AE5, first strand: chain 'Q' and resid 20 through 23 removed outlier: 5.020A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 149 through 150 removed outlier: 3.948A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.478A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS Q 205 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N GLY Q 379 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE Q 207 " --> pdb=" O GLY Q 379 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 220 through 223 removed outlier: 3.755A pdb=" N VAL Q 350 " --> pdb=" O VAL Q 234 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 240 through 242 Processing sheet with id=AF1, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AF2, first strand: chain 'Z' and resid 139 through 140 Processing sheet with id=AF3, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.301A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id=AF5, first strand: chain 'Z' and resid 311 through 313 removed outlier: 9.156A pdb=" N VAL Z 311 " --> pdb=" O LYS Z 287 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE Z 289 " --> pdb=" O VAL Z 311 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU Z 313 " --> pdb=" O PHE Z 289 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL Z 291 " --> pdb=" O LEU Z 313 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP Z 227 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU Z 231 " --> pdb=" O ILE Z 292 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.572A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'a' and resid 9 through 13 removed outlier: 4.412A pdb=" N ILE a 527 " --> pdb=" O ASP d 58 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET d 60 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE a 531 " --> pdb=" O GLN d 62 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.305A pdb=" N ASP a 42 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP g 521 " --> pdb=" O ASP a 42 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 138 through 139 Processing sheet with id=AG1, first strand: chain 'a' and resid 181 through 182 Processing sheet with id=AG2, first strand: chain 'a' and resid 196 through 201 removed outlier: 6.273A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLY a 379 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA a 200 " --> pdb=" O GLY a 379 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.512A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.512A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'g' and resid 254 through 256 removed outlier: 9.065A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG b 255 " --> pdb=" O VAL e 268 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS e 263 " --> pdb=" O ALA h 253 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 486 through 489 Processing sheet with id=AG7, first strand: chain 'b' and resid 17 through 19 removed outlier: 4.449A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE b 521 " --> pdb=" O VAL e 62 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 61 through 64 removed outlier: 7.088A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AH1, first strand: chain 'b' and resid 199 through 205 removed outlier: 3.822A pdb=" N GLY b 377 " --> pdb=" O LYS b 204 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.398A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER b 345 " --> pdb=" O LYS b 236 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS b 236 " --> pdb=" O SER b 345 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS b 347 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS b 289 " --> pdb=" O LYS b 236 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AH4, first strand: chain 'd' and resid 153 through 154 Processing sheet with id=AH5, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.584A pdb=" N LYS d 209 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL d 390 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL d 211 " --> pdb=" O VAL d 390 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLY d 392 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYS d 213 " --> pdb=" O GLY d 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.595A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS d 379 " --> pdb=" O ALA d 359 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA d 359 " --> pdb=" O CYS d 379 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.595A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS d 379 " --> pdb=" O ALA d 359 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA d 359 " --> pdb=" O CYS d 379 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LYS d 245 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU d 299 " --> pdb=" O LYS d 245 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLN d 301 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE d 249 " --> pdb=" O GLN d 301 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU d 298 " --> pdb=" O ILE d 325 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASP d 327 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE d 300 " --> pdb=" O ASP d 327 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 491 through 493 removed outlier: 3.558A pdb=" N SER d 501 " --> pdb=" O GLY d 492 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'e' and resid 26 through 29 removed outlier: 7.242A pdb=" N LEU h 48 " --> pdb=" O ASP e 531 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE e 533 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL h 50 " --> pdb=" O ILE e 533 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LYS e 535 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'e' and resid 153 through 154 Processing sheet with id=AI2, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.400A pdb=" N LYS e 210 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE e 387 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU e 212 " --> pdb=" O ILE e 387 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLY e 389 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS e 214 " --> pdb=" O GLY e 389 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'e' and resid 228 through 230 removed outlier: 6.506A pdb=" N LEU e 358 " --> pdb=" O GLU e 244 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU e 244 " --> pdb=" O LEU e 358 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN e 360 " --> pdb=" O LYS e 242 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS e 242 " --> pdb=" O GLN e 360 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'g' and resid 57 through 60 removed outlier: 6.457A pdb=" N MET g 47 " --> pdb=" O VAL z 518 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU z 520 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'g' and resid 142 through 143 Processing sheet with id=AI6, first strand: chain 'g' and resid 185 through 187 Processing sheet with id=AI7, first strand: chain 'g' and resid 200 through 205 removed outlier: 4.066A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR g 373 " --> pdb=" O LEU g 215 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'g' and resid 218 through 220 