Starting phenix.real_space_refine on Tue Nov 19 00:34:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xl4_38437/11_2024/8xl4_38437.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xl4_38437/11_2024/8xl4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xl4_38437/11_2024/8xl4_38437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xl4_38437/11_2024/8xl4_38437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xl4_38437/11_2024/8xl4_38437.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xl4_38437/11_2024/8xl4_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): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 25.78, per 1000 atoms: 0.51 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: 12.03 Conformation dependent library (CDL) restraints added in 6.4 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: 7.73 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: 29.93 Time building geometry restraints manager: 14.06 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: 6.720 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: 0.040 Extract box with map and model: 1.830 Check model and map are aligned: 0.350 Set scattering table: 0.400 Process input model: 115.490 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.660 ------------------------------------------------------------------------------- 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 : 5.569 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: 0.7208 time to fit residues: 1643.4380 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 : 5.810 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 : 5.265 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: 0.0248 (ttp) cc_final: -0.1015 (ttt) REVERT: A 454 THR cc_start: 0.7586 (m) cc_final: 0.6808 (m) REVERT: A 466 MET cc_start: 0.8375 (mmm) cc_final: 0.7961 (tpt) REVERT: A 566 HIS cc_start: 0.7507 (OUTLIER) cc_final: 0.6089 (m90) REVERT: C 89 THR cc_start: 0.7828 (m) cc_final: 0.7341 (p) REVERT: C 229 MET cc_start: -0.0157 (tmm) cc_final: -0.3263 (ptm) REVERT: C 448 MET cc_start: 0.7405 (ttm) cc_final: 0.6981 (ttt) REVERT: C 696 GLN cc_start: 0.6082 (mm110) cc_final: 0.5838 (mm-40) REVERT: E 186 LYS cc_start: 0.8717 (mttt) cc_final: 0.8474 (pttt) REVERT: E 288 ARG cc_start: 0.6504 (mtm-85) cc_final: 0.6243 (mtm-85) REVERT: E 448 MET cc_start: 0.8425 (ttm) cc_final: 0.8033 (tpp) REVERT: E 466 MET cc_start: 0.8111 (tpp) cc_final: 0.7846 (tpt) REVERT: E 666 MET cc_start: 0.5018 (ttt) cc_final: 0.3636 (tpp) REVERT: F 95 MET cc_start: 0.5976 (mmm) cc_final: 0.5657 (mmt) REVERT: F 214 THR cc_start: 0.8166 (m) cc_final: 0.7753 (p) REVERT: G 549 MET cc_start: 0.6471 (OUTLIER) cc_final: 0.6185 (tpt) REVERT: G 619 ARG cc_start: 0.7022 (ttp-170) cc_final: 0.6572 (ttt-90) REVERT: I 67 LEU cc_start: 0.5814 (mt) cc_final: 0.5470 (tt) REVERT: I 134 THR cc_start: 0.7358 (p) cc_final: 0.6874 (p) REVERT: I 288 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.6508 (ptp-170) REVERT: I 445 TYR cc_start: 0.6941 (m-80) cc_final: 0.6636 (m-10) REVERT: I 463 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7807 (mp) REVERT: I 531 SER cc_start: 0.8042 (t) cc_final: 0.7559 (p) REVERT: I 549 MET cc_start: 0.8050 (tpt) cc_final: 0.7575 (mmt) REVERT: I 693 MET cc_start: 0.6865 (mpp) cc_final: 0.6651 (mpp) REVERT: J 98 ASP cc_start: 0.7908 (m-30) cc_final: 0.7341 (t0) REVERT: J 244 LEU cc_start: 0.8397 (tp) cc_final: 0.8171 (tt) REVERT: K 85 MET cc_start: 0.7606 (tpp) cc_final: 0.7208 (tpp) REVERT: K 97 ASP cc_start: 0.7638 (m-30) cc_final: 0.6731 (t0) REVERT: K 125 ASP cc_start: 0.7598 (p0) cc_final: 0.7371 (p0) REVERT: K 217 MET cc_start: -0.4888 (ttt) cc_final: -0.5825 (ptm) REVERT: K 229 MET cc_start: 0.2263 (ptp) cc_final: 0.0392 (ptp) REVERT: K 316 MET cc_start: 0.4462 (mmp) cc_final: 0.4110 (mmp) REVERT: K 352 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8161 (t) REVERT: K 399 ARG cc_start: 0.6775 (mtp85) cc_final: 0.6532 (mtp180) REVERT: K 459 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6522 (tmt90) REVERT: K 466 MET cc_start: 0.7744 (tpp) cc_final: 0.7168 (tpt) REVERT: K 549 MET cc_start: 0.8271 (tpp) cc_final: 0.7934 (mmt) outliers start: 100 outliers final: 53 residues