Starting phenix.real_space_refine on Wed Jan 15 04:23:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xl4_38437/01_2025/8xl4_38437.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xl4_38437/01_2025/8xl4_38437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xl4_38437/01_2025/8xl4_38437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xl4_38437/01_2025/8xl4_38437.map" model { file = "/net/cci-nas-00/data/ceres_data/8xl4_38437/01_2025/8xl4_38437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xl4_38437/01_2025/8xl4_38437.cif" } resolution = 3.38 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= 0.001 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 292 5.16 5 C 31713 2.51 5 N 8837 2.21 5 O 9574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 50434 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 5147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5147 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 644} Chain: "B" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3873 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "C" Number of atoms: 5147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5147 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 644} Chain: "D" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3873 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "E" Number of atoms: 5147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5147 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 644} Chain: "F" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3873 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "G" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1080 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "H" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3873 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "I" Number of atoms: 5147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5147 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 644} Chain: "J" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3873 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "K" Number of atoms: 5147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5147 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 644} Chain: "L" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3873 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.48, per 1000 atoms: 0.41 Number of scatterers: 50434 At special positions: 0 Unit cell: (186.373, 210.074, 231.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 292 16.00 P 18 15.00 O 9574 8.00 N 8837 7.00 C 31713 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 Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.11 Conformation dependent library (CDL) restraints added in 4.9 seconds 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12010 Finding SS restraints... Secondary structure from input PDB file: 270 helices and 64 sheets defined 40.1% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.93 Creating SS restraints... Processing helix chain 'A' and resid 72 through 86 Processing helix chain 'A' and resid 96 through 99 removed outlier: 4.322A pdb=" N SER A 99 " --> pdb=" O VAL A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 99' Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 167 through 174 removed outlier: 3.548A pdb=" N ILE A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 removed outlier: 3.532A pdb=" N SER A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.895A pdb=" N ALA A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 249 Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 309 through 325 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 458 through 472 Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 518 through 540 Processing helix chain 'A' and resid 641 through 648 removed outlier: 3.904A pdb=" N LYS A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 49 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 91 through 95 removed outlier: 4.152A pdb=" N GLY B 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 134 through 152 Processing helix chain 'B' and resid 170 through 186 Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.707A pdb=" N ALA B 204 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.531A pdb=" N LEU B 210 " --> pdb=" O TYR B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 235 Processing helix chain 'B' and resid 240 through 246 Processing helix chain 'B' and resid 246 through 253 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 315 through 324 removed outlier: 4.262A pdb=" N ILE B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 328 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 367 through 384 Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 407 through 421 removed outlier: 4.006A pdb=" N LYS B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B 415 " --> pdb=" O HIS B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 442 Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 464 through 473 Processing helix chain 'B' and resid 478 through 491 Processing helix chain 'B' and resid 493 through 498 Processing helix chain 'B' and resid 507 through 509 No H-bonds generated for 'chain 'B' and resid 507 through 509' Processing helix chain 'B' and resid 510 through 523 removed outlier: 3.504A pdb=" N VAL B 521 " --> pdb=" O CYS B 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 86 Processing helix chain 'C' and resid 96 through 99 removed outlier: 4.322A pdb=" N SER C 99 " --> pdb=" O VAL C 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 96 through 99' Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 167 through 174 removed outlier: 3.548A pdb=" N ILE C 171 " --> pdb=" O ASP C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.532A pdb=" N SER C 180 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 213 removed outlier: 3.895A pdb=" N ALA C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 249 Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 309 through 325 Processing helix chain 'C' and resid 361 through 366 Processing helix chain 'C' and resid 368 through 379 Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 458 through 472 Processing helix chain 'C' and resid 481 through 489 Processing helix chain 'C' and resid 491 through 497 Processing helix chain 'C' and resid 502 through 508 Processing helix chain 'C' and resid 518 through 540 Processing helix chain 'C' and resid 641 through 648 removed outlier: 3.905A pdb=" N LYS C 648 " --> pdb=" O ALA C 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 49 Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 91 through 95 removed outlier: 4.152A pdb=" N GLY D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 134 through 152 Processing helix chain 'D' and resid 170 through 186 Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.707A pdb=" N ALA D 204 " --> pdb=" O ALA D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 211 removed outlier: 3.531A pdb=" N LEU D 210 " --> pdb=" O TYR D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 235 Processing helix chain 'D' and resid 240 through 246 Processing helix chain 'D' and resid 246 through 253 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 315 through 324 removed outlier: 4.261A pdb=" N ILE D 319 " --> pdb=" O ASN D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 328 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 367 through 384 Processing helix chain 'D' and resid 400 through 405 Processing helix chain 'D' and resid 407 through 421 removed outlier: 4.006A pdb=" N LYS D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU D 415 " --> pdb=" O HIS D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 442 Processing helix chain 'D' and resid 444 through 448 Processing helix chain 'D' and resid 464 through 473 Processing helix chain 'D' and resid 478 through 491 Processing helix chain 'D' and resid 493 through 498 Processing helix chain 'D' and resid 507 through 509 No H-bonds generated for 'chain 'D' and resid 507 through 509' Processing helix chain 'D' and resid 510 through 523 removed outlier: 3.504A pdb=" N VAL D 521 " --> pdb=" O CYS D 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 86 Processing helix chain 'E' and resid 96 through 99 removed outlier: 4.321A pdb=" N SER E 99 " --> pdb=" O VAL E 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 96 through 99' Processing helix chain 'E' and resid 100 through 106 Processing helix chain 'E' and resid 123 through 134 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 167 through 174 removed outlier: 3.548A pdb=" N ILE E 171 " --> pdb=" O ASP E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 187 removed outlier: 3.532A pdb=" N SER E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 213 removed outlier: 3.896A pdb=" N ALA E 209 " --> pdb=" O ALA E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 249 Processing helix chain 'E' and resid 250 through 252 No H-bonds generated for 'chain 'E' and resid 250 through 252' Processing helix chain 'E' and resid 309 through 325 Processing helix chain 'E' and resid 361 through 366 Processing helix chain 'E' and resid 368 through 379 Processing helix chain 'E' and resid 385 through 389 Processing helix chain 'E' and resid 458 through 472 Processing helix chain 'E' and resid 481 through 489 Processing helix chain 'E' and resid 491 through 497 Processing helix chain 'E' and resid 502 through 508 Processing helix chain 'E' and resid 518 through 540 Processing helix chain 'E' and resid 641 through 648 removed outlier: 3.904A pdb=" N LYS E 648 " --> pdb=" O ALA E 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 49 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 91 through 95 removed outlier: 4.152A pdb=" N GLY F 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 128 through 132 Processing helix chain 'F' and resid 134 through 152 Processing helix chain 'F' and resid 170 through 186 Processing helix chain 'F' and resid 201 through 205 removed outlier: 3.708A pdb=" N ALA F 204 " --> pdb=" O ALA F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 211 removed outlier: 3.531A pdb=" N LEU F 210 " --> pdb=" O TYR F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 235 Processing helix chain 'F' and resid 240 through 246 Processing helix chain 'F' and resid 246 through 253 Processing helix chain 'F' and resid 263 through 276 Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 315 through 324 removed outlier: 4.261A pdb=" N ILE F 319 " --> pdb=" O ASN F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 328 Processing helix chain 'F' and resid 361 through 365 Processing helix chain 'F' and resid 367 through 384 Processing helix chain 'F' and resid 400 through 405 Processing helix chain 'F' and resid 407 through 421 removed outlier: 4.006A pdb=" N LYS F 414 " --> pdb=" O ARG F 410 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU F 415 " --> pdb=" O HIS F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 442 Processing helix chain 'F' and resid 444 through 448 Processing helix chain 'F' and resid 464 through 473 Processing helix chain 'F' and resid 478 through 491 Processing helix chain 'F' and resid 493 through 498 Processing helix chain 'F' and resid 507 through 509 No H-bonds generated for 'chain 'F' and resid 507 through 509' Processing helix chain 'F' and resid 510 through 523 removed outlier: 3.504A pdb=" N VAL F 521 " --> pdb=" O CYS F 517 " (cutoff:3.500A) Processing helix chain 'G' and resid 518 through 540 Processing helix chain 'G' and resid 641 through 648 removed outlier: 3.904A pdb=" N LYS G 648 " --> pdb=" O ALA G 644 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 49 Processing helix chain 'H' and resid 51 through 61 Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 91 through 95 removed outlier: 4.152A pdb=" N GLY H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 128 through 132 Processing helix chain 'H' and resid 134 through 152 Processing helix chain 'H' and resid 170 through 186 Processing helix chain 'H' and resid 201 through 205 removed outlier: 3.707A pdb=" N ALA H 204 " --> pdb=" O ALA H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 211 removed outlier: 3.532A pdb=" N LEU H 210 " --> pdb=" O TYR H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 235 Processing helix chain 'H' and resid 240 through 246 Processing helix chain 'H' and resid 246 through 253 Processing helix chain 'H' and resid 263 through 276 Processing helix chain 'H' and resid 299 through 303 Processing helix chain 'H' and resid 315 through 324 removed outlier: 4.262A pdb=" N ILE H 319 " --> pdb=" O ASN H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 328 Processing helix chain 'H' and resid 361 through 365 Processing helix chain 'H' and resid 367 through 384 Processing helix chain 'H' and resid 400 through 405 Processing helix chain 'H' and resid 407 through 421 removed outlier: 4.006A pdb=" N LYS H 414 " --> pdb=" O ARG H 410 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU H 415 " --> pdb=" O HIS H 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 442 Processing helix chain 'H' and resid 444 through 448 Processing helix chain 'H' and resid 464 through 473 Processing helix chain 'H' and resid 478 through 491 Processing helix chain 'H' and resid 493 through 498 Processing helix chain 'H' and resid 507 through 509 No H-bonds generated for 'chain 'H' and resid 507 through 509' Processing helix chain 'H' and resid 510 through 523 removed outlier: 3.504A pdb=" N VAL H 521 " --> pdb=" O CYS H 517 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 86 Processing helix chain 'I' and resid 96 through 99 removed outlier: 4.322A pdb=" N SER I 99 " --> pdb=" O VAL I 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 96 through 99' Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 149 through 158 Processing helix chain 'I' and resid 167 through 174 removed outlier: 3.549A pdb=" N ILE I 171 " --> pdb=" O ASP I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 187 removed outlier: 3.532A pdb=" N SER I 180 " --> pdb=" O ASP I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 213 removed outlier: 3.895A pdb=" N ALA I 209 " --> pdb=" O ALA I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 249 Processing helix chain 'I' and resid 250 through 252 No H-bonds generated for 'chain 'I' and resid 250 through 