Processing sheet with id=AI9, first strand: chain 'g' and resid 310 through 312 removed outlier: 6.361A pdb=" N VAL g 290 " --> pdb=" O ILE g 312 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N VAL g 332 " --> pdb=" O ILE g 238 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU g 240 " --> pdb=" O VAL g 332 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'g' and resid 478 through 480 Processing sheet with id=AJ2, first strand: chain 'h' and resid 14 through 17 removed outlier: 4.300A pdb=" N VAL h 516 " --> pdb=" O ASN q 53 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N MET q 55 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU h 518 " --> pdb=" O MET q 55 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ILE q 57 " --> pdb=" O GLU h 518 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE h 520 " --> pdb=" O ILE q 57 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'h' and resid 195 through 201 removed outlier: 3.889A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AJ5, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ6, first strand: chain 'h' and resid 405 through 407 Processing sheet with id=AJ7, first strand: chain 'h' and resid 475 through 478 Processing sheet with id=AJ8, first strand: chain 'q' and resid 20 through 22 removed outlier: 5.013A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'q' and resid 149 through 150 removed outlier: 3.816A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'q' and resid 202 through 206 removed outlier: 6.622A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'q' and resid 220 through 223 Processing sheet with id=AK3, first strand: chain 'q' and resid 239 through 242 Processing sheet with id=AK4, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AK5, first strand: chain 'z' and resid 139 through 140 Processing sheet with id=AK6, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.369A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'z' and resid 210 through 212 Processing sheet with id=AK8, first strand: chain 'z' and resid 310 through 313 removed outlier: 9.125A pdb=" N VAL z 311 " --> pdb=" O LYS z 287 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP z 227 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL z 290 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE z 292 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU z 231 " --> pdb=" O ILE z 292 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'z' and resid 477 through 479 3998 hydrogen bonds defined for protein. 11430 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 29.20 Time building geometry restraints manager: 15.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22054 1.34 - 1.46: 9457 1.46 - 1.58: 34046 1.58 - 1.69: 48 1.69 - 1.81: 718 Bond restraints: 66323 Sorted by residual: bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" F2 AF3 d 603 " pdb="AL AF3 d 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.34e+01 bond pdb=" F2 AF3 A 603 " pdb="AL AF3 A 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.33e+01 ... (remaining 66318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 88576 2.09 - 4.18: 742 4.18 - 6.27: 231 6.27 - 8.36: 13 8.36 - 10.45: 1 Bond angle restraints: 89563 Sorted by residual: angle pdb=" N ILE a 49 " pdb=" CA ILE a 49 " pdb=" C ILE a 49 " ideal model delta sigma weight residual 113.20 107.26 5.94 9.60e-01 1.09e+00 3.82e+01 angle pdb=" C ALA q 530 " pdb=" CA ALA q 530 " pdb=" CB ALA q 530 " ideal model delta sigma weight residual 117.23 110.29 6.94 1.36e+00 5.41e-01 2.60e+01 angle pdb=" CA ALA q 530 " pdb=" C ALA q 530 " pdb=" N GLY q 531 " ideal model delta sigma weight residual 119.98 116.86 3.12 8.50e-01 1.38e+00 1.35e+01 angle pdb=" C ALA q 151 " pdb=" N LYS q 152 " pdb=" CA LYS q 152 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 121.06 -7.88 2.37e+00 1.78e-01 1.11e+01 ... (remaining 89558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 40343 34.93 - 69.87: 596 69.87 - 104.80: 58 104.80 - 139.74: 9 139.74 - 174.67: 6 Dihedral angle restraints: 41012 sinusoidal: 16493 harmonic: 24519 Sorted by residual: dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual 300.00 125.33 174.67 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 113.28 -173.28 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 129.27 170.73 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 41009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 9515 0.067 - 0.134: 1153 0.134 - 0.201: 19 0.201 - 0.268: 0 0.268 - 0.334: 1 Chirality restraints: 10688 Sorted by residual: chirality pdb=" CB ILE b 11 " pdb=" CA ILE b 11 " pdb=" CG1 ILE b 11 " pdb=" CG2 ILE b 11 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA GLU a 77 " pdb=" N GLU a 77 " pdb=" C GLU a 77 " pdb=" CB GLU a 77 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CB ILE G 363 " pdb=" CA ILE G 363 " pdb=" CG1 ILE G 363 " pdb=" CG2 ILE G 363 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.65e-01 ... (remaining 10685 not shown) Planarity restraints: 11425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP a 47 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C ASP a 47 " 0.040 2.00e-02 2.50e+03 pdb=" O ASP a 47 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP a 48 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO e 441 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 404 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO G 405 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 405 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 405 " 0.027 5.00e-02 4.00e+02 ... (remaining 11422 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 513 2.52 - 3.12: 49330 3.12 - 3.71: 103015 3.71 - 4.31: 144827 4.31 - 4.90: 250018 Nonbonded interactions: 547703 Sorted by model distance: nonbonded pdb="MG MG b 602 " pdb=" F1 AF3 b 603 " model vdw 1.928 2.120 nonbonded pdb=" O1A ADP q 601 " pdb="MG MG q 602 " model vdw 1.946 2.170 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.951 2.120 nonbonded pdb="MG MG z 602 " pdb=" F1 AF3 z 603 " model vdw 1.969 2.120 nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.972 2.120 ... (remaining 547698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = (chain 'G' and (resid 8 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 8 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 2.180 Check model and map are aligned: 0.400 Set scattering table: 0.480 Process input model: 128.710 Find NCS groups from input model: 5.890 Set up NCS constraints: 0.450 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:9.