processed: 788 average time/residue: 0.6408 time to fit residues: 835.7043 Evaluate side-chains 591 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 532 time to evaluate : 5.159 ------------------------------------------------------------------------------- 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 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 463 LEU 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 324 optimal weight: 4.9990 chunk 181 optimal weight: 0.3980 chunk 485 optimal weight: 0.9980 chunk 397 optimal weight: 0.0270 chunk 161 optimal weight: 9.9990 chunk 584 optimal weight: 5.9990 chunk 631 optimal weight: 0.7980 chunk 520 optimal weight: 7.9990 chunk 580 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 469 optimal weight: 5.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- 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 528 GLN ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 GLN ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 528 GLN ** E 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 523 ASN H 115 ASN H 241 GLN H 446 HIS ** I 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 411 HIS ** J 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 446 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 51362 Z= 0.180 Angle : 0.585 12.146 69523 Z= 0.307 Chirality : 0.045 0.288 7874 Planarity : 0.004 0.084 9037 Dihedral : 7.006 68.005 7458 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.42 % Favored : 97.43 % Rotamer: Outliers : 1.87 % Allowed : 10.54 % Favored : 87.59 % 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: 0.72 (0.10), residues: 6497 helix: 0.91 (0.11), residues: 2304 sheet: 0.81 (0.13), residues: 1358 loop : 0.07 (0.12), residues: 2835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 559 HIS 0.010 0.001 HIS E 358 PHE 0.019 0.001 PHE I 337 TYR 0.013 0.001 TYR H 176 ARG 0.012 0.001 ARG J 69 *********************** 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 707 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 606 time to evaluate : 5.688 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: A 188 GLU cc_start: 0.7731 (mm-30) cc_final: 0.6514 (tm-30) REVERT: A 549 MET cc_start: 0.8256 (tpt) cc_final: 0.7953 (mmm) REVERT: B 488 GLU cc_start: 0.7783 (tp30) cc_final: 0.7520 (tp30) REVERT: C 89 THR cc_start: 0.7948 (m) cc_final: 0.7560 (p) REVERT: C 229 MET cc_start: -0.0223 (tmm) cc_final: -0.3235 (ptm) REVERT: C 693 MET cc_start: 0.2346 (mtp) cc_final: 0.1916 (ttm) REVERT: C 696 GLN cc_start: 0.6052 (mm110) cc_final: 0.5848 (mm110) REVERT: D 84 MET cc_start: 0.5407 (pmm) cc_final: 0.4758 (pmm) REVERT: E 288 ARG cc_start: 0.6430 (mtm-85) cc_final: 0.6227 (mtm-85) REVERT: E 350 MET cc_start: 0.6459 (tmm) cc_final: 0.6211 (tmm) REVERT: E 448 MET cc_start: 0.8293 (ttm) cc_final: 0.7983 (tpp) REVERT: E 466 MET cc_start: 0.8137 (tpp) cc_final: 0.7827 (tpt) REVERT: E 666 MET cc_start: 0.5140 (ttt) cc_final: 0.3622 (tpp) REVERT: F 83 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.6088 (t0) REVERT: F 95 MET cc_start: 0.5970 (mmm) cc_final: 0.5628 (mmt) REVERT: F 214 THR cc_start: 0.8168 (m) cc_final: 0.7864 (p) REVERT: F 442 MET cc_start: 0.8247 (mmm) cc_final: 0.7325 (mmm) REVERT: G 549 MET cc_start: 0.6577 (OUTLIER) cc_final: 0.6191 (tpt) REVERT: I 67 LEU cc_start: 0.5650 (OUTLIER) cc_final: 0.5081 (tt) REVERT: I 124 MET cc_start: 0.7762 (pmm) cc_final: 0.6524 (mtm) REVERT: I 336 GLU cc_start: 0.5064 (mt-10) cc_final: 0.4858 (mt-10) REVERT: I 463 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7794 (mp) REVERT: I 531 SER cc_start: 0.8105 (t) cc_final: 0.7598 (p) REVERT: I 549 MET cc_start: 0.7944 (tpt) cc_final: 0.7636 (mmt) REVERT: I 699 MET cc_start: 0.5538 (mpp) cc_final: 0.4904 (mpp) REVERT: J 98 ASP cc_start: 0.7944 (m-30) cc_final: 0.7686 (t70) REVERT: J 197 MET cc_start: 0.5871 (mmm) cc_final: 0.5615 (mmm) REVERT: J 244 LEU cc_start: 0.8354 (tp) cc_final: 0.8113 (tt) REVERT: K 97 ASP cc_start: 0.7789 (m-30) cc_final: 0.7043 (t0) REVERT: K 217 MET cc_start: -0.4729 (ttt) cc_final: -0.5569 (ptm) REVERT: K 350 MET cc_start: 0.8390 (tmm) cc_final: 0.8013 (tmm) REVERT: K 459 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6241 (tmt90) REVERT: K 466 MET cc_start: 0.7502 (tpp) cc_final: 0.7010 (tpt) REVERT: K 538 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8652 (mt) REVERT: K 549 MET cc_start: 0.8319 (tpp) cc_final: 0.8014 (mmt) REVERT: L 423 THR cc_start: 0.7671 (p) cc_final: 0.7363 (t) outliers start: 101 outliers final: 63 residues processed: 674 average time/residue: 0.5895 time to fit residues: 676.2878 Evaluate side-chains 574 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 505 time to evaluate : 5.717 ------------------------------------------------------------------------------- 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 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 669 VAL 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 146 LEU 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 445 LYS Chi-restraints excluded: chain D residue 448 CYS 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 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 G residue 532 LEU Chi-restraints excluded: chain G residue 549 MET Chi-restraints excluded: chain G residue 566 HIS 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 156 ILE Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 537 ILE Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 440 ASP Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 538 LEU Chi-restraints excluded: chain K residue 603 LEU Chi-restraints excluded: chain K residue 616 CYS Chi-restraints excluded: chain K residue 640 THR 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 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 577 optimal weight: 0.7980 chunk 439 optimal weight: 10.0000 chunk 303 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 279 optimal weight: 5.9990 chunk 392 optimal weight: 3.9990 chunk 587 optimal weight: 20.0000 chunk 621 optimal weight: 0.8980 chunk 306 optimal weight: 1.9990 chunk 556 optimal weight: 0.0050 chunk 167 optimal weight: 9.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN C 696 GLN D 100 ASN E 190 ASN F 58 GLN G 647 ASN H 167 GLN I 102 HIS I 169 HIS I 190 ASN ** I 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 139 GLN J 241 GLN J 452 ASN K 169 HIS L 446 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 51362 Z= 0.182 Angle : 0.563 11.866 69523 Z= 0.292 Chirality : 0.045 0.308 7874 Planarity : 0.004 0.089 9037 Dihedral : 6.597 71.902 7453 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.68 % Favored : 97.17 % Rotamer: Outliers : 2.22 % Allowed : 10.95 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.11), residues: 6497 helix: 0.99 (0.11), residues: 2352 sheet: 0.66 (0.14), residues: 1373 loop : 0.08 (0.12), residues: 2772 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 0.023 0.001 PHE A 503 TYR 0.018 0.001 TYR E 473 ARG 0.013 0.001 ARG L 69 *********************** 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 699 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 579 time to evaluate : 5.625 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: A 188 GLU cc_start: 0.7498 (mm-30) cc_final: 0.6452 (tm-30) REVERT: A 344 ASN cc_start: 0.7613 (m110) cc_final: 0.7359 (m-40) REVERT: A 449 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8003 (mt) REVERT: A 549 MET cc_start: 0.8446 (tpt) cc_final: 0.8154 (mmm) REVERT: B 95 MET cc_start: 0.8739 (mmm) cc_final: 0.8473 (mmm) REVERT: C 146 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6373 (mm) REVERT: C 229 MET cc_start: -0.0432 (tmm) cc_final: -0.3256 (ptm) REVERT: C 453 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8683 (mt) REVERT: C 666 MET cc_start: 0.1765 (ttt) cc_final: 0.1399 (ttt) REVERT: C 693 MET cc_start: 0.3035 (mtp) cc_final: 0.2413 (ttm) REVERT: C 695 MET cc_start: 0.5437 (tpp) cc_final: 0.4823 (tmm) REVERT: D 95 MET cc_start: 0.6780 (mmm) cc_final: 0.6509 (mmm) REVERT: E 288 ARG cc_start: 0.6543 (mtm-85) cc_final: 0.6299 (mtm-85) REVERT: E 350 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6061 (tmm) REVERT: E 448 MET cc_start: 0.8279 (ttm) cc_final: 0.7960 (tpp) REVERT: E 466 MET cc_start: 0.8244 (tpp) cc_final: 0.7956 (tpt) REVERT: E 666 MET cc_start: 0.5109 (ttt) cc_final: 0.3637 (tpp) REVERT: E 699 MET