252' Processing helix chain 'I' and resid 309 through 325 Processing helix chain 'I' and resid 361 through 366 Processing helix chain 'I' and resid 368 through 379 Processing helix chain 'I' and resid 385 through 389 Processing helix chain 'I' and resid 458 through 472 Processing helix chain 'I' and resid 481 through 489 Processing helix chain 'I' and resid 491 through 497 Processing helix chain 'I' and resid 502 through 508 Processing helix chain 'I' and resid 518 through 540 Processing helix chain 'I' and resid 641 through 648 removed outlier: 3.904A pdb=" N LYS I 648 " --> pdb=" O ALA I 644 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 49 Processing helix chain 'J' and resid 51 through 61 Processing helix chain 'J' and resid 65 through 74 Processing helix chain 'J' and resid 91 through 95 removed outlier: 4.152A pdb=" N GLY J 94 " --> pdb=" O ALA J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 101 Processing helix chain 'J' and resid 128 through 132 Processing helix chain 'J' and resid 134 through 152 Processing helix chain 'J' and resid 170 through 186 Processing helix chain 'J' and resid 201 through 205 removed outlier: 3.708A pdb=" N ALA J 204 " --> pdb=" O ALA J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 211 removed outlier: 3.531A pdb=" N LEU J 210 " --> pdb=" O TYR J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 235 Processing helix chain 'J' and resid 240 through 246 Processing helix chain 'J' and resid 246 through 253 Processing helix chain 'J' and resid 263 through 276 Processing helix chain 'J' and resid 299 through 303 Processing helix chain 'J' and resid 315 through 324 removed outlier: 4.262A pdb=" N ILE J 319 " --> pdb=" O ASN J 315 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 328 Processing helix chain 'J' and resid 361 through 365 Processing helix chain 'J' and resid 367 through 384 Processing helix chain 'J' and resid 400 through 405 Processing helix chain 'J' and resid 407 through 421 removed outlier: 4.006A pdb=" N LYS J 414 " --> pdb=" O ARG J 410 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU J 415 " --> pdb=" O HIS J 411 " (cutoff:3.500A) Processing helix chain 'J' and resid 437 through 442 Processing helix chain 'J' and resid 444 through 448 Processing helix chain 'J' and resid 464 through 473 Processing helix chain 'J' and resid 478 through 491 Processing helix chain 'J' and resid 493 through 498 Processing helix chain 'J' and resid 507 through 509 No H-bonds generated for 'chain 'J' and resid 507 through 509' Processing helix chain 'J' and resid 510 through 523 removed outlier: 3.504A pdb=" N VAL J 521 " --> pdb=" O CYS J 517 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 86 Processing helix chain 'K' and resid 96 through 99 removed outlier: 4.323A pdb=" N SER K 99 " --> pdb=" O VAL K 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 96 through 99' Processing helix chain 'K' and resid 100 through 106 Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 149 through 158 Processing helix chain 'K' and resid 167 through 174 removed outlier: 3.548A pdb=" N ILE K 171 " --> pdb=" O ASP K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 187 removed outlier: 3.532A pdb=" N SER K 180 " --> pdb=" O ASP K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 213 removed outlier: 3.895A pdb=" N ALA K 209 " --> pdb=" O ALA K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 249 Processing helix chain 'K' and resid 250 through 252 No H-bonds generated for 'chain 'K' and resid 250 through 252' Processing helix chain 'K' and resid 309 through 325 Processing helix chain 'K' and resid 361 through 366 Processing helix chain 'K' and resid 368 through 379 Processing helix chain 'K' and resid 385 through 389 Processing helix chain 'K' and resid 458 through 472 Processing helix chain 'K' and resid 481 through 489 Processing helix chain 'K' and resid 491 through 497 Processing helix chain 'K' and resid 502 through 508 Processing helix chain 'K' and resid 518 through 540 Processing helix chain 'K' and resid 641 through 648 removed outlier: 3.905A pdb=" N LYS K 648 " --> pdb=" O ALA K 644 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 49 Processing helix chain 'L' and resid 51 through 61 Processing helix chain 'L' and resid 65 through 74 Processing helix chain 'L' and resid 91 through 95 removed outlier: 4.152A pdb=" N GLY L 94 " --> pdb=" O ALA L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 101 Processing helix chain 'L' and resid 128 through 132 Processing helix chain 'L' and resid 134 through 152 Processing helix chain 'L' and resid 170 through 186 Processing helix chain 'L' and resid 201 through 205 removed outlier: 3.707A pdb=" N ALA L 204 " --> pdb=" O ALA L 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 211 removed outlier: 3.531A pdb=" N LEU L 210 " --> pdb=" O TYR L 206 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 235 Processing helix chain 'L' and resid 240 through 246 Processing helix chain 'L' and resid 246 through 253 Processing helix chain 'L' and resid 263 through 276 Processing helix chain 'L' and resid 299 through 303 Processing helix chain 'L' and resid 315 through 324 removed outlier: 4.261A pdb=" N ILE L 319 " --> pdb=" O ASN L 315 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 328 Processing helix chain 'L' and resid 361 through 365 Processing helix chain 'L' and resid 367 through 384 Processing helix chain 'L' and resid 400 through 405 Processing helix chain 'L' and resid 407 through 421 removed outlier: 4.006A pdb=" N LYS L 414 " --> pdb=" O ARG L 410 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU L 415 " --> pdb=" O HIS L 411 " (cutoff:3.500A) Processing helix chain 'L' and resid 437 through 442 Processing helix chain 'L' and resid 444 through 448 Processing helix chain 'L' and resid 464 through 473 Processing helix chain 'L' and resid 478 through 491 Processing helix chain 'L' and resid 493 through 498 Processing helix chain 'L' and resid 507 through 509 No H-bonds generated for 'chain 'L' and resid 507 through 509' Processing helix chain 'L' and resid 510 through 523 removed outlier: 3.504A pdb=" N VAL L 521 " --> pdb=" O CYS L 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 113 removed outlier: 3.821A pdb=" N ILE A 92 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 138 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 230 through 232 Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 351 removed outlier: 5.399A pdb=" N PHE A 347 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU A 338 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N HIS A 269 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU A 289 " --> pdb=" O HIS A 269 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU A 271 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU A 287 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN A 273 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER A 291 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL A 300 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN A 293 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS A 298 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 14.033A pdb=" N GLN A 297 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 10.667A pdb=" N TYR A 401 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 299 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA5, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AA6, first strand: chain 'A' and resid 419 through 421 Processing sheet with id=AA7, first strand: chain 'A' and resid 559 through 564 removed outlier: 6.608A pdb=" N SER A 626 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG A 619 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN A 624 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 661 through 663 removed outlier: 7.230A pdb=" N LEU A 662 " --> pdb=" O LEU A 724 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 695 through 700 removed outlier: 7.844A pdb=" N ILE A 687 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL A 673 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 689 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 81 removed outlier: 6.427A pdb=" N VAL B 155 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU B 195 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY B 157 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 217 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR B 214 " --> pdb=" O ARG B 259 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N PHE B 261 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET B 216 " --> pdb=" O PHE B 261 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 330 through 331 removed outlier: 5.963A pdb=" N ASP B 393 " --> pdb=" O ASN B 357 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 388 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL B 429 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR B 390 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR B 431 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL B 392 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS B 433 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU B 459 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARG B 432 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ALA B 461 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA B 434 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 330 through 331 removed outlier: 5.963A pdb=" N ASP B 393 " --> pdb=" O ASN B 357 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 388 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL B 429 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR B 390 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR B 431 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL B 392 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS B 433 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 451 " --> pdb=" O LYS B 426 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP B 504 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 108 through 113 removed outlier: 3.821A pdb=" N ILE C 92 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 138 " --> pdb=" O LYS C 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 230 through 232 Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 351 removed outlier: 5.399A pdb=" N PHE C 347 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU C 338 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N HIS C 269 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU C 289 " --> pdb=" O HIS C 269 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU C 271 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU C 287 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN C 273 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER C 291 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL C 300 " --> pdb=" O SER C 291 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN C 293 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS C 298 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 14.034A pdb=" N GLN C 297 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 10.667A pdb=" N TYR C 401 " --> pdb=" O GLN C 297 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL C 299 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB8, first strand: chain 'C' and resid 415 through 416 Processing sheet with id=AB9, first strand: chain 'C' and resid 419 through 421 Processing sheet with id=AC1, first strand: chain 'C' and resid 559 through 564 removed outlier: 6.608A pdb=" N SER C 626 " --> pdb=" O LEU C 617 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG C 619 " --> pdb=" O ASN C 624 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN C 624 " --> pdb=" O ARG C 619 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 661 through 663 removed outlier: 7.230A pdb=" N LEU C 662 " --> pdb=" O LEU C 724 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 695 through 700 removed outlier: 7.844A pdb=" N ILE C 687 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL C 673 " --> pdb=" O ILE C 687 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 689 " --> pdb=" O VAL C 671 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.428A pdb=" N VAL D 155 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU D 195 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLY D 157 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 217 " --> pdb=" O ILE D 196 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR D 214 " --> pdb=" O ARG D 259 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N PHE D 261 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET D 216 " --> pdb=" O PHE D 261 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 330 through 331 removed outlier: 5.962A pdb=" N ASP D 393 " --> pdb=" O ASN D 357 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU D 388 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL D 429 " --> pdb=" O LEU D 388 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR D 390 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR D 431 " --> pdb=" O THR D 390 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL D 392 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS D 433 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU D 459 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARG D 432 " --> pdb=" O GLU D 459 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA D 461 " --> pdb=" O ARG D 432 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA D 434 " --> pdb=" O ALA D 461 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 330 through 331 removed outlier: 5.962A pdb=" N ASP D 393 " --> pdb=" O ASN D 357 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU D 388 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL D 429 " --> pdb=" O LEU D 388 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR D 390 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR D 431 " --> pdb=" O THR D 390 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL D 392 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS D 433 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR D 451 " --> pdb=" O LYS D 426 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP D 504 " --> pdb=" O ASN D 452 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 108 through 113 removed outlier: 3.820A