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 66323 Z= 0.292 Angle : 0.535 10.450 89563 Z= 0.264 Chirality : 0.041 0.334 10688 Planarity : 0.003 0.055 11425 Dihedral : 13.773 174.674 25130 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.09), residues: 8486 helix: 2.39 (0.08), residues: 4349 sheet: 0.19 (0.16), residues: 1129 loop : -0.43 (0.11), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 168 HIS 0.013 0.001 HIS z 161 PHE 0.022 0.001 PHE H 174 TYR 0.012 0.001 TYR q 468 ARG 0.006 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 561 time to evaluate : 6.441 Fit side-chains REVERT: A 47 ASP cc_start: 0.7861 (t0) cc_final: 0.7655 (t0) REVERT: A 344 MET cc_start: 0.8893 (mpp) cc_final: 0.8522 (mmm) REVERT: A 508 ILE cc_start: 0.9091 (tp) cc_final: 0.8886 (tp) REVERT: B 17 ASP cc_start: 0.8219 (t0) cc_final: 0.7795 (t70) REVERT: E 29 MET cc_start: 0.7945 (mmm) cc_final: 0.7739 (mmm) REVERT: E 464 GLU cc_start: 0.8732 (tt0) cc_final: 0.8445 (tp30) REVERT: E 501 MET cc_start: 0.9317 (mmp) cc_final: 0.8983 (mmp) REVERT: G 113 LEU cc_start: 0.9064 (mt) cc_final: 0.8796 (mp) REVERT: H 14 ASP cc_start: 0.8485 (t70) cc_final: 0.8271 (t0) REVERT: H 81 ASP cc_start: 0.8499 (m-30) cc_final: 0.8147 (m-30) REVERT: Q 41 GLN cc_start: 0.8791 (tp40) cc_final: 0.8302 (tp40) REVERT: Q 249 MET cc_start: 0.8389 (pmm) cc_final: 0.8081 (pmm) REVERT: Q 296 LYS cc_start: 0.8555 (tmmt) cc_final: 0.8308 (ttpp) REVERT: a 209 MET cc_start: 0.8383 (mtm) cc_final: 0.8099 (mtp) REVERT: a 416 GLU cc_start: 0.8237 (mp0) cc_final: 0.7933 (mp0) REVERT: b 139 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7778 (tm-30) REVERT: b 353 MET cc_start: 0.9036 (tpt) cc_final: 0.8753 (tpp) REVERT: e 4 MET cc_start: 0.4429 (mmt) cc_final: 0.4156 (tmm) REVERT: e 464 GLU cc_start: 0.8539 (tp30) cc_final: 0.8213 (tp30) REVERT: g 52 ASP cc_start: 0.8019 (t0) cc_final: 0.7790 (t0) REVERT: h 524 ARG cc_start: 0.7636 (tmt170) cc_final: 0.7036 (tmm160) REVERT: q 41 GLN cc_start: 0.8818 (tp-100) cc_final: 0.8476 (tm-30) REVERT: z 44 MET cc_start: 0.8798 (mmm) cc_final: 0.8486 (mmm) outliers start: 0 outliers final: 0 residues processed: 561 average time/residue: 1.6114 time to fit residues: 1155.3402 Evaluate side-chains 432 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 6.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 713 optimal weight: 9.9990 chunk 640 optimal weight: 6.9990 chunk 355 optimal weight: 6.9990 chunk 218 optimal weight: 7.9990 chunk 432 optimal weight: 8.9990 chunk 342 optimal weight: 2.9990 chunk 662 optimal weight: 8.9990 chunk 256 optimal weight: 0.9990 chunk 402 optimal weight: 8.9990 chunk 492 optimal weight: 0.3980 chunk 767 optimal weight: 6.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 73 GLN H 283 HIS Z 84 GLN ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 423 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN z 161 HIS ** z 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 346 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.062473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.052133 restraints weight = 175709.759| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 2.90 r_work: 0.2473 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 66323 Z= 0.333 Angle : 0.605 10.778 89563 Z= 0.301 Chirality : 0.044 0.171 10688 Planarity : 0.003 0.062 11425 Dihedral : 7.445 176.998 9216 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.69 % Allowed : 6.00 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.09), residues: 8486 helix: 2.35 (0.08), residues: 4392 sheet: 0.10 (0.16), residues: 1095 loop : -0.51 (0.11), residues: 2999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 168 HIS 0.012 0.001 HIS z 161 PHE 0.025 0.001 PHE H 174 TYR 0.018 0.001 TYR E 446 ARG 0.007 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 457 time to evaluate : 6.042 Fit side-chains REVERT: A 344 MET cc_start: 0.9418 (mpp) cc_final: 0.9029 (mmm) REVERT: A 508 ILE cc_start: 0.9042 (tp) cc_final: 0.8829 (tp) REVERT: B 62 MET cc_start: 0.8614 (ttm) cc_final: 0.8334 (ttm) REVERT: D 57 MET cc_start: 0.9273 (mmm) cc_final: 0.8884 (mmm) REVERT: D 67 ASP cc_start: 0.8406 (m-30) cc_final: 0.8145 (m-30) REVERT: E 464 GLU cc_start: 0.9162 (tt0) cc_final: 0.8675 (tp30) REVERT: E 532 ASP cc_start: 0.7947 (m-30) cc_final: 0.7613 (m-30) REVERT: E 533 ILE cc_start: 0.9308 (mm) cc_final: 0.9105 (tp) REVERT: G 47 MET cc_start: 0.9284 (mtp) cc_final: 0.8891 (mtp) REVERT: G 54 MET cc_start: 0.8800 (mmm) cc_final: 0.8518 (mpp) REVERT: G 59 MET cc_start: 0.9351 (ttp) cc_final: 0.9002 (ttp) REVERT: G 167 ARG cc_start: 0.8905 (mmp-170) cc_final: 0.8555 (mmp80) REVERT: G 521 ASP cc_start: 0.7949 (t70) cc_final: 0.7641 (t70) REVERT: H 14 ASP cc_start: 0.8669 (t70) cc_final: 0.8396 (t0) REVERT: H 81 ASP cc_start: 0.8859 (m-30) cc_final: 0.8490 (m-30) REVERT: Q 41 GLN cc_start: 0.9146 (tp40) cc_final: 0.8671 (tp40) REVERT: Q 249 MET cc_start: 0.8684 (pmm) cc_final: 0.8244 (pmm) REVERT: Q 296 LYS cc_start: 0.8389 (tmmt) cc_final: 0.8153 (ttpp) REVERT: Z 69 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8928 (mp) REVERT: Z 415 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: a 209 MET cc_start: 0.9211 (mtm) cc_final: 0.8913 (mtp) REVERT: a 416 GLU cc_start: 0.8413 (mp0) cc_final: 0.8154 (mp0) REVERT: b 139 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8242 (tm-30) REVERT: e 4 MET cc_start: 0.3933 (mmt) cc_final: 0.3693 (tmm) REVERT: e 440 CYS cc_start: 0.8740 (t) cc_final: 0.8540 (t) REVERT: e 464 GLU cc_start: 0.8995 (tp30) cc_final: 0.8703 (tp30) REVERT: g 47 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8560 (mtp) REVERT: g 527 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8664 (mtmm) REVERT: g 528 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8318 (tmmt) REVERT: h 70 ASP cc_start: 0.8309 (m-30) cc_final: 0.8091 (t0) REVERT: h 524 ARG cc_start: 0.7924 (tmt170) cc_final: 0.7369 (tmm160) REVERT: q 26 GLU cc_start: 0.8729 (tt0) cc_final: 0.8506 (pm20) REVERT: q 41 GLN cc_start: 0.9070 (tp-100) cc_final: 0.8753 (tm-30) REVERT: q 152 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8585 (ptmm) REVERT: q 522 ASP cc_start: 0.9187 (t0) cc_final: 0.8983 (t0) REVERT: z 190 MET cc_start: 0.9304 (mmp) cc_final: 0.8994 (mmp) REVERT: z 244 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8340 (t) outliers start: 49 outliers final: 12 residues processed: 477 average time/residue: 1.5653 time to fit residues: 963.1030 Evaluate side-chains 442 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 423 time to evaluate : 6.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain b residue 11 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 527 LYS Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 367 optimal weight: 10.0000 chunk 589 optimal weight: 7.9990 chunk 632 optimal weight: 6.9990 chunk 829 optimal weight: 5.9990 chunk 637 optimal weight: 2.9990 chunk 680 optimal weight: 4.9990 chunk 746 optimal weight: 10.0000 chunk 575 optimal weight: 1.9990 chunk 705 optimal weight: 5.9990 chunk 634 optimal weight: 6.9990 chunk 600 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 472 GLN H 117 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN z 84 GLN z 161 HIS ** z 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.061313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.050641 restraints weight = 208774.050| |-----------------------------------------------------------------------------| r_work (start): 0.2582 rms_B_bonded: 3.16 r_work: 0.2428 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2432 r_free = 0.2432 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2432 r_free = 0.2432 