pdb=" N ILE E 92 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA E 138 " --> pdb=" O LYS E 65 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 230 through 232 Processing sheet with id=AC9, first strand: chain 'E' and resid 345 through 351 removed outlier: 5.399A pdb=" N PHE E 347 " --> pdb=" O LEU E 338 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU E 338 " --> pdb=" O PHE E 347 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N HIS E 269 " --> pdb=" O GLU E 289 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU E 289 " --> pdb=" O HIS E 269 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU E 271 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU E 287 " --> pdb=" O GLU E 271 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN E 273 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER E 291 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL E 300 " --> pdb=" O SER E 291 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN E 293 " --> pdb=" O LYS E 298 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS E 298 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 14.033A pdb=" N GLN E 297 " --> pdb=" O TYR E 401 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N TYR E 401 " --> pdb=" O GLN E 297 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL E 299 " --> pdb=" O ARG E 399 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 403 through 404 Processing sheet with id=AD2, first strand: chain 'E' and resid 415 through 416 Processing sheet with id=AD3, first strand: chain 'E' and resid 419 through 421 Processing sheet with id=AD4, first strand: chain 'E' and resid 559 through 564 removed outlier: 6.608A pdb=" N SER E 626 " --> pdb=" O LEU E 617 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG E 619 " --> pdb=" O ASN E 624 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN E 624 " --> pdb=" O ARG E 619 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 661 through 663 removed outlier: 7.231A pdb=" N LEU E 662 " --> pdb=" O LEU E 724 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 695 through 700 removed outlier: 7.845A pdb=" N ILE E 687 " --> pdb=" O VAL E 673 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL E 673 " --> pdb=" O ILE E 687 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 689 " --> pdb=" O VAL E 671 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 80 through 81 removed outlier: 6.428A pdb=" N VAL F 155 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU F 195 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLY F 157 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL F 217 " --> pdb=" O ILE F 196 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR F 214 " --> pdb=" O ARG F 259 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N PHE F 261 " --> pdb=" O THR F 214 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET F 216 " --> pdb=" O PHE F 261 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 330 through 331 removed outlier: 5.963A pdb=" N ASP F 393 " --> pdb=" O ASN F 357 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU F 388 " --> pdb=" O VAL F 427 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL F 429 " --> pdb=" O LEU F 388 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR F 390 " --> pdb=" O VAL F 429 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR F 431 " --> pdb=" O THR F 390 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL F 392 " --> pdb=" O THR F 431 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS F 433 " --> pdb=" O VAL F 392 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU F 459 " --> pdb=" O ILE F 430 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARG F 432 " --> pdb=" O GLU F 459 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA F 461 " --> pdb=" O ARG F 432 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA F 434 " --> pdb=" O ALA F 461 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 330 through 331 removed outlier: 5.963A pdb=" N ASP F 393 " --> pdb=" O ASN F 357 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU F 388 " --> pdb=" O VAL F 427 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL F 429 " --> pdb=" O LEU F 388 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR F 390 " --> pdb=" O VAL F 429 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR F 431 " --> pdb=" O THR F 390 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL F 392 " --> pdb=" O THR F 431 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS F 433 " --> pdb=" O VAL F 392 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR F 451 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP F 504 " --> pdb=" O ASN F 452 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 559 through 564 removed outlier: 6.608A pdb=" N SER G 626 " --> pdb=" O LEU G 617 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG G 619 " --> pdb=" O ASN G 624 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN G 624 " --> pdb=" O ARG G 619 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 80 through 81 removed outlier: 6.427A pdb=" N VAL H 155 " --> pdb=" O ILE H 193 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU H 195 " --> pdb=" O VAL H 155 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLY H 157 " --> pdb=" O LEU H 195 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL H 217 " --> pdb=" O ILE H 196 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR H 214 " --> pdb=" O ARG H 259 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N PHE H 261 " --> pdb=" O THR H 214 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET H 216 " --> pdb=" O PHE H 261 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 330 through 331 removed outlier: 5.962A pdb=" N ASP H 393 " --> pdb=" O ASN H 357 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU H 388 " --> pdb=" O VAL H 427 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL H 429 " --> pdb=" O LEU H 388 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR H 390 " --> pdb=" O VAL H 429 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR H 431 " --> pdb=" O THR H 390 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL H 392 " --> pdb=" O THR H 431 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS H 433 " --> pdb=" O VAL H 392 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU H 459 " --> pdb=" O ILE H 430 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARG H 432 " --> pdb=" O GLU H 459 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ALA H 461 " --> pdb=" O ARG H 432 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA H 434 " --> pdb=" O ALA H 461 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 330 through 331 removed outlier: 5.962A pdb=" N ASP H 393 " --> pdb=" O ASN H 357 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU H 388 " --> pdb=" O VAL H 427 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL H 429 " --> pdb=" O LEU H 388 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR H 390 " --> pdb=" O VAL H 429 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR H 431 " --> pdb=" O THR H 390 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL H 392 " --> pdb=" O THR H 431 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS H 433 " --> pdb=" O VAL H 392 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR H 451 " --> pdb=" O LYS H 426 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP H 504 " --> pdb=" O ASN H 452 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 108 through 113 removed outlier: 3.822A pdb=" N ILE I 92 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA I 138 " --> pdb=" O LYS I 65 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 230 through 232 Processing sheet with id=AE7, first strand: chain 'I' and resid 345 through 351 removed outlier: 5.399A pdb=" N PHE I 347 " --> pdb=" O LEU I 338 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU I 338 " --> pdb=" O PHE I 347 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N HIS I 269 " --> pdb=" O GLU I 289 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU I 289 " --> pdb=" O HIS I 269 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU I 271 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU I 287 " --> pdb=" O GLU I 271 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN I 273 " --> pdb=" O LEU I 285 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER I 291 " --> pdb=" O VAL I 300 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL I 300 " --> pdb=" O SER I 291 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN I 293 " --> pdb=" O LYS I 298 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS I 298 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 14.033A pdb=" N GLN I 297 " --> pdb=" O TYR I 401 " (cutoff:3.500A) removed outlier: 10.667A pdb=" N TYR I 401 " --> pdb=" O GLN I 297 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL I 299 " --> pdb=" O ARG I 399 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 403 through 404 Processing sheet with id=AE9, first strand: chain 'I' and resid 415 through 416 Processing sheet with id=AF1, first strand: chain 'I' and resid 419 through 421 Processing sheet with id=AF2, first strand: chain 'I' and resid 559 through 564 removed outlier: 6.608A pdb=" N SER I 626 " --> pdb=" O LEU I 617 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG I 619 " --> pdb=" O ASN I 624 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN I 624 " --> pdb=" O ARG I 619 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 661 through 663 removed outlier: 7.231A pdb=" N LEU I 662 " --> pdb=" O LEU I 724 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 695 through 700 removed outlier: 7.844A pdb=" N ILE I 687 " --> pdb=" O VAL I 673 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL I 673 " --> pdb=" O ILE I 687 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL I 689 " --> pdb=" O VAL I 671 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 80 through 81 removed outlier: 6.428A pdb=" N VAL J 155 " --> pdb=" O ILE J 193 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU J 195 " --> pdb=" O VAL J 155 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY J 157 " --> pdb=" O LEU J 195 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL J 217 " --> pdb=" O ILE J 196 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR J 214 " --> pdb=" O ARG J 259 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N PHE J 261 " --> pdb=" O THR J 214 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET J 216 " --> pdb=" O PHE J 261 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 330 through 331 removed outlier: 5.963A pdb=" N ASP J 393 " --> pdb=" O ASN J 357 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU J 388 " --> pdb=" O VAL J 427 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL J 429 " --> pdb=" O LEU J 388 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR J 390 " --> pdb=" O VAL J 429 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR J 431 " --> pdb=" O THR J 390 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL J 392 " --> pdb=" O THR J 431 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS J 433 " --> pdb=" O VAL J 392 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU J 459 " --> pdb=" O ILE J 430 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARG J 432 " --> pdb=" O GLU J 459 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA J 461 " --> pdb=" O ARG J 432 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA J 434 " --> pdb=" O ALA J 461 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 330 through 331 removed outlier: 5.963A pdb=" N ASP J 393 " --> pdb=" O ASN J 357 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU J 388 " --> pdb=" O VAL J 427 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL J 429 " --> pdb=" O LEU J 388 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR J 390 " --> pdb=" O VAL J 429 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR J 431 " --> pdb=" O THR J 390 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL J 392 " --> pdb=" O THR J 431 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS J 433 " --> pdb=" O VAL J 392 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR J 451 " --> pdb=" O LYS J 426 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP J 504 " --> pdb=" O ASN J 452 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 108 through 113 removed outlier: 3.822A pdb=" N ILE K 92 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA K 138 " --> pdb=" O LYS K 65 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 230 through 232 Processing sheet with id=AG1, first strand: chain 'K' and resid 345 through 351 removed outlier: 5.400A pdb=" N PHE K 347 " --> pdb=" O LEU K 338 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU K 338 " --> pdb=" O PHE K 347 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N HIS K 269 " --> pdb=" O GLU K 289 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU K 289 " --> pdb=" O HIS K 269 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU K 271 " --> pdb=" O GLU K 287 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU K 287 " --> pdb=" O GLU K 271 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN K 273 " --> pdb=" O LEU K 285 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER K 291 " --> pdb=" O VAL K 300 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL K 300 " --> pdb=" O SER K 291 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN K 293 " --> pdb=" O LYS K 298 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS K 298 " --> pdb=" O GLN K 293 " (cutoff:3.500A) removed outlier: 14.033A pdb=" N GLN K 297 " --> pdb=" O TYR K 401 " (cutoff:3.500A) removed outlier: 10.667A pdb=" N TYR K 401 " --> pdb=" O GLN K 297 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL K 299 " --> pdb=" O ARG K 399 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 403 through 404 Processing sheet with id=AG3, first strand: chain 'K' and resid 415 through 416 Processing sheet with id=AG4, first strand: chain 'K' and resid 419 through 421 Processing sheet with id=AG5, first strand: chain 'K' and resid 559 through 564 removed outlier: 6.607A pdb=" N SER K 626 " --> pdb=" O LEU K 617 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG K 619 " --> pdb=" O ASN K 624 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN K 624 " --> pdb=" O ARG K 619 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 661 through 663 removed outlier: 7.230A pdb=" N LEU K 662 " --> pdb=" O LEU K 724 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 695 through 700 removed outlier: 7.844A pdb=" N ILE K 687 " --> pdb=" O VAL K 673 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL K 673 " --> pdb=" O ILE K 687 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL K 689 " --> pdb=" O VAL K 671 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 80 through 81 removed outlier: 6.427A pdb=" N VAL L 155 " --> pdb=" O ILE L 193 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU L 195 " --> pdb=" O VAL L 155 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLY L 157 " --> pdb=" O LEU L 195 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL L 217 " --> pdb=" O ILE L 196 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR L 214 " --> pdb=" O ARG L 259 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N PHE L 261 " --> pdb=" O THR L 214 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET L 216 " --> pdb=" O PHE L 261 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 330 through 331 removed outlier: 5.963A pdb=" N ASP L 393 " --> pdb=" O ASN L 357 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU L 388 " --> pdb=" O VAL L 427 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL L 429 " --> pdb=" O LEU L 388 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR L 390 " --> pdb=" O VAL L 429 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR L 431 " --> pdb=" O THR L 390 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL L 392 " --> pdb=" O THR L 431 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS L 433 " --> pdb=" O VAL L 392 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLU L 459 " --> pdb=" O ILE L 430 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARG L 432 " --> pdb=" O GLU L 459 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA L 461 " --> pdb=" O ARG L 432 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA L 434 " --> pdb=" O ALA L 461 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 330 through 331 removed outlier: 5.963A pdb=" N ASP L 393 " --> pdb=" O ASN L 357 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU L 388 " --> pdb=" O VAL L 427 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL L 429 " --> pdb=" O LEU L 388 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR L 390 " --> pdb=" O VAL L 429 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR L 431 " --> pdb=" O THR L 390 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL L 392 " --> pdb=" O THR L 431 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS L 433 " --> pdb=" O VAL L 392 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR L 451 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP L 504 " --> pdb=" O ASN L 452 " (cutoff:3.500A) 2456 hydrogen bonds defined for protein. 6708 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: 21.45 Time building geometry restraints manager: 10.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 9702 1.32 - 1.44: 11879 1.44 - 1.57: 29278 1.57 - 1.69: 41 1.69 - 1.81: 462 Bond restraints: 51362 Sorted by residual: bond pdb=" C3 BTN E 801 " pdb=" O3 BTN E 801 " ideal model delta sigma weight residual 1.220 1.410 -0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" C3 BTN I 801 " pdb=" O3 BTN I 801 " ideal model delta sigma weight residual 1.220 1.409 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" C3 BTN C 801 " pdb=" O3 BTN C 801 " ideal model delta sigma weight residual 1.220 1.409 -0.189 2.00e-02 2.50e+03 8.93e+01 bond pdb=" C3 BTN K 801 " pdb=" O3 BTN K 801 " ideal model delta sigma weight residual 1.220 1.409 -0.189 2.00e-02 2.50e+03 8.90e+01 bond pdb=" C3 BTN A 801 " pdb=" O3 BTN A 801 " ideal model delta sigma weight residual 1.220 1.408 -0.188 2.00e-02 2.50e+03 8.88e+01 ... (remaining 51357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 68477 3.28 - 6.56: 854 6.56 - 9.84: 155 9.84 - 13.11: 25 13.11 - 16.39: 12 Bond angle restraints: 69523 Sorted by residual: angle pdb=" P1A ACO B 601 " pdb=" O3A ACO B 601 " pdb=" P2A ACO B 601 " ideal model delta sigma weight residual 136.83 120.44 16.39 1.00e+00 1.00e+00 2.69e+02 angle pdb=" P1A ACO H 601 " pdb=" O3A ACO H 601 " pdb=" P2A ACO H 601 " ideal model delta sigma weight residual 136.83 120.44 16.39 1.00e+00 1.00e+00 2.69e+02 angle pdb=" P1A ACO F 601 " pdb=" O3A ACO F 601 " pdb=" P2A ACO F 601 " ideal model delta sigma weight residual 136.83 120.45 16.38 1.00e+00 1.00e+00 2.68e+02 angle pdb=" P1A ACO J 601 " pdb=" O3A ACO J 601 " pdb=" P2A ACO J 601 " ideal model delta sigma weight residual 136.83 120.51 16.32 1.00e+00 1.00e+00 2.67e+02 angle pdb=" P1A ACO D 601 " pdb=" O3A ACO D 601 " pdb=" P2A ACO D 601 " ideal model delta sigma weight residual 136.83 120.52 16.31 1.00e+00 1.00e+00 2.66e+02 ... (remaining 69518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 29705 17.94 - 35.89: 1088 35.89 - 53.83: 346 53.83 - 71.78: 107 71.78 - 89.72: 47 Dihedral angle restraints: 31293 sinusoidal: 12620 harmonic: 18673 Sorted by residual: dihedral pdb=" CA VAL L 121 " pdb=" C VAL L 121 " pdb=" N PHE L 122 " pdb=" CA PHE L 122 " ideal model delta harmonic sigma weight residual 180.00 161.31 18.69 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA VAL H 121 " pdb=" C VAL H 121 " pdb=" N PHE H 122 " pdb=" CA PHE H 122 " ideal model delta harmonic sigma weight residual 180.00 161.31 18.69 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA VAL D 121 " pdb=" C VAL D 121 " pdb=" N PHE D 122 " pdb=" CA PHE D 122 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 31290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 5993 0.077 - 0.154: 1720 0.154 - 0.231: 146 0.231 - 0.308: 10 0.308 - 0.385: 5 Chirality restraints: 7874 Sorted by residual: chirality pdb=" C2 BTN E 801 " pdb=" C4 BTN E 801 " pdb=" C7 BTN E 801 " pdb=" S1 BTN E 801 " both_signs ideal model delta sigma weight residual False 3.08 2.70 0.38 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" C2 BTN C 801 " pdb=" C4 BTN C 801 " pdb=" C7 BTN C 801 " pdb=" S1 BTN C 801 " both_signs ideal model delta sigma weight residual False 3.08 2.70 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" C2 BTN I 801 " pdb=" C4 BTN I 801 " pdb=" C7 BTN I 801 " pdb=" S1 BTN I 801 " both_signs ideal model delta sigma weight residual False 3.08 2.70 0.38 2.00e-01 2.50e+01 3.67e+00 ... (remaining 7871 not shown) Planarity restraints: 9037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P ACO H 601 " 0.356 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C9P ACO H 601 " -0.090 2.00e-02 2.50e+03 pdb=" CAP ACO H 601 " 0.149 2.00e-02 2.50e+03 pdb=" N8P ACO H 601 " -0.538 2.00e-02 2.50e+03 pdb=" O9P ACO H 601 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO F 601 " -0.349 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C9P ACO F 601 " 0.090 2.00e-02 2.50e+03 pdb=" CAP ACO F 601 " -0.167 2.00e-02 2.50e+03 pdb=" N8P ACO F 601 " 0.523 2.00e-02 2.50e+03 pdb=" O9P ACO F 601 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO B 601 " -0.349 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C9P ACO B 601 " 0.090 2.00e-02 2.50e+03 pdb=" CAP ACO B 601 " -0.167 2.00e-02 2.50e+03 pdb=" N8P ACO B 601 " 0.523 2.00e-02 2.50e+03 pdb=" O9P ACO B 601 " -0.097 2.00e-02 2.50e+03 ... (remaining 9034 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 11018 2.78 - 3.31: 46653 3.31 - 3.84: 82018 3.84 - 4.37: 100704 4.37 - 4.90: 169718 Nonbonded interactions: 410111 Sorted by model distance: nonbonded pdb=" ND2 ASN B 536 " pdb=" OD1 ASP D 212 " model vdw 2.254 3.120 nonbonded pdb=" O GLY B 162 " pdb=" C6P ACO B 601 " model vdw 2.254 3.440 nonbonded pdb=" OD1 ASP B 212 " pdb=" ND2 ASN D 536 " model vdw 2.254 3.120 nonbonded pdb=" OH TYR J 206 " pdb=" CZ PHE L 397 " model vdw 2.270 3.340 nonbonded pdb=" ND2 ASN J 536 " pdb=" OD1 ASP L 212 " model vdw 2.298 3.120 ... (remaining 410106 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' selection = chain 'C' selection = chain 'E' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } 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=1.00 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: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.410 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 88.370 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 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 : 0.010 0.190 51362 Z= 0.660 Angle : 1.045 16.393 69523 Z= 0.704 Chirality : 0.064 0.385 7874 Planarity : 0.010 0.304 9037 Dihedral : 11.962 89.722 19283 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.72 % Allowed : 2.72 % Favored : 96.55 % Rotamer: Outliers : 1.98 % Allowed : 1.52 % Favored : 96.50 % 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: -0.32 (0.10), residues: 6497 helix: -0.70 (0.10), residues: 2241 sheet: 0.95 (0.13), residues: 1368 loop : -0.23 (0.11), residues: 2888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 394 HIS 0.001 0.000 HIS K 566 PHE 0.002 0.000 PHE J 330 TYR 0.002 0.000 TYR H 453 ARG 0.003 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1496 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1389 time to evaluate : 4.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 THR cc_start: 0.7535 (m) cc_final: 0.5833 (p) REVERT: A 338 LEU cc_start: 0.6024 (mt) cc_final: 0.5235 (tp) REVERT: A 454 THR cc_start: 0.7434 (m) cc_final: 0.6926 (m) REVERT: D 435 TYR cc_start: 0.8115 (m-80) cc_final: 0.7045 (m-80) REVERT: E 156 LEU cc_start: 0.7114 (tp) cc_final: 0.6250 (tp) REVERT: E 229 MET cc_start: 0.2395 (mtt) cc_final: 0.1659 (ppp) REVERT: E 457 SER cc_start: 0.7553 (p) cc_final: 0.7321 (m) REVERT: E 666 MET cc_start: 0.4763 (ttt) cc_final: 0.3169 (mmp) REVERT: F 95 MET cc_start: 0.6072 (mmm) cc_final: 0.5811 (mmm) REVERT: F 214 THR cc_start: 0.7929 (m) cc_final: 0.7607 (p) REVERT: F 316 MET cc_start: 0.7592 (tpp) cc_final: 0.7138 (tpt) REVERT: G 642 LEU cc_start: 0.8477 (tp) cc_final: 0.8228 (mp) REVERT: H 145 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7842 (mmm) REVERT: H 167 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8282 (mp10) REVERT: H 265 VAL cc_start: 0.8773 (t) cc_final: 0.8392 (p) REVERT: K 217 MET cc_start: -0.5410 (ttt) cc_final: -0.6019 (ptm) REVERT: K 316 MET cc_start: 0.4383 (mmp) cc_final: 0.4078 (mmt) REVERT: K 466 MET cc_start: 0.7460 (tpp) cc_final: 0.7221 (tpt) REVERT: K 471 ASP cc_start: 0.5627 (m-30) cc_final: 0.5373 (p0) REVERT: L 95 MET cc_start: 0.7703 (mmm) cc_final: 0.7284 (mmm) outliers start: 107 outliers final: 11 residues processed: 1460 average time/residue: 0.5853 time to fit residues: 1331.3420 Evaluate side-chains 667 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 654 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 499 ARG Chi-restraints excluded: chain E residue 566 HIS Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain H residue 54 ARG Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain J residue 445 LYS Chi-restraints excluded: chain K residue 459 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 542 optimal weight: 9.9990 chunk 487 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 328 optimal weight: 0.3980 chunk 260 optimal weight: 6.9990 chunk 503 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 306 optimal weight: 0.7980 chunk 375 optimal weight: 0.9980 chunk 583 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS A 269 HIS A 358 HIS A 392 ASN A 577 ASN A 591 ASN A 611 GLN B 115 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN C 140 HIS ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN E 419 GLN E 421 GLN F 139 GLN F 478 ASN F 528 GLN G 558 ASN G 570 HIS G 597 ASN H 115 ASN H 507 GLN I 140 HIS I 169 HIS I 611 GLN J 115 ASN K 140 HIS ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 GLN K 392 ASN K 425 HIS K 611 GLN L 321 HIS L 446 HIS L 536 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.145476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.108876 restraints weight = 124738.893| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.28 r_work: 0.3626 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 51362 Z= 0.225 Angle : 0.659 10.770 69523 Z= 0.352 Chirality : 0.046 0.225 7874 Planarity : 0.005 0.105 9037 Dihedral : 7.844 68.325 7487 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.20 % Favored : 97.65 % Rotamer: Outliers : 1.85 % Allowed : 8.88 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.10), residues: 6497 helix: 0.68 (0.11), residues: 2287 sheet: 0.98 (0.14), residues: 1343 loop : 0.04 (0.12), residues: 2867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 559 HIS 0.012 0.001 HIS K 358 PHE 0.023 0.002 PHE D 85 TYR 0.019 0.001 TYR H 176 ARG 0.008 0.001 ARG L 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 720 time to evaluate : 4.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.0122 (ttp) cc_final: -0.1211 (ttt) REVERT: A 273 GLN cc_start: 0.8237 (tt0) cc_final: 0.7346 (tm-30) REVERT: A 448 MET cc_start: 0.8031 (ttm) cc_final: 0.7742 (ttm) REVERT: A 454 THR cc_start: 0.7889 (m) cc_final: 0.6899 (m) REVERT: A 466 MET cc_start: 0.8374 (mmm) cc_final: 0.8038 (tpt) REVERT: A 566 HIS cc_start: 0.8161 (OUTLIER) cc_final: 0.6854 (m90) REVERT: A 693 MET cc_start: 0.3064 (OUTLIER) cc_final: 0.2624 (mtm) REVERT: A 695 MET cc_start: 0.4770 (tpp) cc_final: 0.4554 (tpp) REVERT: B 269 CYS cc_start: 0.8713 (m) cc_final: 0.8502 (m) REVERT: C 89 THR cc_start: 0.8557 (m) cc_final: 0.7837 (p) REVERT: C 108 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7624 (tm-30) REVERT: C 124 MET cc_start: 0.8340 (mpp) cc_final: 0.7983 (mpp) REVERT: C 229 MET cc_start: -0.0613 (tmm) cc_final: -0.2698 (ptm) REVERT: C 448 MET cc_start: 0.7890 (ttm) cc_final: 0.7518 (ttt) REVERT: C 505 SER cc_start: 0.8710 (m) cc_final: 0.8487 (p) REVERT: C 696 GLN cc_start: 0.6099 (mm110) cc_final: 0.5830 (mm-40) REVERT: E 174 MET cc_start: 0.6378 (tpt) cc_final: 0.6014 (tpp) REVERT: E 186 LYS cc_start: 0.8931 (mttt) cc_final: 0.8647 (pttt) REVERT: E 266 ASN cc_start: 0.7006 (m-40) cc_final: 0.6565 (t0) REVERT: E 268 ARG cc_start: 0.5271 (mpt180) cc_final: 0.4928 (mmt90) REVERT: E 271 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7816 (mt-10) REVERT: E 288 ARG cc_start: 0.7722 (mtm-85) cc_final: 0.7360 (mtm-85) REVERT: E 448 MET cc_start: 0.8717 (ttm) cc_final: 0.7988 (tpp) REVERT: E 466 MET cc_start: 0.8523 (tpp) cc_final: 0.7882 (tpt) REVERT: E 666 MET cc_start: 0.4419 (ttt) cc_final: 0.2665 (tpp) REVERT: F 83 ASP cc_start: 0.7439 (m-30) cc_final: 0.7025 (t0) REVERT: F 95 MET cc_start: 0.5931 (mmm) cc_final: 0.5460 (mmt) REVERT: F 214 THR cc_start: 0.8709 (m) cc_final: 0.8159 (p) REVERT: F 253 MET cc_start: 0.8300 (ttt) cc_final: 0.7996 (ttp) REVERT: G 522 LYS cc_start: 0.8571 (mtmt) cc_final: 0.8305 (mttt) REVERT: G 549 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6380 (tpt) REVERT: G 560 GLU cc_start: 0.8572 (tt0) cc_final: 0.8087 (tt0) REVERT: G 566 HIS cc_start: 0.6586 (m-70) cc_final: 0.6172 (t-90) REVERT: G 619 ARG cc_start: 0.7722 (ttp-170) cc_final: 0.6876 (ttt-90) REVERT: H 504 ASP cc_start: 0.7478 (t0) cc_final: 0.7007 (t70) REVERT: I 67 LEU cc_start: 0.6138 (mt) cc_final: 0.5612 (tt) REVERT: I 134 THR cc_start: 0.7884 (p) cc_final: 0.7437 (p) REVERT: I 150 LYS cc_start: 0.7518 (mtpt) cc_final: 0.7286 (mmmm) REVERT: I 273 GLN cc_start: 0.8424 (tt0) cc_final: 0.8039 (tp40) REVERT: I 288 ARG cc_start: 0.5725 (OUTLIER) cc_final: 0.4852 (ptp-170) REVERT: I 358 HIS cc_start: 0.8567 (p-80) cc_final: 0.8140 (p90) REVERT: I 373 MET cc_start: 0.7306 (tpt) cc_final: 0.7062 (tpt) REVERT: I 394 TRP cc_start: 0.6727 (m100) cc_final: 0.6517 (m100) REVERT: I 445 TYR cc_start: 0.7865 (m-80) cc_final: 0.7587 (m-10) REVERT: I 531 SER cc_start: 0.8463 (t) cc_final: 0.7866 (p) REVERT: I 549 MET cc_start: 0.8268 (tpt) cc_final: 0.7930 (mmt) REVERT: I 693 MET cc_start: 0.7369 (mpp) cc_final: 0.7125 (mpp) REVERT: J 98 ASP cc_start: 0.7993 (m-30) cc_final: 0.7422 (t0) REVERT: J 233 SER cc_start: 0.8363 (m) cc_final: 0.8148 (p) REVERT: J 244 LEU cc_start: 0.8915 (tp) cc_final: 0.8632 (tt) REVERT: J 450 ASP cc_start: 0.7596 (m-30) cc_final: 0.7381 (m-30) REVERT: K 85 MET cc_start: 0.8403 (tpp) cc_final: 0.7761 (tpp) REVERT: K 97 ASP cc_start: 0.7687 (m-30) cc_final: 0.6645 (t0) REVERT: K 125 ASP cc_start: 0.8316 (p0) cc_final: 0.7959 (p0) REVERT: K 156 LEU cc_start: 0.8357 (tt) cc_final: 0.8071 (pp) REVERT: K 217 MET cc_start: -0.5719 (ttt) cc_final: -0.5951 (ptm) REVERT: K 229 MET cc_start: 0.0689 (ptp) cc_final: -0.0609 (ptp) REVERT: K 301 GLU cc_start: 0.7316 (mp0) cc_final: 0.7060 (mp0) REVERT: K 316 MET cc_start: 0.4410 (mmp) cc_final: 0.4130 (mmp) REVERT: K 352 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7973 (t) REVERT: K 418 SER cc_start: 0.8815 (m) cc_final: 0.8532 (p) REVERT: K 459 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6732 (tmt90) REVERT: K 466 MET cc_start: 0.7653 (tpp) cc_final: 0.6919 (tpt) REVERT: K 471 ASP cc_start: 0.6338 (m-30) cc_final: 0.5815 (p0) REVERT: K 549 MET cc_start: 0.8539 (tpp) cc_final: 0.8197 (mmt) REVERT: L 311 THR cc_start: 0.8696 (p) cc_final: 0.8387 (t) outliers start: 100 outliers final: 53 residues processed: 788 average time/residue: 0.5168 time to fit residues: 670.9264 Evaluate side-chains 597 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 538 time to evaluate : 4.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 566 HIS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 547 SER Chi-restraints excluded: chain G residue 549 MET Chi-restraints excluded: chain G residue 572 VAL Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 607 VAL Chi-restraints excluded: chain G residue 653 LYS Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 288 ARG Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 352 THR Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 616 CYS Chi-restraints excluded: chain K residue 671 VAL Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 390 THR Chi-restraints excluded: chain L residue 516 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 463 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 503 optimal weight: 0.8980 chunk 621 optimal weight: 0.8980 chunk 454 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 590 optimal weight: 6.9990 chunk 587 optimal weight: 6.9990 chunk 574 optimal weight: 0.6980 chunk 448 optimal weight: 0.1980 chunk 169 optimal weight: 10.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 344 ASN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN B 528 GLN ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 GLN ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN D 528 GLN ** E 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 523 ASN H 115 ASN H 167 GLN H 241 GLN H 446 HIS I 102 HIS ** I 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 139 GLN J 241 GLN ** J 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 HIS L 241 GLN L 446 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.142221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.104702 restraints weight = 126062.324| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.27 r_work: 0.3568 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 51362 Z= 0.226 Angle : 0.596 12.574 69523 Z= 0.313 Chirality : 0.045 0.300 7874 Planarity : 0.004 0.080 9037 Dihedral : 6.940 67.251 7461 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.63 % Favored : 97.21 % Rotamer: Outliers : 2.09 % Allowed : 10.58 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.10), residues: 6497 helix: 0.86 (0.11), residues: 2346 sheet: 0.83 (0.14), residues: 1330 loop : 0.00 (0.12), residues: 2821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 559 HIS 0.011 0.001 HIS E 358 PHE 0.019 0.001 PHE C 152 TYR 0.015 0.001 TYR H 176 ARG 0.007 0.001 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 593 time to evaluate : 4.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7698 (mm-30) cc_final: 0.6708 (tm-30) REVERT: A 273 GLN cc_start: 0.8186 (tt0) cc_final: 0.7511 (tm-30) REVERT: A 449 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8486 (mt) REVERT: A 454 THR cc_start: 0.8043 (m) cc_final: 0.7792 (m) REVERT: A 549 MET cc_start: 0.8575 (tpt) cc_final: 0.8042 (mmm) REVERT: A 693 MET cc_start: 0.4412 (mtm) cc_final: 0.4021 (mtm) REVERT: A 695 MET cc_start: 0.5217 (tpp) cc_final: 0.4929 (tpp) REVERT: B 95 MET cc_start: 0.9047 (mmm) cc_final: 0.8835 (mmm) REVERT: B 488 GLU cc_start: 0.8718 (tp30) cc_final: 0.8221 (tp30) REVERT: B 504 ASP cc_start: 0.8036 (t0) cc_final: 0.7705 (t70) REVERT: C 64 ASP cc_start: 0.7878 (m-30) cc_final: 0.7533 (m-30) REVERT: C 89 THR cc_start: 0.8770 (m) cc_final: 0.8357 (p) REVERT: C 108 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7651 (tm-30) REVERT: C 124 MET cc_start: 0.8374 (mpp) cc_final: 0.8089 (mtp) REVERT: C 229 MET cc_start: -0.0563 (tmm) cc_final: -0.2715 (ptm) REVERT: C 505 SER cc_start: 0.8720 (m) cc_final: 0.8516 (p) REVERT: C 666 MET cc_start: 0.3427 (ttt) cc_final: 0.3152 (ttt) REVERT: C 693 MET cc_start: 0.3185 (mtp) cc_final: 0.2456 (ttm) REVERT: C 696 GLN cc_start: 0.6498 (mm110) cc_final: 0.6278 (mm110) REVERT: E 174 MET cc_start: 0.6348 (tpt) cc_final: 0.6079 (tpp) REVERT: E 186 LYS cc_start: 0.8789 (mttt) cc_final: 0.8554 (pttt) REVERT: E 266 ASN cc_start: 0.7063 (m-40) cc_final: 0.6844 (t0) REVERT: E 271 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7738 (mt-10) REVERT: E 448 MET cc_start: 0.8593 (ttm) cc_final: 0.8052 (tpp) REVERT: E 466 MET cc_start: 0.8554 (tpp) cc_final: 0.7923 (tpt) REVERT: E 666 MET cc_start: 0.5006 (ttt) cc_final: 0.3073 (tpp) REVERT: F 83 ASP cc_start: 0.7625 (m-30) cc_final: 0.7229 (t0) REVERT: F 95 MET cc_start: 0.5905 (mmm) cc_final: 0.5486 (mmt) REVERT: F 214 THR cc_start: 0.8746 (m) cc_final: 0.8380 (p) REVERT: F 253 MET cc_start: 0.8359 (ttt) cc_final: 0.8047 (ttp) REVERT: F 442 MET cc_start: 0.8690 (mmm) cc_final: 0.7750 (mmm) REVERT: G 549 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.6364 (tpt) REVERT: G 566 HIS cc_start: 0.6308 (m-70) cc_final: 0.5997 (t-90) REVERT: H 504 ASP cc_start: 0.7477 (t0) cc_final: 0.7026 (t0) REVERT: H 518 ASP cc_start: 0.8252 (m-30) cc_final: 0.8022 (m-30) REVERT: I 74 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8232 (pt) REVERT: I 124 MET cc_start: 0.8602 (pmm) cc_final: 0.7238 (mtt) REVERT: I 358 HIS cc_start: 0.8379 (p-80) cc_final: 0.8045 (p90) REVERT: I 531 SER cc_start: 0.8543 (t) cc_final: 0.7939 (p) REVERT: I 549 MET cc_start: 0.8145 (tpt) cc_final: 0.7862 (mmt) REVERT: I 666 MET cc_start: 0.4194 (mmp) cc_final: 0.3789 (mmm) REVERT: I 693 MET cc_start: 0.7565 (mpp) cc_final: 0.7347 (mpp) REVERT: I 699 MET cc_start: 0.5340 (mpp) cc_final: 0.4610 (mpp) REVERT: J 98 ASP cc_start: 0.8062 (m-30) cc_final: 0.7494 (t0) REVERT: J 233 SER cc_start: 0.8407 (m) cc_final: 0.8141 (p) REVERT: J 244 LEU cc_start: 0.8928 (tp) cc_final: 0.8632 (tt) REVERT: J 499 ARG cc_start: 0.9005 (mtt-85) cc_final: 0.8665 (mtt-85) REVERT: K 88 LYS cc_start: 0.7410 (mmtm) cc_final: 0.7160 (mmmt) REVERT: K 97 ASP cc_start: 0.7868 (m-30) cc_final: 0.7001 (t0) REVERT: K 174 MET cc_start: 0.7667 (mmm) cc_final: 0.7304 (mmm) REVERT: K 217 MET cc_start: -0.5305 (ttt) cc_final: -0.5664 (ptm) REVERT: K 350 MET cc_start: 0.8407 (tmm) cc_final: 0.8013 (tmm) REVERT: K 418 SER cc_start: 0.8774 (m) cc_final: 0.8538 (p) REVERT: K 459 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.6495 (tmt90) REVERT: K 549 MET cc_start: 0.8641 (tpp) cc_final: 0.8339 (mmt) REVERT: K 559 TRP cc_start: 0.8069 (m100) cc_final: 0.7828 (m-90) REVERT: L 101 LYS cc_start: 0.6689 (mmmt) cc_final: 0.6439 (mmtt) outliers start: 113 outliers final: 72 residues processed: 670 average time/residue: 0.4790 time to fit residues: 544.5139 Evaluate side-chains 581 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 505 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 566 HIS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 499 ILE Chi-restraints excluded: chain E residue 566 HIS Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 669 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 547 SER Chi-restraints excluded: chain G residue 549 MET Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 607 VAL Chi-restraints excluded: chain G residue 653 LYS Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 288 ARG Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 704 THR Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 432 ASP Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 501 THR Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 603 LEU Chi-restraints excluded: chain K residue 616 CYS Chi-restraints excluded: chain K residue 671 VAL Chi-restraints excluded: chain L residue 302 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 390 THR Chi-restraints excluded: chain L residue 516 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 176 optimal weight: 20.0000 chunk 591 optimal weight: 7.9990 chunk 187 optimal weight: 8.9990 chunk 233 optimal weight: 7.9990 chunk 582 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 571 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 599 optimal weight: 4.9990 chunk 317 optimal weight: 3.9990 chunk 314 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS C 696 GLN D 100 ASN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN D 446 HIS E 140 HIS E 190 ASN ** E 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN F 241 GLN F 258 HIS H 88 HIS H 192 GLN H 476 HIS I 169 HIS I 480 HIS ** I 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 697 ASN J 88 HIS ** J 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 476 HIS K 102 HIS K 279 HIS L 88 HIS L 446 HIS L 528 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.137452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.100285 restraints weight = 123422.091| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.11 r_work: 0.3361 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 51362 Z= 0.512 Angle : 0.746 15.839 69523 Z= 0.392 Chirality : 0.050 0.260 7874 Planarity : 0.006 0.093 9037 Dihedral : 7.138 69.504 7453 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.22 % Favored : 96.63 % Rotamer: Outliers : 2.96 % Allowed : 11.15 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.10), residues: 6497 helix: 0.41 (0.11), residues: 2341 sheet: 0.37 (0.13), residues: 1326 loop : -0.35 (0.12), residues: 2830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 559 HIS 0.013 0.002 HIS D 258 PHE 0.033 0.003 PHE H 329 TYR 0.028 0.002 TYR B 222 ARG 0.019 0.001 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 524 time to evaluate : 4.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.6803 (OUTLIER) cc_final: 0.6237 (m-30) REVERT: A 188 GLU cc_start: 0.7411 (mm-30) cc_final: 0.6668 (tm-30) REVERT: A 273 GLN cc_start: 0.8342 (tt0) cc_final: 0.8136 (tp-100) REVERT: A 454 THR cc_start: 0.8517 (m) cc_final: 0.8155 (m) REVERT: A 516 MET cc_start: 0.8825 (tpp) cc_final: 0.8450 (pmm) REVERT: A 531 SER cc_start: 0.9044 (m) cc_final: 0.8596 (p) REVERT: A 693 MET cc_start: 0.5057 (mtm) cc_final: 0.4848 (mtm) REVERT: B 95 MET cc_start: 0.9073 (mmm) cc_final: 0.8853 (mmm) REVERT: B 488 GLU cc_start: 0.8762 (tp30) cc_final: 0.8442 (tp30) REVERT: C 64 ASP cc_start: 0.8190 (m-30) cc_final: 0.7833 (m-30) REVERT: C 229 MET cc_start: -0.0501 (tmm) cc_final: -0.3264 (ptm) REVERT: C 231 ILE cc_start: 0.5816 (mm) cc_final: 0.5213 (mt) REVERT: C 448 MET cc_start: 0.7943 (ttm) cc_final: 0.7511 (tmm) REVERT: C 650 MET cc_start: 0.8591 (mmp) cc_final: 0.8358 (mmp) REVERT: C 666 MET cc_start: 0.4018 (ttt) cc_final: 0.3505 (mtt) REVERT: C 693 MET cc_start: 0.3548 (mtp) cc_final: 0.3156 (ttm) REVERT: C 695 MET cc_start: 0.6327 (tpp) cc_final: 0.5336 (ttp) REVERT: E 124 MET cc_start: 0.7062 (pmm) cc_final: 0.6537 (pmm) REVERT: E 271 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7580 (mt-10) REVERT: E 288 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.7452 (ptp-110) REVERT: E 448 MET cc_start: 0.8643 (ttm) cc_final: 0.8190 (tpp) REVERT: E 466 MET cc_start: 0.8541 (tpp) cc_final: 0.8105 (tpt) REVERT: E 666 MET cc_start: 0.4804 (ttt) cc_final: 0.3062 (tpp) REVERT: E 693 MET cc_start: 0.6709 (tpp) cc_final: 0.6275 (ttm) REVERT: E 699 MET cc_start: 0.2570 (mtp) cc_final: 0.2329 (ptp) REVERT: F 58 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: F 95 MET cc_start: 0.6110 (mmm) cc_final: 0.5812 (mmt) REVERT: F 253 MET cc_start: 0.8345 (ttt) cc_final: 0.8030 (tpt) REVERT: G 566 HIS cc_start: 0.6280 (m-70) cc_final: 0.6030 (t-90) REVERT: G 650 MET cc_start: 0.8694 (mmp) cc_final: 0.8471 (mmp) REVERT: H 95 MET cc_start: 0.8805 (mmp) cc_final: 0.8360 (mmt) REVERT: H 504 ASP cc_start: 0.7985 (t0) cc_final: 0.7578 (t70) REVERT: I 74 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8316 (pt) REVERT: I 124 MET cc_start: 0.8580 (pmm) cc_final: 0.7063 (mtm) REVERT: I 358 HIS cc_start: 0.8533 (p-80) cc_final: 0.8047 (p90) REVERT: I 549 MET cc_start: 0.8474 (tpt) cc_final: 0.7952 (mmt) REVERT: I 666 MET cc_start: 0.4101 (mmp) cc_final: 0.3782 (mmm) REVERT: I 693 MET cc_start: 0.7579 (mpp) cc_final: 0.7366 (mpp) REVERT: K 88 LYS cc_start: 0.7712 (mmtm) cc_final: 0.7422 (mmmt) REVERT: K 97 ASP cc_start: 0.8160 (m-30) cc_final: 0.7425 (t0) REVERT: K 174 MET cc_start: 0.7953 (mmm) cc_final: 0.7342 (mmm) REVERT: K 217 MET cc_start: -0.4919 (ttt) cc_final: -0.5378 (ptm) REVERT: K 259 LEU cc_start: 0.5370 (mt) cc_final: 0.5000 (tp) REVERT: K 316 MET cc_start: 0.4448 (mmp) cc_final: 0.3820 (mmt) REVERT: K 350 MET cc_start: 0.8137 (tmm) cc_final: 0.7669 (tmm) REVERT: K 352 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7922 (t) REVERT: K 399 ARG cc_start: 0.7440 (mtp180) cc_final: 0.7222 (mtp85) REVERT: K 459 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6522 (tmt90) REVERT: K 653 LYS cc_start: 0.4088 (pttt) cc_final: 0.3821 (pttp) REVERT: L 101 LYS cc_start: 0.7460 (mmmt) cc_final: 0.6997 (mmtt) REVERT: L 316 MET cc_start: 0.8085 (ttm) cc_final: 0.7847 (ttm) outliers start: 160 outliers final: 98 residues processed: 632 average time/residue: 0.4662 time to fit residues: 501.6582 Evaluate side-chains 557 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 454 time to evaluate : 4.