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 66323 Z= 0.380 Angle : 0.610 9.731 89563 Z= 0.303 Chirality : 0.044 0.176 10688 Planarity : 0.003 0.062 11425 Dihedral : 7.369 176.356 9216 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.89 % Allowed : 8.03 % Favored : 91.09 % 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: 1.50 (0.09), residues: 8486 helix: 2.29 (0.08), residues: 4395 sheet: -0.03 (0.16), residues: 1086 loop : -0.56 (0.11), residues: 3005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 304 HIS 0.012 0.001 HIS z 161 PHE 0.020 0.001 PHE H 174 TYR 0.018 0.001 TYR z 498 ARG 0.008 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 442 time to evaluate : 6.078 Fit side-chains REVERT: A 156 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8555 (mpp) REVERT: A 306 MET cc_start: 0.9340 (mtp) cc_final: 0.8977 (mtm) REVERT: B 62 MET cc_start: 0.8531 (ttm) cc_final: 0.8278 (ttm) REVERT: D 57 MET cc_start: 0.9199 (mmm) cc_final: 0.8911 (mmm) REVERT: E 464 GLU cc_start: 0.9162 (tt0) cc_final: 0.8668 (tp30) REVERT: E 533 ILE cc_start: 0.9321 (mm) cc_final: 0.9114 (tp) REVERT: G 54 MET cc_start: 0.8848 (mmm) cc_final: 0.8564 (mpp) REVERT: G 167 ARG cc_start: 0.8997 (mmp-170) cc_final: 0.8718 (mmp80) REVERT: H 14 ASP cc_start: 0.8726 (t70) cc_final: 0.8422 (t0) REVERT: H 81 ASP cc_start: 0.8873 (m-30) cc_final: 0.8522 (m-30) REVERT: H 227 MET cc_start: 0.9408 (mpp) cc_final: 0.9171 (mmm) REVERT: Q 249 MET cc_start: 0.8690 (pmm) cc_final: 0.8250 (pmm) REVERT: Q 296 LYS cc_start: 0.8513 (tmmt) cc_final: 0.8263 (ttpp) REVERT: Z 10 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7529 (ptpp) REVERT: Z 15 ARG cc_start: 0.8851 (ttm110) cc_final: 0.8320 (ttp-110) REVERT: Z 161 HIS cc_start: 0.6489 (OUTLIER) cc_final: 0.6055 (t70) REVERT: Z 415 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8345 (mp0) REVERT: a 209 MET cc_start: 0.9239 (mtm) cc_final: 0.8939 (mtp) REVERT: a 416 GLU cc_start: 0.8479 (mp0) cc_final: 0.8205 (mp0) REVERT: d 48 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8641 (pp) REVERT: d 222 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: e 4 MET cc_start: 0.3856 (mmt) cc_final: 0.3645 (tmm) REVERT: e 29 MET cc_start: 0.8505 (mtp) cc_final: 0.8095 (mtm) REVERT: e 207 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.9042 (mt-10) REVERT: e 440 CYS cc_start: 0.8766 (t) cc_final: 0.8476 (t) REVERT: e 464 GLU cc_start: 0.9054 (tp30) cc_final: 0.8761 (tp30) REVERT: g 46 MET cc_start: 0.9249 (mmm) cc_final: 0.8879 (mmm) REVERT: g 47 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8484 (mtp) REVERT: g 528 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8248 (tmmt) REVERT: h 70 ASP cc_start: 0.8352 (m-30) cc_final: 0.8142 (t0) REVERT: h 524 ARG cc_start: 0.7987 (tmt170) cc_final: 0.7554 (tmm160) REVERT: q 41 GLN cc_start: 0.9055 (tp-100) cc_final: 0.8755 (tm-30) REVERT: q 522 ASP cc_start: 0.9314 (t0) cc_final: 0.8960 (t0) REVERT: z 244 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8323 (t) outliers start: 63 outliers final: 21 residues processed: 477 average time/residue: 1.5632 time to fit residues: 971.5554 Evaluate side-chains 450 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 419 time to evaluate : 6.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 10 LYS Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 11 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 207 GLU Chi-restraints excluded: chain e residue 533 ILE Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 173 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 519 optimal weight: 1.9990 chunk 817 optimal weight: 0.9990 chunk 630 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 686 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 587 optimal weight: 6.9990 chunk 703 optimal weight: 10.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN A 56 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 514 ASN b 227 ASN ** d 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN z 161 HIS z 218 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.063721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.053041 restraints weight = 192418.376| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 3.18 r_work: 0.2479 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2485 r_free = 0.2485 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2485 r_free = 0.2485 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 66323 Z= 0.176 Angle : 0.543 9.790 89563 Z= 0.267 Chirality : 0.041 0.171 10688 Planarity : 0.003 0.060 11425 Dihedral : 7.083 177.234 9216 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.84 % Allowed : 9.42 % Favored : 89.74 % 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: 1.64 (0.09), residues: 8486 helix: 2.42 (0.08), residues: 4398 sheet: 0.06 (0.16), residues: 1067 loop : -0.53 (0.11), residues: 3021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 168 HIS 0.014 0.001 HIS z 161 PHE 0.020 0.001 PHE H 174 TYR 0.012 0.001 TYR E 420 ARG 0.006 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 463 time to evaluate : 6.156 Fit side-chains revert: symmetry clash REVERT: N 267 ASP cc_start: 0.6580 (t0) cc_final: 0.6311 (t0) REVERT: A 156 MET cc_start: 0.8862 (mpp) cc_final: 0.8595 (mpp) REVERT: A 306 MET cc_start: 0.9287 (mtp) cc_final: 0.8938 (mtm) REVERT: A 508 ILE cc_start: 0.9021 (tp) cc_final: 0.8816 (tp) REVERT: B 62 MET cc_start: 0.8414 (ttm) cc_final: 0.8155 (ttm) REVERT: D 28 ASP cc_start: 0.8504 (t0) cc_final: 0.7869 (t0) REVERT: D 57 MET cc_start: 0.9158 (mmm) cc_final: 0.8871 (mmm) REVERT: D 467 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8831 (tm-30) REVERT: E 464 GLU cc_start: 0.9167 (tt0) cc_final: 0.8682 (tp30) REVERT: G 47 MET cc_start: 0.9204 (mtm) cc_final: 0.8956 (mtp) REVERT: G 54 MET cc_start: 0.8854 (mmm) cc_final: 0.8571 (mpp) REVERT: G 59 MET cc_start: 0.9409 (ttp) cc_final: 0.9102 (ttp) REVERT: G 167 ARG cc_start: 0.8926 (mmp-170) cc_final: 0.8612 (mmp80) REVERT: G 429 MET cc_start: 0.8472 (mtm) cc_final: 0.8169 (ptm) REVERT: H 14 ASP cc_start: 0.8677 (t70) cc_final: 0.8403 (t0) REVERT: H 81 ASP cc_start: 0.8826 (m-30) cc_final: 0.8471 (m-30) REVERT: H 227 MET cc_start: 0.9373 (mpp) cc_final: 0.9156 (mmm) REVERT: Q 41 GLN cc_start: 0.9157 (tp40) cc_final: 0.8736 (tp40) REVERT: Q 61 GLU cc_start: 0.9330 (mt-10) cc_final: 0.9080 (mp0) REVERT: Q 249 MET cc_start: 0.8665 (pmm) cc_final: 0.8178 (pmm) REVERT: Q 296 LYS cc_start: 0.8465 (tmmt) cc_final: 0.8179 (ttpp) REVERT: Q 311 MET cc_start: 0.9106 (ttp) cc_final: 0.8830 (ttp) REVERT: Z 15 ARG cc_start: 0.8816 (ttm110) cc_final: 0.8282 (ttp-110) REVERT: Z 415 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8333 (mp0) REVERT: a 209 MET cc_start: 0.9251 (mtm) cc_final: 0.8952 (mtp) REVERT: a 416 GLU cc_start: 0.8452 (mp0) cc_final: 0.8156 (mp0) REVERT: b 182 LEU cc_start: 0.9033 (tp) cc_final: 0.8769 (tt) REVERT: b 445 MET cc_start: 0.8935 (tpp) cc_final: 0.8732 (tpp) REVERT: d 222 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: e 4 MET cc_start: 0.3835 (mmt) cc_final: 0.3511 (tmm) REVERT: e 464 GLU cc_start: 0.9062 (tp30) cc_final: 0.8762 (tp30) REVERT: g 47 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8350 (mtp) REVERT: g 527 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8631 (mtmm) REVERT: g 528 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8242 (tmmt) REVERT: h 524 ARG cc_start: 0.7914 (tmt170) cc_final: 0.7518 (tmm160) REVERT: q 41 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8724 (tm-30) REVERT: q 152 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8493 (ptmm) REVERT: q 200 ASP cc_start: 0.8999 (t70) cc_final: 0.8764 (t0) REVERT: q 522 ASP cc_start: 0.9347 (t0) cc_final: 0.9055 (t0) REVERT: z 244 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8225 (t) outliers start: 60 outliers final: 15 residues processed: 495 average time/residue: 1.4950 time to fit residues: 965.0395 Evaluate side-chains 461 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 440 time to evaluate : 5.