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 566 HIS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain E residue 281 ASN Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 588 SER Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 654 VAL Chi-restraints excluded: chain E residue 669 VAL Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 516 CYS Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 547 SER Chi-restraints excluded: chain G residue 549 MET Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 607 VAL Chi-restraints excluded: chain G residue 653 LYS Chi-restraints excluded: chain H residue 390 THR Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 537 ILE Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 288 ARG Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 468 ASP Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 697 ASN Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 519 LEU Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 147 SER Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 352 THR Chi-restraints excluded: chain K residue 432 ASP Chi-restraints excluded: chain K residue 435 ILE Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 501 THR Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 575 SER Chi-restraints excluded: chain K residue 603 LEU Chi-restraints excluded: chain K residue 616 CYS Chi-restraints excluded: chain K residue 671 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 311 THR Chi-restraints excluded: chain L residue 390 THR Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 516 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 366 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 92 optimal weight: 0.0970 chunk 128 optimal weight: 5.9990 chunk 279 optimal weight: 0.9980 chunk 321 optimal weight: 1.9990 chunk 515 optimal weight: 0.6980 chunk 635 optimal weight: 0.7980 chunk 345 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 285 optimal weight: 8.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN A 371 GLN B 446 HIS C 102 HIS ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 528 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 452 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.142528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.105373 restraints weight = 126435.852| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.19 r_work: 0.3438 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 51362 Z= 0.176 Angle : 0.577 14.568 69523 Z= 0.300 Chirality : 0.044 0.211 7874 Planarity : 0.004 0.090 9037 Dihedral : 6.723 76.335 7453 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.76 % Favored : 97.09 % Rotamer: Outliers : 2.09 % Allowed : 12.30 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.10), residues: 6497 helix: 0.81 (0.11), residues: 2342 sheet: 0.62 (0.14), residues: 1331 loop : -0.31 (0.12), residues: 2824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 559 HIS 0.011 0.001 HIS E 358 PHE 0.021 0.001 PHE K 345 TYR 0.016 0.001 TYR K 346 ARG 0.006 0.000 ARG I 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 535 time to evaluate : 4.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6163 (m-30) REVERT: A 128 MET cc_start: 0.8511 (mmm) cc_final: 0.8032 (mmm) REVERT: A 454 THR cc_start: 0.8305 (m) cc_final: 0.7941 (m) REVERT: A 455 TYR cc_start: 0.7853 (p90) cc_final: 0.7575 (p90) REVERT: A 473 TYR cc_start: 0.7002 (OUTLIER) cc_final: 0.5928 (t80) REVERT: A 516 MET cc_start: 0.8799 (tpp) cc_final: 0.8323 (pmm) REVERT: A 531 SER cc_start: 0.8926 (m) cc_final: 0.8531 (p) REVERT: A 693 MET cc_start: 0.5164 (mtm) cc_final: 0.4821 (mtm) REVERT: B 95 MET cc_start: 0.9056 (mmm) cc_final: 0.8729 (mmm) REVERT: B 488 GLU cc_start: 0.8723 (tp30) cc_final: 0.8326 (tp30) REVERT: C 64 ASP cc_start: 0.8193 (m-30) cc_final: 0.7885 (m-30) REVERT: C 152 PHE cc_start: 0.8904 (t80) cc_final: 0.8420 (t80) REVERT: C 229 MET cc_start: -0.1328 (tmm) cc_final: -0.3190 (ptm) REVERT: C 231 ILE cc_start: 0.5876 (mm) cc_final: 0.5286 (mt) REVERT: C 666 MET cc_start: 0.3942 (ttt) cc_final: 0.3533 (mtt) REVERT: C 693 MET cc_start: 0.3700 (mtp) cc_final: 0.3396 (ttp) REVERT: C 699 MET cc_start: 0.5778 (mmp) cc_final: 0.5422 (ptt) REVERT: E 124 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6713 (pmm) REVERT: E 174 MET cc_start: 0.7097 (tpt) cc_final: 0.6847 (tpp) REVERT: E 288 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.7376 (mtm-85) REVERT: E 466 MET cc_start: 0.8506 (tpp) cc_final: 0.8015 (tpt) REVERT: E 666 MET cc_start: 0.4598 (ttt) cc_final: 0.2606 (mmp) REVERT: E 699 MET cc_start: 0.2667 (OUTLIER) cc_final: 0.2432 (ptp) REVERT: F 83 ASP cc_start: 0.8364 (m-30) cc_final: 0.7878 (t0) REVERT: F 95 MET cc_start: 0.6027 (mmm) cc_final: 0.5650 (mmt) REVERT: F 253 MET cc_start: 0.8343 (ttt) cc_final: 0.8047 (tpt) REVERT: F 504 ASP cc_start: 0.8885 (t0) cc_final: 0.8613 (t70) REVERT: G 522 LYS cc_start: 0.8744 (mtmt) cc_final: 0.8439 (mttt) REVERT: G 566 HIS cc_start: 0.6119 (m-70) cc_final: 0.5878 (t-90) REVERT: G 610 THR cc_start: 0.7720 (OUTLIER) cc_final: 0.7430 (p) REVERT: G 650 MET cc_start: 0.8666 (mmp) cc_final: 0.8452 (mmp) REVERT: H 504 ASP cc_start: 0.7878 (t0) cc_final: 0.7392 (t0) REVERT: I 74 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8279 (pt) REVERT: I 124 MET cc_start: 0.8633 (pmm) cc_final: 0.7307 (mtm) REVERT: I 191 THR cc_start: 0.5701 (OUTLIER) cc_final: 0.5275 (p) REVERT: I 358 HIS cc_start: 0.8620 (p-80) cc_final: 0.8289 (p90) REVERT: I 531 SER cc_start: 0.8644 (t) cc_final: 0.8119 (p) REVERT: I 636 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8600 (t) REVERT: I 666 MET cc_start: 0.4175 (mmp) cc_final: 0.3879 (mmm) REVERT: I 693 MET cc_start: 0.7543 (mpp) cc_final: 0.7312 (mpp) REVERT: J 308 LEU cc_start: 0.8494 (mp) cc_final: 0.7914 (tt) REVERT: K 88 LYS cc_start: 0.7510 (mmtm) cc_final: 0.7217 (mmtm) REVERT: K 97 ASP cc_start: 0.7933 (m-30) cc_final: 0.7281 (t0) REVERT: K 152 PHE cc_start: 0.8647 (m-80) cc_final: 0.8006 (m-80) REVERT: K 174 MET cc_start: 0.7825 (mmm) cc_final: 0.7550 (mmm) REVERT: K 217 MET cc_start: -0.4871 (ttt) cc_final: -0.5297 (ptm) REVERT: K 316 MET cc_start: 0.4318 (mmp) cc_final: 0.3714 (mmt) REVERT: K 350 MET cc_start: 0.8251 (tmm) cc_final: 0.7542 (tmm) REVERT: K 466 MET cc_start: 0.7572 (tpp) cc_final: 0.6946 (tpt) outliers start: 113 outliers final: 75 residues processed: 613 average time/residue: 0.4772 time to fit residues: 498.7252 Evaluate side-chains 566 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 483 time to evaluate : 4.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 566 HIS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 566 HIS Chi-restraints excluded: chain E residue 588 SER Chi-restraints excluded: chain E residue 603 LEU Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 699 MET Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 516 CYS Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 547 SER Chi-restraints excluded: chain G residue 549 MET Chi-restraints excluded: chain G residue 576 ASN Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 607 VAL Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain H residue 244 LEU Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 636 VAL Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 519 LEU Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 369 LEU Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 432 ASP Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 603 LEU Chi-restraints excluded: chain K residue 671 VAL Chi-restraints excluded: chain L residue 197 MET Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 390 THR Chi-restraints excluded: chain L residue 511 THR Chi-restraints excluded: chain L residue 516 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 380 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 101 optimal weight: 0.1980 chunk 596 optimal weight: 0.6980 chunk 500 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 533 optimal weight: 5.9990 chunk 309 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 581 optimal weight: 0.0020 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN B 446 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 GLN G 647 ASN H 483 GLN I 169 HIS K 102 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.139651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.100014 restraints weight = 121729.809| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.41 r_work: 0.3480 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 51362 Z= 0.155 Angle : 0.554 14.147 69523 Z= 0.286 Chirality : 0.044 0.239 7874 Planarity : 0.004 0.078 9037 Dihedral : 6.463 78.593 7449 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.92 % Favored : 96.94 % Rotamer: Outliers : 2.07 % Allowed : 12.65 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.11), residues: 6497 helix: 1.00 (0.11), residues: 2348 sheet: 0.74 (0.14), residues: 1346 loop : -0.32 (0.12), residues: 2803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 559 HIS 0.008 0.001 HIS E 358 PHE 0.021 0.001 PHE I 503 TYR 0.017 0.001 TYR A 455 ARG 0.007 0.000 ARG F 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 533 time to evaluate : 4.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7881 (tm-30) REVERT: A 149 ASN cc_start: 0.6565 (t0) cc_final: 0.5941 (t0) REVERT: A 152 PHE cc_start: 0.7792 (t80) cc_final: 0.7420 (t80) REVERT: A 454 THR cc_start: 0.8375 (m) cc_final: 0.8035 (m) REVERT: A 455 TYR cc_start: 0.7890 (p90) cc_final: 0.7655 (p90) REVERT: A 693 MET cc_start: 0.5380 (mtm) cc_final: 0.4769 (mtm) REVERT: B 95 MET cc_start: 0.9102 (mmm) cc_final: 0.8696 (mmm) REVERT: B 466 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8796 (mtpp) REVERT: B 488 GLU cc_start: 0.8724 (tp30) cc_final: 0.8282 (tp30) REVERT: C 64 ASP cc_start: 0.8078 (m-30) cc_final: 0.7787 (m-30) REVERT: C 124 MET cc_start: 0.8265 (pmm) cc_final: 0.8017 (mtm) REVERT: C 229 MET cc_start: -0.1423 (tmm) cc_final: -0.3006 (ptm) REVERT: C 231 ILE cc_start: 0.5920 (mm) cc_final: 0.5352 (mt) REVERT: C 666 MET cc_start: 0.3330 (ttt) cc_final: 0.3038 (mtt) REVERT: C 699 MET cc_start: 0.5904 (mmp) cc_final: 0.5474 (ptt) REVERT: E 124 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6829 (pmm) REVERT: E 174 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6841 (tpp) REVERT: E 288 ARG cc_start: 0.7635 (mtm-85) cc_final: 0.7396 (mtm-85) REVERT: E 466 MET cc_start: 0.8580 (tpp) cc_final: 0.8064 (tpt) REVERT: E 666 MET cc_start: 0.4930 (ttt) cc_final: 0.2816 (mmp) REVERT: E 699 MET cc_start: 0.2776 (OUTLIER) cc_final: 0.2523 (ptp) REVERT: F 83 ASP cc_start: 0.8240 (m-30) cc_final: 0.7772 (t0) REVERT: F 95 MET cc_start: 0.6206 (mmm) cc_final: 0.5849 (mmt) REVERT: F 253 MET cc_start: 0.8355 (ttt) cc_final: 0.8075 (tpt) REVERT: F 442 MET cc_start: 0.8798 (mmm) cc_final: 0.8293 (mmm) REVERT: F 504 ASP cc_start: 0.8727 (t0) cc_final: 0.8509 (t70) REVERT: G 522 LYS cc_start: 0.8724 (mtmt) cc_final: 0.8422 (mttt) REVERT: G 577 ASN cc_start: 0.8184 (t0) cc_final: 0.7886 (t0) REVERT: G 610 THR cc_start: 0.7706 (m) cc_final: 0.7450 (p) REVERT: H 504 ASP cc_start: 0.7755 (t0) cc_final: 0.7259 (t0) REVERT: I 74 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8349 (pt) REVERT: I 124 MET cc_start: 0.8571 (pmm) cc_final: 0.7465 (mtm) REVERT: I 531 SER cc_start: 0.8538 (t) cc_final: 0.8036 (p) REVERT: I 666 MET cc_start: 0.4488 (mmp) cc_final: 0.4211 (mmm) REVERT: I 693 MET cc_start: 0.7642 (mpp) cc_final: 0.7398 (mpp) REVERT: J 147 GLN cc_start: 0.8695 (mt0) cc_final: 0.8310 (tt0) REVERT: J 308 LEU cc_start: 0.8462 (mp) cc_final: 0.7870 (tt) REVERT: K 88 LYS cc_start: 0.7397 (mmtm) cc_final: 0.7182 (mmtm) REVERT: K 97 ASP cc_start: 0.7978 (m-30) cc_final: 0.7308 (t0) REVERT: K 152 PHE cc_start: 0.8396 (m-80) cc_final: 0.7954 (m-80) REVERT: K 174 MET cc_start: 0.7797 (mmm) cc_final: 0.7593 (mmm) REVERT: K 217 MET cc_start: -0.4851 (ttt) cc_final: -0.5240 (ptm) REVERT: K 316 MET cc_start: 0.4716 (mmp) cc_final: 0.4406 (mmt) REVERT: K 350 MET cc_start: 0.8294 (tmm) cc_final: 0.7498 (tmm) REVERT: K 373 MET cc_start: 0.8541 (mtm) cc_final: 0.8330 (mtm) REVERT: K 466 MET cc_start: 0.7547 (tpp) cc_final: 0.6935 (tpt) REVERT: K 496 LYS cc_start: 0.7822 (ttpp) cc_final: 0.7515 (ttpp) REVERT: K 549 MET cc_start: 0.8485 (tpp) cc_final: 0.8103 (mtp) REVERT: L 101 LYS cc_start: 0.7317 (mmtt) cc_final: 0.6793 (mmtt) outliers start: 112 outliers final: 89 residues processed: 613 average time/residue: 0.4646 time to fit residues: 489.7008 Evaluate side-chains 580 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 486 time to evaluate : 4.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 466 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 566 HIS Chi-restraints excluded: chain E residue 588 SER Chi-restraints excluded: chain E residue 603 LEU Chi-restraints excluded: chain E residue 699 MET Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 516 CYS Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 547 SER Chi-restraints excluded: chain G residue 549 MET Chi-restraints excluded: chain G residue 576 ASN Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 607 VAL Chi-restraints excluded: chain G residue 647 ASN Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 636 VAL Chi-restraints excluded: chain I residue 640 THR Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 310 SER Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 519 LEU Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 369 LEU Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 432 ASP Chi-restraints excluded: chain K residue 452 LEU Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 648 LYS Chi-restraints excluded: chain K residue 671 VAL Chi-restraints excluded: chain L residue 197 MET Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 390 THR Chi-restraints excluded: chain L residue 516 CYS Chi-restraints excluded: chain L residue 537 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 589 optimal weight: 20.0000 chunk 484 optimal weight: 4.9990 chunk 300 optimal weight: 0.8980 chunk 177 optimal weight: 7.9990 chunk 624 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 592 optimal weight: 0.0030 chunk 457 optimal weight: 3.9990 chunk 327 optimal weight: 0.9990 chunk 202 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN B 446 HIS C 371 GLN D 528 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.142502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.105561 restraints weight = 127018.365| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.08 r_work: 0.3435 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 51362 Z= 0.211 Angle : 0.572 13.882 69523 Z= 0.295 Chirality : 0.044 0.220 7874 Planarity : 0.004 0.065 9037 Dihedral : 6.445 79.165 7449 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 2.39 % Allowed : 13.13 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.11), residues: 6497 helix: 1.06 (0.11), residues: 2347 sheet: 0.61 (0.14), residues: 1335 loop : -0.33 (0.12), residues: 2815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 559 HIS 0.009 0.001 HIS E 358 PHE 0.022 0.001 PHE B 93 TYR 0.017 0.001 TYR D 417 ARG 0.014 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 496 time to evaluate : 4.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.6153 (m-30) REVERT: A 124 MET cc_start: 0.8728 (tpp) cc_final: 0.8235 (tpp) REVERT: A 128 MET cc_start: 0.8452 (mmm) cc_final: 0.8113 (mmm) REVERT: A 129 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7908 (tm-30) REVERT: A 149 ASN cc_start: 0.6448 (t0) cc_final: 0.6156 (t0) REVERT: A 152 PHE cc_start: 0.7787 (t80) cc_final: 0.7515 (t80) REVERT: A 269 HIS cc_start: 0.7442 (m90) cc_final: 0.7162 (m-70) REVERT: A 454 THR cc_start: 0.8364 (m) cc_final: 0.8018 (m) REVERT: A 455 TYR cc_start: 0.7868 (p90) cc_final: 0.7645 (p90) REVERT: A 473 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.5969 (t80) REVERT: A 516 MET cc_start: 0.8701 (tpp) cc_final: 0.8455 (pmm) REVERT: A 531 SER cc_start: 0.8877 (m) cc_final: 0.8490 (p) REVERT: A 693 MET cc_start: 0.5428 (mtm) cc_final: 0.4802 (mtm) REVERT: B 95 MET cc_start: 0.9117 (mmm) cc_final: 0.8861 (mmm) REVERT: B 488 GLU cc_start: 0.8770 (tp30) cc_final: 0.8376 (tp30) REVERT: C 64 ASP cc_start: 0.8124 (m-30) cc_final: 0.7835 (m-30) REVERT: C 124 MET cc_start: 0.8349 (pmm) cc_final: 0.8101 (mtm) REVERT: C 229 MET cc_start: -0.1250 (tmm) cc_final: -0.2742 (ptm) REVERT: C 231 ILE cc_start: 0.5933 (mm) cc_final: 0.5401 (mt) REVERT: C 448 MET cc_start: 0.7435 (tmm) cc_final: 0.6875 (ttt) REVERT: C 695 MET cc_start: 0.5956 (tpp) cc_final: 0.4944 (tmm) REVERT: C 696 GLN cc_start: 0.5723 (mm110) cc_final: 0.5412 (mm-40) REVERT: E 124 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6825 (pmm) REVERT: E 174 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6937 (tpp) REVERT: E 288 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.7340 (mtm-85) REVERT: E 466 MET cc_start: 0.8602 (tpp) cc_final: 0.8154 (tpt) REVERT: E 666 MET cc_start: 0.4127 (ttt) cc_final: 0.3521 (mmp) REVERT: E 699 MET cc_start: 0.2549 (OUTLIER) cc_final: 0.2331 (ptp) REVERT: F 83 ASP cc_start: 0.8315 (m-30) cc_final: 0.7925 (t0) REVERT: F 95 MET cc_start: 0.6160 (mmm) cc_final: 0.5776 (mmt) REVERT: F 253 MET cc_start: 0.8445 (ttt) cc_final: 0.8108 (tpt) REVERT: F 504 ASP cc_start: 0.8885 (t0) cc_final: 0.8658 (t70) REVERT: G 522 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8407 (mttt) REVERT: G 549 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6179 (tpt) REVERT: G 560 GLU cc_start: 0.8285 (tt0) cc_final: 0.8063 (tt0) REVERT: G 610 THR cc_start: 0.7616 (m) cc_final: 0.7371 (p) REVERT: H 504 ASP cc_start: 0.7863 (t0) cc_final: 0.7376 (t0) REVERT: I 74 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8290 (pt) REVERT: I 124 MET cc_start: 0.8482 (pmm) cc_final: 0.7291 (mtm) REVERT: I 319 GLN cc_start: 0.6483 (mm-40) cc_final: 0.6039 (pt0) REVERT: I 448 MET cc_start: 0.7918 (tpt) cc_final: 0.7382 (tpt) REVERT: I 531 SER cc_start: 0.8684 (t) cc_final: 0.8135 (p) REVERT: I 666 MET cc_start: 0.4664 (mmp) cc_final: 0.4182 (mtm) REVERT: I 693 MET cc_start: 0.7600 (mpp) cc_final: 0.7355 (mpp) REVERT: J 308 LEU cc_start: 0.8535 (mp) cc_final: 0.7932 (tt) REVERT: K 97 ASP cc_start: 0.8055 (m-30) cc_final: 0.7412 (t0) REVERT: K 152 PHE cc_start: 0.8386 (m-80) cc_final: 0.8050 (m-80) REVERT: K 174 MET cc_start: 0.7873 (mmm) cc_final: 0.7653 (mmm) REVERT: K 217 MET cc_start: -0.4906 (ttt) cc_final: -0.5232 (ptm) REVERT: K 316 MET cc_start: 0.4876 (mmp) cc_final: 0.4561 (mmt) REVERT: K 350 MET cc_start: 0.8209 (tmm) cc_final: 0.7417 (tmm) REVERT: K 373 MET cc_start: 0.8611 (mtm) cc_final: 0.8394 (mtm) REVERT: K 466 MET cc_start: 0.7585 (tpp) cc_final: 0.6975 (tpt) REVERT: K 549 MET cc_start: 0.8581 (tpp) cc_final: 0.8219 (mtp) REVERT: L 101 LYS cc_start: 0.7576 (mmtt) cc_final: 0.6936 (mmtt) outliers start: 129 outliers final: 97 residues processed: 594 average time/residue: 0.4696 time to fit residues: 479.6940 Evaluate side-chains 569 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 465 time to evaluate : 4.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 566 HIS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 281 ASN Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 566 HIS Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 588 SER Chi-restraints excluded: chain E residue 603 LEU Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 699 MET Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 516 CYS Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 547 SER Chi-restraints excluded: chain G residue 549 MET Chi-restraints excluded: chain G residue 576 ASN Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 607 VAL Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 636 VAL Chi-restraints excluded: chain I residue 640 THR Chi-restraints excluded: chain I residue 650 MET Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 519 LEU Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 369 LEU Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 432 ASP Chi-restraints excluded: chain K residue 501 THR Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 603 LEU Chi-restraints excluded: chain K residue 616 CYS Chi-restraints excluded: chain K residue 648 LYS Chi-restraints excluded: chain K residue 671 VAL Chi-restraints excluded: chain L residue 197 MET Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 390 THR Chi-restraints excluded: chain L residue 511 THR Chi-restraints excluded: chain L residue 516 CYS Chi-restraints excluded: chain L residue 537 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 471 optimal weight: 3.9990 chunk 439 optimal weight: 9.9990 chunk 554 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 381 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 615 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 286 ASN B 192 GLN B 241 GLN B 446 HIS ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 HIS D 528 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 ASN G 647 ASN K 102 HIS ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 392 ASN ** K 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.134743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.097883 restraints weight = 126418.595| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.13 r_work: 0.3408 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 51362 Z= 0.304 Angle : 0.605 14.453 69523 Z= 0.314 Chirality : 0.045 0.251 7874 Planarity : 0.004 0.070 9037 Dihedral : 6.560 78.988 7449 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.24 % Rotamer: Outliers : 2.57 % Allowed : 13.10 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.11), residues: 6497 helix: 1.02 (0.11), residues: 2312 sheet: 0.50 (0.14), residues: 1371 loop : -0.43 (0.12), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 559 HIS 0.010 0.001 HIS E 358 PHE 0.024 0.002 PHE B 93 TYR 0.021 0.002 TYR J 176 ARG 0.026 0.001 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 493 time to evaluate : 4.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.6117 (m-30) REVERT: A 124 MET cc_start: 0.8699 (tpp) cc_final: 0.8339 (tpp) REVERT: A 129 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8022 (tm-30) REVERT: A 149 ASN cc_start: 0.6530 (t0) cc_final: 0.6235 (t0) REVERT: A 152 PHE cc_start: 0.7817 (t80) cc_final: 0.7612 (t80) REVERT: A 350 MET cc_start: 0.8629 (tpp) cc_final: 0.8203 (tpp) REVERT: A 394 TRP cc_start: 0.7680 (OUTLIER) cc_final: 0.7320 (t-100) REVERT: A 454 THR cc_start: 0.8416 (m) cc_final: 0.8054 (m) REVERT: A 455 TYR cc_start: 0.7827 (p90) cc_final: 0.7588 (p90) REVERT: A 473 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.6088 (t80) REVERT: A 516 MET cc_start: 0.8761 (tpp) cc_final: 0.8365 (pmm) REVERT: A 531 SER cc_start: 0.8921 (m) cc_final: 0.8508 (p) REVERT: A 693 MET cc_start: 0.5644 (mtm) cc_final: 0.5029 (mtm) REVERT: B 488 GLU cc_start: 0.8725 (tp30) cc_final: 0.8350 (tp30) REVERT: B 518 ASP cc_start: 0.7872 (m-30) cc_final: 0.7658 (m-30) REVERT: C 64 ASP cc_start: 0.8262 (m-30) cc_final: 0.7978 (m-30) REVERT: C 124 MET cc_start: 0.8460 (pmm) cc_final: 0.8175 (mtm) REVERT: C 229 MET cc_start: -0.0822 (tmm) cc_final: -0.2649 (ptm) REVERT: C 231 ILE cc_start: 0.6238 (mm) cc_final: 0.5645 (mt) REVERT: C 394 TRP cc_start: 0.8799 (OUTLIER) cc_final: 0.8485 (t-100) REVERT: C 448 MET cc_start: 0.7776 (tmm) cc_final: 0.7223 (ttt) REVERT: C 695 MET cc_start: 0.5964 (tpp) cc_final: 0.4846 (ttp) REVERT: E 124 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6899 (pmm) REVERT: E 174 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6804 (tpp) REVERT: E 217 MET cc_start: -0.1228 (ttt) cc_final: -0.1640 (ttt) REVERT: E 289 GLU cc_start: 0.7905 (tt0) cc_final: 0.6969 (tm-30) REVERT: E 342 LYS cc_start: 0.8208 (mttt) cc_final: 0.7850 (tttt) REVERT: E 466 MET cc_start: 0.8523 (tpp) cc_final: 0.8059 (tpt) REVERT: E 666 MET cc_start: 0.4858 (ttt) cc_final: 0.3538 (mmp) REVERT: E 699 MET cc_start: 0.3388 (OUTLIER) cc_final: 0.3039 (ptp) REVERT: F 83 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8025 (t0) REVERT: F 95 MET cc_start: 0.6277 (mmm) cc_final: 0.6035 (mmt) REVERT: F 253 MET cc_start: 0.8447 (ttt) cc_final: 0.8098 (tpt) REVERT: G 522 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8414 (mttt) REVERT: G 610 THR cc_start: 0.7628 (m) cc_final: 0.7383 (p) REVERT: H 504 ASP cc_start: 0.7915 (t0) cc_final: 0.7631 (t0) REVERT: I 74 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8336 (pt) REVERT: I 124 MET cc_start: 0.8491 (pmm) cc_final: 0.7262 (mtm) REVERT: I 426 LEU cc_start: 0.8785 (mt) cc_final: 0.8104 (tt) REVERT: I 448 MET cc_start: 0.7816 (tpt) cc_final: 0.7493 (tpt) REVERT: I 666 MET cc_start: 0.4672 (mmp) cc_final: 0.4217 (mtm) REVERT: I 693 MET cc_start: 0.7818 (mpp) cc_final: 0.7591 (mpp) REVERT: J 308 LEU cc_start: 0.8534 (mp) cc_final: 0.7895 (tt) REVERT: K 97 ASP cc_start: 0.7905 (m-30) cc_final: 0.7318 (t0) REVERT: K 152 PHE cc_start: 0.8294 (m-80) cc_final: 0.7926 (m-80) REVERT: K 174 MET cc_start: 0.7992 (mmm) cc_final: 0.7682 (mmm) REVERT: K 217 MET cc_start: -0.4137 (ttt) cc_final: -0.4954 (ptm) REVERT: K 316 MET cc_start: 0.4806 (mmp) cc_final: 0.4537 (mmt) REVERT: K 350 MET cc_start: 0.8206 (tmm) cc_final: 0.7369 (tmm) REVERT: K 473 TYR cc_start: 0.7137 (OUTLIER) cc_final: 0.6334 (t80) REVERT: L 101 LYS cc_start: 0.7826 (mmtt) cc_final: 0.7064 (mmtt) outliers start: 139 outliers final: 106 residues processed: 594 average time/residue: 0.4770 time to fit residues: 485.4698 Evaluate side-chains 580 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 464 time to evaluate : 4.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 566 HIS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 625 MET Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 394 TRP Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 281 ASN Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 588 SER Chi-restraints excluded: chain E residue 603 LEU Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 699 MET Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 516 CYS Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 547 SER Chi-restraints excluded: chain G residue 549 MET Chi-restraints excluded: chain G residue 576 ASN Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 607 VAL Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 636 VAL Chi-restraints excluded: chain I residue 650 MET Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 310 SER Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 519 LEU Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 432 ASP Chi-restraints excluded: chain K residue 435 ILE Chi-restraints excluded: chain K residue 473 TYR Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 603 LEU Chi-restraints excluded: chain K residue 616 CYS Chi-restraints excluded: chain K residue 648 LYS Chi-restraints excluded: chain K residue 671 VAL Chi-restraints excluded: chain L residue 197 MET Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 390 THR Chi-restraints excluded: chain L residue 511 THR Chi-restraints excluded: chain L residue 516 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 509 optimal weight: 2.9990 chunk 627 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 318 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 294 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 445 optimal weight: 4.9990 chunk 293 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 GLN ** K 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.139490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.102456 restraints weight = 126163.505| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.18 r_work: 0.3407 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 51362 Z= 0.222 Angle : 0.584 14.472 69523 Z= 0.302 Chirality : 0.044 0.258 7874 Planarity : 0.004 0.077 9037 Dihedral : 6.493 81.319 7449 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.58 % Rotamer: Outliers : 2.22 % Allowed : 13.82 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.11), residues: 6497 helix: 1.03 (0.11), residues: 2337 sheet: 0.61 (0.14), residues: 1315 loop : -0.49 (0.12), residues: 2845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 559 HIS 0.008 0.001 HIS E 358 PHE 0.027 0.001 PHE B 93 TYR 0.021 0.001 TYR J 176 ARG 0.012 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 493 time to evaluate : 4.