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 481 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 831 optimal weight: 5.9990 chunk 617 optimal weight: 9.9990 chunk 576 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 448 optimal weight: 7.9990 chunk 502 optimal weight: 7.9990 chunk 764 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 788 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN H 501 ASN Q 397 ASN d 301 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN g 526 HIS h 501 ASN z 68 GLN z 161 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.060498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.049599 restraints weight = 231510.251| |-----------------------------------------------------------------------------| r_work (start): 0.2553 rms_B_bonded: 3.43 r_work: 0.2387 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2394 r_free = 0.2394 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2394 r_free = 0.2394 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 66323 Z= 0.464 Angle : 0.644 11.490 89563 Z= 0.319 Chirality : 0.045 0.173 10688 Planarity : 0.004 0.058 11425 Dihedral : 7.171 175.429 9216 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.08 % Allowed : 10.42 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.09), residues: 8486 helix: 2.29 (0.08), residues: 4389 sheet: -0.11 (0.16), residues: 1105 loop : -0.59 (0.11), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 304 HIS 0.013 0.001 HIS z 161 PHE 0.019 0.002 PHE h 174 TYR 0.018 0.002 TYR z 498 ARG 0.009 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 429 time to evaluate : 6.803 Fit side-chains revert: symmetry clash REVERT: N 267 ASP cc_start: 0.6575 (t0) cc_final: 0.6251 (t0) REVERT: A 156 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8669 (mpp) REVERT: A 306 MET cc_start: 0.9231 (mtp) cc_final: 0.8754 (mtm) REVERT: B 62 MET cc_start: 0.8557 (ttm) cc_final: 0.8339 (ttm) REVERT: D 57 MET cc_start: 0.9077 (mmm) cc_final: 0.8720 (mmm) REVERT: E 464 GLU cc_start: 0.9181 (tt0) cc_final: 0.8702 (tp30) REVERT: G 47 MET cc_start: 0.9184 (mtm) cc_final: 0.8960 (mtp) REVERT: G 167 ARG cc_start: 0.9061 (mmp-170) cc_final: 0.8845 (mmp80) REVERT: H 14 ASP cc_start: 0.8670 (t70) cc_final: 0.8396 (t0) REVERT: H 81 ASP cc_start: 0.8884 (m-30) cc_final: 0.8537 (m-30) REVERT: H 185 MET cc_start: 0.8671 (mtm) cc_final: 0.8105 (ptm) REVERT: Q 249 MET cc_start: 0.8748 (pmm) cc_final: 0.8248 (pmm) REVERT: Q 296 LYS cc_start: 0.8627 (tmmt) cc_final: 0.8378 (ttpp) REVERT: Q 311 MET cc_start: 0.9164 (ttp) cc_final: 0.8855 (ttp) REVERT: Z 15 ARG cc_start: 0.8863 (ttm110) cc_final: 0.8324 (ttp-110) REVERT: Z 161 HIS cc_start: 0.6473 (OUTLIER) cc_final: 0.6056 (t70) REVERT: a 209 MET cc_start: 0.9286 (mtm) cc_final: 0.9009 (mtp) REVERT: a 416 GLU cc_start: 0.8519 (mp0) cc_final: 0.8214 (mp0) REVERT: d 222 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: e 4 MET cc_start: 0.3882 (mmt) cc_final: 0.3471 (tmm) REVERT: e 80 MET cc_start: 0.9170 (mmt) cc_final: 0.8961 (mtt) REVERT: e 464 GLU cc_start: 0.9114 (tp30) cc_final: 0.8875 (tm-30) REVERT: g 47 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8461 (mtp) REVERT: g 528 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8286 (tmmt) REVERT: q 41 GLN cc_start: 0.9082 (tp-100) cc_final: 0.8802 (tm-30) REVERT: q 522 ASP cc_start: 0.9376 (t0) cc_final: 0.8997 (t0) REVERT: z 244 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8311 (t) outliers start: 77 outliers final: 36 residues processed: 471 average time/residue: 1.5037 time to fit residues: 922.7010 Evaluate side-chains 454 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 412 time to evaluate : 5.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain b residue 11 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 387 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 533 ILE Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 643 optimal weight: 1.9990 chunk 832 optimal weight: 6.9990 chunk 787 optimal weight: 0.0000 chunk 531 optimal weight: 2.9990 chunk 755 optimal weight: 0.0470 chunk 77 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 chunk 586 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 355 optimal weight: 5.9990 chunk 249 optimal weight: 0.9990 overall best weight: 0.5886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN H 501 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN z 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.065291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.054360 restraints weight = 222479.116| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 3.39 r_work: 0.2490 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2498 r_free = 0.2498 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2498 r_free = 0.2498 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 66323 Z= 0.142 Angle : 0.538 10.956 89563 Z= 0.265 Chirality : 0.041 0.170 10688 Planarity : 0.003 0.059 11425 Dihedral : 6.899 177.484 9216 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.73 % Allowed : 11.36 % Favored : 87.90 % 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: 1.68 (0.09), residues: 8486 helix: 2.45 (0.08), residues: 4410 sheet: 0.01 (0.16), residues: 1104 loop : -0.51 (0.11), residues: 2972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 168 HIS 0.016 0.001 HIS z 161 PHE 0.020 0.001 PHE H 174 TYR 0.012 0.001 TYR Q 505 ARG 0.008 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 466 time to evaluate : 6.077 Fit side-chains REVERT: N 267 ASP cc_start: 0.6432 (t0) cc_final: 0.6123 (t0) REVERT: A 156 MET cc_start: 0.8907 (mpp) cc_final: 0.8574 (mpp) REVERT: A 306 MET cc_start: 0.9193 (mtp) cc_final: 0.8815 (mtm) REVERT: A 508 ILE cc_start: 0.8984 (tp) cc_final: 0.8780 (tp) REVERT: B 408 TYR cc_start: 0.9036 (m-80) cc_final: 0.8637 (m-80) REVERT: D 28 ASP cc_start: 0.8416 (t0) cc_final: 0.7768 (t0) REVERT: D 57 MET cc_start: 0.9083 (mmm) cc_final: 0.8702 (mmm) REVERT: D 374 LEU cc_start: 0.9591 (tp) cc_final: 0.9368 (tm) REVERT: E 464 GLU cc_start: 0.9169 (tt0) cc_final: 0.8706 (tp30) REVERT: G 47 MET cc_start: 0.9122 (mtm) cc_final: 0.8881 (mtp) REVERT: G 54 MET cc_start: 0.8914 (mmm) cc_final: 0.8620 (mpp) REVERT: G 167 ARG cc_start: 0.8986 (mmp-170) cc_final: 0.8746 (mmp80) REVERT: G 358 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7886 (mm-30) REVERT: G 429 MET cc_start: 0.8413 (mtm) cc_final: 0.7984 (ptm) REVERT: H 14 ASP cc_start: 0.8645 (t70) cc_final: 0.8376 (t0) REVERT: H 45 MET cc_start: 0.9032 (mmm) cc_final: 0.8822 (mmm) REVERT: H 81 ASP cc_start: 0.8849 (m-30) cc_final: 0.8509 (m-30) REVERT: H 185 MET cc_start: 0.8594 (mtm) cc_final: 0.8360 (ptm) REVERT: Q 41 GLN cc_start: 0.9161 (tp40) cc_final: 0.8751 (tp40) REVERT: Q 249 MET cc_start: 0.8693 (pmm) cc_final: 0.8130 (pmm) REVERT: Q 296 LYS cc_start: 0.8477 (tmmt) cc_final: 0.8202 (ttpp) REVERT: Q 311 MET cc_start: 0.9155 (ttp) cc_final: 0.8897 (ttp) REVERT: Z 15 ARG cc_start: 0.8852 (ttm110) cc_final: 0.8231 (ttp-110) REVERT: Z 415 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8335 (mp0) REVERT: a 209 MET cc_start: 0.9252 (mtm) cc_final: 0.8939 (mtp) REVERT: a 416 GLU cc_start: 0.8457 (mp0) cc_final: 0.8140 (mp0) REVERT: b 182 LEU cc_start: 0.8951 (tp) cc_final: 0.8707 (tt) REVERT: b 385 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8743 (tp30) REVERT: b 445 MET cc_start: 0.8871 (tpp) cc_final: 0.8666 (tpp) REVERT: d 222 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: e 4 MET cc_start: 0.3876 (mmt) cc_final: 0.3355 (tmm) REVERT: e 80 MET cc_start: 0.9129 (mmt) cc_final: 0.8873 (mtp) REVERT: e 464 GLU cc_start: 0.9084 (tp30) cc_final: 0.8793 (tp30) REVERT: g 47 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8372 (mtp) REVERT: g 151 MET cc_start: 0.9202 (tpp) cc_final: 0.8926 (tpt) REVERT: g 528 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8189 (tmmt) REVERT: h 524 ARG cc_start: 0.7958 (tmt170) cc_final: 0.7550 (tmm160) REVERT: q 41 GLN cc_start: 0.8987 (tp-100) cc_final: 0.8630 (tm-30) REVERT: q 200 ASP cc_start: 0.8997 (t70) cc_final: 0.8754 (t0) REVERT: q 522 ASP cc_start: 0.9371 (t0) cc_final: 0.9046 (t0) REVERT: z 244 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8137 (t) outliers start: 52 outliers final: 19 residues processed: 494 average time/residue: 1.4863 time to fit residues: 960.8495 Evaluate side-chains 472 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 447 time to evaluate : 6.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 341 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 385 GLU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 387 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 287 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 416 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 169 optimal weight: 3.9990 chunk 361 optimal weight: 8.9990 chunk 758 optimal weight: 9.9990 chunk 500 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 285 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN H 501 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN h 501 ASN z 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.060694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.049783 restraints weight = 233210.283| |-----------------------------------------------------------------------------| r_work (start): 0.2557 rms_B_bonded: 3.43 r_work: 0.2392 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2399 r_free = 0.2399 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2399 r_free = 0.2399 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 66323 Z= 0.457 Angle : 0.646 11.967 89563 Z= 0.318 Chirality : 0.045 0.171 10688 Planarity : 0.004 0.057 11425 Dihedral : 6.996 170.209 9216 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.97 % Allowed : 11.52 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.09), residues: 8486 helix: 2.33 (0.08), residues: 4397 sheet: -0.11 (0.15), residues: 1115 loop : -0.56 (0.11), residues: 2974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP e 304 HIS 0.014 0.001 HIS z 161 PHE 0.019 0.002 PHE a 167 TYR 0.020 0.002 TYR E 446 ARG 0.006 0.000 ARG z 323 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 432 time to evaluate : 6.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 267 ASP cc_start: 0.6555 (t0) cc_final: 0.6188 (t0) REVERT: A 47 ASP cc_start: 0.8009 (t0) cc_final: 0.7755 (t0) REVERT: A 156 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8604 (mpp) REVERT: A 306 MET cc_start: 0.9190 (mtp) cc_final: 0.8704 (mtm) REVERT: D 57 MET cc_start: 0.9080 (mmm) cc_final: 0.8792 (mmm) REVERT: E 464 GLU cc_start: 0.9175 (tt0) cc_final: 0.8709 (tp30) REVERT: G 47 MET cc_start: 0.9102 (mtm) cc_final: 0.8872 (mtp) REVERT: G 167 ARG cc_start: 0.9052 (mmp-170) cc_final: 0.8844 (mmp80) REVERT: G 429 MET cc_start: 0.8675 (mtm) cc_final: 0.7970 (ptm) REVERT: H 14 ASP cc_start: 0.8695 (t70) cc_final: 0.8437 (t0) REVERT: H 81 ASP cc_start: 0.8881 (m-30) cc_final: 0.8535 (m-30) REVERT: H 185 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8513 (ttp) REVERT: H 370 CYS cc_start: 0.8715 (OUTLIER) cc_final: 0.7758 (p) REVERT: Q 249 MET cc_start: 0.8751 (pmm) cc_final: 0.8129 (pmm) REVERT: Q 296 LYS cc_start: 0.8649 (tmmt) cc_final: 0.8340 (ttpp) REVERT: Z 15 ARG cc_start: 0.8831 (ttm110) cc_final: 0.8356 (ttp-110) REVERT: Z 161 HIS cc_start: 0.6463 (OUTLIER) cc_final: 0.6111 (t70) REVERT: a 209 MET cc_start: 0.9286 (mtm) cc_final: 0.8927 (mtp) REVERT: a 416 GLU cc_start: 0.8503 (mp0) cc_final: 0.8262 (mp0) REVERT: d 222 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: e 4 MET cc_start: 0.3942 (mmt) cc_final: 0.3372 (tmm) REVERT: e 21 ASP cc_start: 0.8714 (t0) cc_final: 0.8224 (t0) REVERT: e 464 GLU cc_start: 0.9098 (tp30) cc_final: 0.8850 (tm-30) REVERT: g 46 MET cc_start: 0.9220 (mmm) cc_final: 0.8879 (mmm) REVERT: g 47 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8384 (mtp) REVERT: g 151 MET cc_start: 0.9264 (tpp) cc_final: 0.8959 (tpt) REVERT: g 528 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8290 (tmmt) REVERT: h 57 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8543 (p) REVERT: q 41 GLN cc_start: 0.9060 (tp-100) cc_final: 0.8811 (tm-30) REVERT: q 152 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8423 (pmtt) REVERT: q 200 ASP cc_start: 0.9048 (t70) cc_final: 0.8806 (t0) REVERT: q 522 ASP cc_start: 0.9421 (t0) cc_final: 0.9018 (t0) REVERT: z 244 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8271 (t) outliers start: 69 outliers final: 34 residues processed: 473 average time/residue: 1.5618 time to fit residues: 961.1178 Evaluate side-chains 463 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 419 time to evaluate : 5.