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.6460 (OUTLIER) cc_final: 0.6002 (m-30) REVERT: A 129 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7963 (tm-30) REVERT: A 149 ASN cc_start: 0.6587 (t0) cc_final: 0.6228 (t0) REVERT: A 152 PHE cc_start: 0.7928 (t80) cc_final: 0.7532 (t80) REVERT: A 350 MET cc_start: 0.8555 (tpp) cc_final: 0.8082 (tpp) REVERT: A 373 MET cc_start: 0.7391 (mmp) cc_final: 0.7183 (mmm) REVERT: A 394 TRP cc_start: 0.7667 (OUTLIER) cc_final: 0.7277 (t-100) REVERT: A 449 ILE cc_start: 0.8897 (mm) cc_final: 0.8480 (mt) REVERT: A 454 THR cc_start: 0.8439 (m) cc_final: 0.8098 (m) REVERT: A 455 TYR cc_start: 0.7831 (p90) cc_final: 0.7620 (p90) REVERT: A 473 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.6089 (t80) REVERT: A 516 MET cc_start: 0.8831 (tpp) cc_final: 0.8406 (pmm) REVERT: A 531 SER cc_start: 0.8907 (m) cc_final: 0.8509 (p) REVERT: A 693 MET cc_start: 0.5481 (mtm) cc_final: 0.4842 (mtm) REVERT: B 488 GLU cc_start: 0.8649 (tp30) cc_final: 0.8259 (tp30) REVERT: B 518 ASP cc_start: 0.8043 (m-30) cc_final: 0.7837 (m-30) REVERT: C 64 ASP cc_start: 0.8195 (m-30) cc_final: 0.7905 (m-30) REVERT: C 124 MET cc_start: 0.8328 (pmm) cc_final: 0.8097 (mtm) REVERT: C 229 MET cc_start: -0.1228 (tmm) cc_final: -0.2634 (ptm) REVERT: C 231 ILE cc_start: 0.5987 (mm) cc_final: 0.5450 (mt) REVERT: C 394 TRP cc_start: 0.8826 (OUTLIER) cc_final: 0.8460 (t-100) REVERT: C 448 MET cc_start: 0.7797 (tmm) cc_final: 0.7182 (ttt) REVERT: C 695 MET cc_start: 0.5734 (tpp) cc_final: 0.4816 (ttp) REVERT: C 699 MET cc_start: 0.5998 (mmp) cc_final: 0.5656 (ptt) REVERT: D 84 MET cc_start: 0.7296 (pmm) cc_final: 0.6872 (pmm) REVERT: E 124 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6866 (pmm) REVERT: E 174 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6881 (tpp) REVERT: E 289 GLU cc_start: 0.7911 (tt0) cc_final: 0.6898 (tm-30) REVERT: E 342 LYS cc_start: 0.8198 (mttt) cc_final: 0.7847 (tttt) REVERT: E 466 MET cc_start: 0.8510 (tpp) cc_final: 0.8067 (tpt) REVERT: E 666 MET cc_start: 0.4539 (ttt) cc_final: 0.3416 (mmp) REVERT: E 699 MET cc_start: 0.2599 (OUTLIER) cc_final: 0.2332 (ptp) REVERT: F 83 ASP cc_start: 0.8364 (m-30) cc_final: 0.7958 (t0) REVERT: F 95 MET cc_start: 0.6182 (mmm) cc_final: 0.5911 (mmt) REVERT: F 253 MET cc_start: 0.8456 (ttt) cc_final: 0.8074 (tpt) REVERT: G 522 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8442 (mttt) REVERT: G 610 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.7341 (p) REVERT: H 504 ASP cc_start: 0.7925 (t0) cc_final: 0.7636 (t0) REVERT: I 74 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8275 (pt) REVERT: I 85 MET cc_start: 0.7151 (mtp) cc_final: 0.6925 (mtp) REVERT: I 124 MET cc_start: 0.8491 (pmm) cc_final: 0.7303 (mtm) REVERT: I 287 GLU cc_start: 0.4355 (pm20) cc_final: 0.3962 (pm20) REVERT: I 531 SER cc_start: 0.8671 (t) cc_final: 0.8111 (p) REVERT: I 666 MET cc_start: 0.4472 (mmp) cc_final: 0.4042 (mtt) REVERT: I 693 MET cc_start: 0.7665 (mpp) cc_final: 0.7401 (mpp) REVERT: J 308 LEU cc_start: 0.8557 (mp) cc_final: 0.7932 (tt) REVERT: K 97 ASP cc_start: 0.7880 (m-30) cc_final: 0.7179 (t0) REVERT: K 152 PHE cc_start: 0.8235 (m-80) cc_final: 0.7811 (m-80) REVERT: K 174 MET cc_start: 0.7909 (mmm) cc_final: 0.7641 (mmm) REVERT: K 350 MET cc_start: 0.8203 (tmm) cc_final: 0.7339 (tmm) REVERT: L 101 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7043 (mmtt) outliers start: 120 outliers final: 98 residues processed: 586 average time/residue: 0.4569 time to fit residues: 460.4477 Evaluate side-chains 570 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 463 time to evaluate : 4.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 566 HIS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 394 TRP Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 281 ASN Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 588 SER Chi-restraints excluded: chain E residue 603 LEU Chi-restraints excluded: chain E residue 613 THR Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 699 MET Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 516 CYS Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 547 SER Chi-restraints excluded: chain G residue 549 MET Chi-restraints excluded: chain G residue 576 ASN Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 607 VAL Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 636 VAL Chi-restraints excluded: chain I residue 650 MET Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 310 SER Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 519 LEU Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 432 ASP Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 603 LEU Chi-restraints excluded: chain K residue 616 CYS Chi-restraints excluded: chain K residue 648 LYS Chi-restraints excluded: chain K residue 671 VAL Chi-restraints excluded: chain L residue 197 MET Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 390 THR Chi-restraints excluded: chain L residue 511 THR Chi-restraints excluded: chain L residue 516 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 183 optimal weight: 10.0000 chunk 308 optimal weight: 2.9990 chunk 309 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 390 optimal weight: 0.8980 chunk 479 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 chunk 608 optimal weight: 0.5980 chunk 473 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN D 41 ASN D 528 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 169 HIS I 269 HIS K 273 GLN ** K 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 536 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.141829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.105152 restraints weight = 126906.608| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.15 r_work: 0.3429 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 51362 Z= 0.174 Angle : 0.580 14.793 69523 Z= 0.297 Chirality : 0.044 0.276 7874 Planarity : 0.004 0.081 9037 Dihedral : 6.393 82.361 7449 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.42 % Favored : 96.51 % Rotamer: Outliers : 2.09 % Allowed : 14.02 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.11), residues: 6497 helix: 1.11 (0.11), residues: 2337 sheet: 0.60 (0.14), residues: 1315 loop : -0.42 (0.12), residues: 2845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 559 HIS 0.008 0.001 HIS K 358 PHE 0.039 0.001 PHE L 380 TYR 0.024 0.001 TYR J 176 ARG 0.010 0.000 ARG A 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12994 Ramachandran restraints generated. 6497 Oldfield, 0 Emsley, 6497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 497 time to evaluate : 4.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.6422 (OUTLIER) cc_final: 0.5968 (m-30) REVERT: A 124 MET cc_start: 0.8773 (tpp) cc_final: 0.8391 (tpp) REVERT: A 149 ASN cc_start: 0.6452 (t0) cc_final: 0.6111 (t0) REVERT: A 152 PHE cc_start: 0.8038 (t80) cc_final: 0.7439 (t80) REVERT: A 229 MET cc_start: -0.0625 (tpp) cc_final: -0.1299 (tpp) REVERT: A 350 MET cc_start: 0.8525 (tpp) cc_final: 0.8037 (tpp) REVERT: A 373 MET cc_start: 0.7384 (mmp) cc_final: 0.7154 (mmm) REVERT: A 394 TRP cc_start: 0.7644 (OUTLIER) cc_final: 0.7290 (t-100) REVERT: A 451 LYS cc_start: 0.8399 (mtpt) cc_final: 0.8028 (mtmm) REVERT: A 454 THR cc_start: 0.8437 (m) cc_final: 0.8111 (m) REVERT: A 473 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.5921 (t80) REVERT: A 516 MET cc_start: 0.8836 (tpp) cc_final: 0.8418 (pmm) REVERT: A 531 SER cc_start: 0.8873 (m) cc_final: 0.8482 (p) REVERT: A 693 MET cc_start: 0.5429 (mtm) cc_final: 0.4805 (mtm) REVERT: B 488 GLU cc_start: 0.8646 (tp30) cc_final: 0.8256 (tp30) REVERT: C 64 ASP cc_start: 0.8186 (m-30) cc_final: 0.7904 (m-30) REVERT: C 124 MET cc_start: 0.8282 (pmm) cc_final: 0.8050 (mtm) REVERT: C 229 MET cc_start: -0.1094 (tmm) cc_final: -0.2446 (ptm) REVERT: C 231 ILE cc_start: 0.6105 (mm) cc_final: 0.5612 (mt) REVERT: C 394 TRP cc_start: 0.8840 (OUTLIER) cc_final: 0.8441 (t-100) REVERT: C 448 MET cc_start: 0.7801 (tmm) cc_final: 0.7213 (ttt) REVERT: C 695 MET cc_start: 0.5545 (tpp) cc_final: 0.4702 (ttp) REVERT: C 699 MET cc_start: 0.6006 (mmp) cc_final: 0.5657 (ptt) REVERT: D 84 MET cc_start: 0.7410 (pmm) cc_final: 0.6983 (pmm) REVERT: E 124 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6877 (pmm) REVERT: E 174 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6834 (tpp) REVERT: E 289 GLU cc_start: 0.7879 (tt0) cc_final: 0.6979 (tm-30) REVERT: E 342 LYS cc_start: 0.8163 (mttt) cc_final: 0.7820 (tttt) REVERT: E 466 MET cc_start: 0.8526 (tpp) cc_final: 0.7832 (tpp) REVERT: E 666 MET cc_start: 0.4753 (ttt) cc_final: 0.3345 (mmp) REVERT: F 83 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7917 (t0) REVERT: F 95 MET cc_start: 0.6131 (mmm) cc_final: 0.5858 (mmt) REVERT: F 253 MET cc_start: 0.8461 (ttt) cc_final: 0.8077 (tpt) REVERT: G 577 ASN cc_start: 0.8125 (t0) cc_final: 0.7880 (t0) REVERT: H 504 ASP cc_start: 0.7878 (t0) cc_final: 0.7587 (t0) REVERT: I 74 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8249 (pt) REVERT: I 124 MET cc_start: 0.8491 (pmm) cc_final: 0.7291 (mtm) REVERT: I 271 GLU cc_start: 0.4825 (mt-10) cc_final: 0.4462 (mp0) REVERT: I 287 GLU cc_start: 0.4253 (pm20) cc_final: 0.3966 (pm20) REVERT: I 426 LEU cc_start: 0.8665 (mt) cc_final: 0.8049 (tt) REVERT: I 531 SER cc_start: 0.8571 (t) cc_final: 0.8028 (p) REVERT: I 666 MET cc_start: 0.4523 (mmp) cc_final: 0.4095 (mtt) REVERT: I 693 MET cc_start: 0.7725 (mpp) cc_final: 0.7432 (mpp) REVERT: J 242 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7978 (pp20) REVERT: J 308 LEU cc_start: 0.8575 (mp) cc_final: 0.7960 (tt) REVERT: K 97 ASP cc_start: 0.7833 (m-30) cc_final: 0.7155 (t0) REVERT: K 151 GLU cc_start: 0.8781 (pm20) cc_final: 0.8519 (pm20) REVERT: K 152 PHE cc_start: 0.8205 (m-80) cc_final: 0.7584 (m-80) REVERT: K 174 MET cc_start: 0.7871 (mmm) cc_final: 0.7614 (mmm) REVERT: K 350 MET cc_start: 0.8215 (tmm) cc_final: 0.7395 (tmm) REVERT: K 466 MET cc_start: 0.7721 (tpp) cc_final: 0.6863 (tpp) REVERT: L 101 LYS cc_start: 0.7765 (mmtt) cc_final: 0.6979 (mmtt) outliers start: 113 outliers final: 94 residues processed: 578 average time/residue: 0.4648 time to fit residues: 461.6221 Evaluate side-chains 579 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 477 time to evaluate : 4.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 566 HIS Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 699 MET Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 394 TRP Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 445 LYS Chi-restraints excluded: chain D residue 448 CYS Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 281 ASN Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 585 VAL Chi-restraints excluded: chain E residue 588 SER Chi-restraints excluded: chain E residue 603 LEU Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 516 CYS Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 547 SER Chi-restraints excluded: chain G residue 576 ASN Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 607 VAL Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 636 VAL Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain I residue 650 MET Chi-restraints excluded: chain J residue 144 ILE Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 310 SER Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 519 LEU Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain K residue 501 THR Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 603 LEU Chi-restraints excluded: chain K residue 616 CYS Chi-restraints excluded: chain K residue 648 LYS Chi-restraints excluded: chain K residue 671 VAL Chi-restraints excluded: chain L residue 197 MET Chi-restraints excluded: chain L residue 299 VAL Chi-restraints excluded: chain L residue 390 THR Chi-restraints excluded: chain L residue 511 THR Chi-restraints excluded: chain L residue 516 CYS Chi-restraints excluded: chain L residue 537 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 473 optimal weight: 4.9990 chunk 319 optimal weight: 7.9990 chunk 295 optimal weight: 6.9990 chunk 306 optimal weight: 0.6980 chunk 176 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 403 optimal weight: 5.9990 chunk 642 optimal weight: 4.9990 chunk 361 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 483 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.139025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.101676 restraints weight = 121654.658| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.18 r_work: 0.3374 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 51362 Z= 0.311 Angle : 0.633 14.882 69523 Z= 0.326 Chirality : 0.046 0.255 7874 Planarity : 0.005 0.083 9037 Dihedral : 6.513 79.891 7449 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.99 % Favored : 95.94 % Rotamer: Outliers : 2.15 % Allowed : 14.15 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.11), residues: 6497 helix: 0.96 (0.11), residues: 2368 sheet: 0.48 (0.14), residues: 1346 loop : -0.55 (0.12), residues: 2783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 394 HIS 0.011 0.001 HIS K 358 PHE 0.026 0.002 PHE B 93 TYR 0.031 0.002 TYR J 176 ARG 0.013 0.001 ARG A 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24749.93 seconds wall clock time: 425 minutes 17.26 seconds (25517.26 seconds total)