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 185 MET Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 341 LEU Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 185 ARG Chi-restraints excluded: chain b residue 11 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 387 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 533 ILE Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 542 optimal weight: 5.9990 chunk 773 optimal weight: 0.8980 chunk 613 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 317 optimal weight: 0.0670 chunk 656 optimal weight: 7.9990 chunk 506 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 488 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN H 501 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 467 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN h 501 ASN z 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.064744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.054152 restraints weight = 197975.063| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 3.19 r_work: 0.2501 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 66323 Z= 0.147 Angle : 0.549 11.946 89563 Z= 0.269 Chirality : 0.041 0.183 10688 Planarity : 0.003 0.057 11425 Dihedral : 6.788 172.751 9216 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.86 % Allowed : 12.05 % Favored : 87.09 % 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: 1.68 (0.09), residues: 8486 helix: 2.45 (0.08), residues: 4405 sheet: 0.00 (0.16), residues: 1090 loop : -0.50 (0.11), residues: 2991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 168 HIS 0.016 0.001 HIS z 161 PHE 0.023 0.001 PHE H 174 TYR 0.023 0.001 TYR E 446 ARG 0.006 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 459 time to evaluate : 6.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 267 ASP cc_start: 0.6377 (t0) cc_final: 0.6050 (t0) REVERT: A 156 MET cc_start: 0.8950 (mpp) cc_final: 0.8495 (mpp) REVERT: A 306 MET cc_start: 0.9184 (mtp) cc_final: 0.8802 (mtm) REVERT: A 508 ILE cc_start: 0.9024 (tp) cc_final: 0.8819 (tp) REVERT: A 528 ASP cc_start: 0.9035 (p0) cc_final: 0.8691 (p0) REVERT: D 28 ASP cc_start: 0.8428 (t0) cc_final: 0.7778 (t0) REVERT: D 57 MET cc_start: 0.9077 (mmm) cc_final: 0.8662 (mmm) REVERT: D 60 MET cc_start: 0.9292 (ttp) cc_final: 0.9044 (ttm) REVERT: D 374 LEU cc_start: 0.9604 (tp) cc_final: 0.9386 (tm) REVERT: E 464 GLU cc_start: 0.9139 (tt0) cc_final: 0.8676 (tp30) REVERT: G 47 MET cc_start: 0.9010 (mtm) cc_final: 0.8771 (mtp) REVERT: G 113 LEU cc_start: 0.9062 (mt) cc_final: 0.8672 (mp) REVERT: G 167 ARG cc_start: 0.8989 (mmp-170) cc_final: 0.8762 (mmp80) REVERT: G 358 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7868 (mm-30) REVERT: G 429 MET cc_start: 0.8462 (mtm) cc_final: 0.7984 (ptm) REVERT: H 14 ASP cc_start: 0.8646 (t70) cc_final: 0.8377 (t0) REVERT: H 81 ASP cc_start: 0.8837 (m-30) cc_final: 0.8489 (m-30) REVERT: H 185 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8393 (ttp) REVERT: Q 41 GLN cc_start: 0.9166 (tp40) cc_final: 0.8744 (tp40) REVERT: Q 249 MET cc_start: 0.8687 (pmm) cc_final: 0.8107 (pmm) REVERT: Q 296 LYS cc_start: 0.8571 (tmmt) cc_final: 0.8262 (ttpp) REVERT: Q 318 LYS cc_start: 0.8441 (pptt) cc_final: 0.8183 (pptt) REVERT: Z 15 ARG cc_start: 0.8850 (ttm110) cc_final: 0.8369 (ttp-110) REVERT: Z 415 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8324 (mp0) REVERT: a 209 MET cc_start: 0.9256 (mtm) cc_final: 0.8937 (mtp) REVERT: a 416 GLU cc_start: 0.8449 (mp0) cc_final: 0.8127 (mp0) REVERT: d 222 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: e 21 ASP cc_start: 0.8671 (t0) cc_final: 0.8161 (t0) REVERT: e 464 GLU cc_start: 0.9090 (tp30) cc_final: 0.8851 (tp30) REVERT: g 47 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8391 (mtp) REVERT: g 151 MET cc_start: 0.9271 (tpp) cc_final: 0.8945 (tpt) REVERT: g 391 LEU cc_start: 0.9442 (mt) cc_final: 0.9183 (mt) REVERT: g 528 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8268 (tmmt) REVERT: h 57 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8420 (p) REVERT: q 41 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8626 (tm-30) REVERT: q 152 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8310 (pmtt) REVERT: q 200 ASP cc_start: 0.8987 (t70) cc_final: 0.8737 (t0) REVERT: q 522 ASP cc_start: 0.9394 (t0) cc_final: 0.9074 (t0) REVERT: z 244 VAL cc_start: 0.8478 (OUTLIER) cc_final: 0.8154 (t) outliers start: 61 outliers final: 26 residues processed: 497 average time/residue: 1.4937 time to fit residues: 971.3465 Evaluate side-chains 477 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 443 time to evaluate : 5.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 185 MET Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 341 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain a residue 185 ARG Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 387 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 538 THR Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 145 LYS Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 212 optimal weight: 0.0470 chunk 404 optimal weight: 8.9990 chunk 798 optimal weight: 3.9990 chunk 347 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 817 optimal weight: 5.9990 chunk 268 optimal weight: 0.9980 chunk 188 optimal weight: 0.4980 chunk 558 optimal weight: 7.9990 chunk 311 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.7082 ------------------------------------------------------------------------------- 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** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN z 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.064018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.053482 restraints weight = 198628.188| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 3.11 r_work: 0.2518 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 66323 Z= 0.193 Angle : 0.555 13.624 89563 Z= 0.270 Chirality : 0.041 0.207 10688 Planarity : 0.003 0.055 11425 Dihedral : 6.619 167.055 9216 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.66 % Allowed : 12.25 % Favored : 87.09 % 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: 1.71 (0.09), residues: 8486 helix: 2.48 (0.08), residues: 4408 sheet: 0.02 (0.16), residues: 1093 loop : -0.50 (0.11), residues: 2985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.015 0.001 HIS z 161 PHE 0.022 0.001 PHE H 174 TYR 0.025 0.001 TYR B 297 ARG 0.008 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 448 time to evaluate : 6.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 267 ASP cc_start: 0.6539 (t0) cc_final: 0.6205 (t0) REVERT: A 156 MET cc_start: 0.9043 (mpp) cc_final: 0.8578 (mpp) REVERT: A 306 MET cc_start: 0.9198 (mtp) cc_final: 0.8832 (mtm) REVERT: A 508 ILE cc_start: 0.9116 (tp) cc_final: 0.8914 (tp) REVERT: D 28 ASP cc_start: 0.8444 (t0) cc_final: 0.7727 (t0) REVERT: D 57 MET cc_start: 0.9113 (mmm) cc_final: 0.8806 (mmm) REVERT: E 464 GLU cc_start: 0.9123 (tt0) cc_final: 0.8685 (tp30) REVERT: G 47 MET cc_start: 0.9094 (mtm) cc_final: 0.8879 (mtp) REVERT: G 167 ARG cc_start: 0.9012 (mmp-170) cc_final: 0.8802 (mmp80) REVERT: G 358 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8026 (mm-30) REVERT: G 429 MET cc_start: 0.8507 (mtm) cc_final: 0.8111 (ptm) REVERT: H 14 ASP cc_start: 0.8696 (t70) cc_final: 0.8447 (t0) REVERT: H 81 ASP cc_start: 0.8870 (m-30) cc_final: 0.8519 (m-30) REVERT: Q 249 MET cc_start: 0.8704 (pmm) cc_final: 0.8076 (pmm) REVERT: Q 296 LYS cc_start: 0.8631 (tmmt) cc_final: 0.8338 (ttpp) REVERT: Z 15 ARG cc_start: 0.8878 (ttm110) cc_final: 0.8430 (ttp-110) REVERT: Z 415 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: a 209 MET cc_start: 0.9246 (mtm) cc_final: 0.8959 (mtp) REVERT: a 416 GLU cc_start: 0.8445 (mp0) cc_final: 0.8127 (mp0) REVERT: d 222 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: e 21 ASP cc_start: 0.8730 (t0) cc_final: 0.8240 (t0) REVERT: e 464 GLU cc_start: 0.9119 (tp30) cc_final: 0.8779 (tm-30) REVERT: g 47 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8573 (mtp) REVERT: g 151 MET cc_start: 0.9326 (tpp) cc_final: 0.9004 (tpt) REVERT: g 528 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8257 (tmmt) REVERT: h 57 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8615 (p) REVERT: q 41 GLN cc_start: 0.8977 (tp-100) cc_final: 0.8640 (tm-30) REVERT: q 152 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8293 (pmtt) REVERT: q 200 ASP cc_start: 0.8983 (t70) cc_final: 0.8732 (t0) REVERT: q 522 ASP cc_start: 0.9326 (t0) cc_final: 0.9039 (t0) REVERT: z 244 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8271 (t) outliers start: 47 outliers final: 29 residues processed: 478 average time/residue: 1.5013 time to fit residues: 940.7404 Evaluate side-chains 478 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 442 time to evaluate : 5.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 341 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 387 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 538 THR Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 533 ILE Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 145 LYS Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 454 optimal weight: 4.9990 chunk 686 optimal weight: 7.9990 chunk 510 optimal weight: 7.9990 chunk 705 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 294 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 435 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 356 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN H 501 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.061270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.050539 restraints weight = 214428.349| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 3.23 r_work: 0.2443 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2440 r_free = 0.2440 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2440 r_free = 0.2440 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 66323 Z= 0.399 Angle : 0.635 12.932 89563 Z= 0.313 Chirality : 0.044 0.197 10688 Planarity : 0.003 0.055 11425 Dihedral : 6.775 166.811 9216 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.66 % Allowed : 12.46 % Favored : 86.88 % 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: 8486 helix: 2.36 (0.08), residues: 4399 sheet: -0.09 (0.16), residues: 1106 loop : -0.56 (0.11), residues: 2981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 304 HIS 0.014 0.001 HIS z 161 PHE 0.021 0.002 PHE H 174 TYR 0.020 0.002 TYR E 446 ARG 0.009 0.000 ARG E 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16972 Ramachandran restraints generated. 8486 Oldfield, 0 Emsley, 8486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 428 time to evaluate : 6.141 Fit side-chains revert: symmetry clash REVERT: N 267 ASP cc_start: 0.6571 (t0) cc_final: 0.6199 (t0) REVERT: A 156 MET cc_start: 0.9135 (mpp) cc_final: 0.8724 (mpp) REVERT: A 306 MET cc_start: 0.9209 (mtp) cc_final: 0.8746 (mtm) REVERT: D 57 MET cc_start: 0.9017 (mmm) cc_final: 0.8761 (mmm) REVERT: E 464 GLU cc_start: 0.9166 (tt0) cc_final: 0.8725 (tp30) REVERT: G 47 MET cc_start: 0.9222 (mtm) cc_final: 0.8995 (mtp) REVERT: G 270 MET cc_start: 0.9035 (mtm) cc_final: 0.8754 (mtt) REVERT: H 14 ASP cc_start: 0.8771 (t70) cc_final: 0.8528 (t0) REVERT: H 81 ASP cc_start: 0.8902 (m-30) cc_final: 0.8547 (m-30) REVERT: Q 249 MET cc_start: 0.8749 (pmm) cc_final: 0.8212 (pmm) REVERT: Q 296 LYS cc_start: 0.8750 (tmmt) cc_final: 0.8489 (ttpp) REVERT: Z 15 ARG cc_start: 0.8910 (ttm110) cc_final: 0.8376 (ttp-110) REVERT: a 47 ASP cc_start: 0.8514 (t0) cc_final: 0.8294 (t0) REVERT: a 209 MET cc_start: 0.9262 (mtm) cc_final: 0.8995 (mtp) REVERT: a 416 GLU cc_start: 0.8501 (mp0) cc_final: 0.8262 (mp0) REVERT: d 222 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: e 21 ASP cc_start: 0.8772 (t0) cc_final: 0.8310 (t0) REVERT: e 464 GLU cc_start: 0.9149 (tp30) cc_final: 0.8874 (tm-30) REVERT: g 47 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8656 (mtp) REVERT: g 73 GLN cc_start: 0.8761 (mp10) cc_final: 0.8366 (mp10) REVERT: g 151 MET cc_start: 0.9345 (tpp) cc_final: 0.9039 (tpt) REVERT: g 528 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8302 (tmmt) REVERT: h 57 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8712 (p) REVERT: q 41 GLN cc_start: 0.9061 (tp-100) cc_final: 0.8802 (tm-30) REVERT: q 152 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8430 (pmtt) REVERT: q 200 ASP cc_start: 0.8982 (t70) cc_final: 0.8726 (t0) REVERT: q 522 ASP cc_start: 0.9367 (t0) cc_final: 0.9036 (t0) REVERT: z 244 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8403 (t) outliers start: 47 outliers final: 33 residues processed: 460 average time/residue: 1.5095 time to fit residues: 905.1250 Evaluate side-chains 459 residues out of total 7100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 420 time to evaluate : 6.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 341 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain b residue 11 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 214 LEU Chi-restraints excluded: chain d residue 222 GLU Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 387 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 538 THR Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 533 ILE Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 145 LYS Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 618 optimal weight: 6.9990 chunk 796 optimal weight: 1.9990 chunk 569 optimal weight: 2.9990 chunk 338 optimal weight: 2.9990 chunk 535 optimal weight: 6.9990 chunk 440 optimal weight: 7.9990 chunk 520 optimal weight: 6.9990 chunk 808 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 346 optimal weight: 7.9990 chunk 322 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 GLN G 390 ASN H 501 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.063122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.052663 restraints weight = 193383.963| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 3.05 r_work: 0.2496 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2495 r_free = 0.2495 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2495 r_free = 0.2495 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 66323 Z= 0.215 Angle : 0.570 13.837 89563 Z= 0.279 Chirality : 0.042 0.176 10688 Planarity : 0.003 0.055 11425 Dihedral : 6.631 164.986 9216 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.68 % Allowed : 12.56 % Favored : 86.76 % 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: 1.64 (0.09), residues: 8486 helix: 2.43 (0.08), residues: 4396 sheet: -0.04 (0.16), residues: 1086 loop : -0.50 (0.11), residues: 3004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 168 HIS 0.016 0.001 HIS z 161 PHE 0.025 0.001 PHE H 174 TYR 0.022 0.001 TYR E 446 ARG 0.006 0.000 ARG g 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29329.63 seconds wall clock time: 514 minutes 18.83 seconds (30858.83 seconds total)