cc_start: 0.4758 (mtp) cc_final: 0.4298 (ptp) REVERT: F 83 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.6282 (t0) REVERT: F 133 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7352 (tt) REVERT: G 549 MET cc_start: 0.6689 (OUTLIER) cc_final: 0.6176 (tpt) REVERT: I 124 MET cc_start: 0.7655 (pmm) cc_final: 0.6848 (mtt) REVERT: I 169 HIS cc_start: 0.6590 (OUTLIER) cc_final: 0.6109 (t-90) REVERT: I 191 THR cc_start: 0.4173 (OUTLIER) cc_final: 0.3725 (p) REVERT: I 531 SER cc_start: 0.8055 (t) cc_final: 0.7588 (p) REVERT: I 549 MET cc_start: 0.8063 (tpt) cc_final: 0.7767 (mmt) REVERT: I 666 MET cc_start: 0.4569 (mmp) cc_final: 0.4311 (mmm) REVERT: I 693 MET cc_start: 0.6966 (mpp) cc_final: 0.6746 (mpp) REVERT: I 699 MET cc_start: 0.5452 (mpp) cc_final: 0.5007 (mpp) REVERT: J 98 ASP cc_start: 0.8040 (m-30) cc_final: 0.7396 (t0) REVERT: J 244 LEU cc_start: 0.8354 (tp) cc_final: 0.8099 (tt) REVERT: K 97 ASP cc_start: 0.7832 (m-30) cc_final: 0.7092 (t0) REVERT: K 174 MET cc_start: 0.7172 (mmm) cc_final: 0.6761 (mmm) REVERT: K 217 MET cc_start: -0.4727 (ttt) cc_final: -0.5499 (ptm) REVERT: K 316 MET cc_start: 0.4230 (mmp) cc_final: 0.3606 (mmt) REVERT: K 350 MET cc_start: 0.8328 (tmm) cc_final: 0.7865 (tmm) REVERT: K 459 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6141 (tmt90) REVERT: K 466 MET cc_start: 0.7445 (tpp) cc_final: 0.7008 (tpt) REVERT: K 549 MET cc_start: 0.8415 (tpp) cc_final: 0.8106 (mmt) REVERT: L 423 THR cc_start: 0.7859 (p) cc_final: 0.7549 (t) outliers start: 120 outliers final: 73 residues processed: 657 average time/residue: 0.5897 time to fit residues: 662.2013 Evaluate side-chains 578 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 495 time to evaluate : 5.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 A residue 690 ILE 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 89 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 178 ILE 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 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 421 GLU 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 350 MET Chi-restraints excluded: chain E residue 429 VAL 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 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 669 VAL Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 133 LEU 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 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 647 ASN Chi-restraints excluded: chain G residue 653 LYS Chi-restraints excluded: chain H residue 145 MET 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 169 HIS 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 704 THR Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 451 THR 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 538 LEU 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 306 VAL Chi-restraints excluded: chain L residue 347 MET Chi-restraints excluded: chain L residue 390 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 517 optimal weight: 3.9990 chunk 352 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 462 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 530 optimal weight: 3.9990 chunk 429 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 317 optimal weight: 1.9990 chunk 557 optimal weight: 0.1980 chunk 156 optimal weight: 5.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS B 88 HIS ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS D 241 GLN D 446 HIS D 528 GLN E 140 HIS ** E 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN F 258 HIS H 88 HIS ** I 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 697 ASN J 88 HIS L 446 HIS L 528 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 51362 Z= 0.324 Angle : 0.629 14.423 69523 Z= 0.328 Chirality : 0.046 0.320 7874 Planarity : 0.005 0.091 9037 Dihedral : 6.631 73.002 7453 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.00 % Favored : 96.84 % Rotamer: Outliers : 2.68 % Allowed : 11.49 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.10), residues: 6497 helix: 0.86 (0.11), residues: 2347 sheet: 0.57 (0.13), residues: 1356 loop : -0.16 (0.12), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 559 HIS 0.044 0.002 HIS I 169 PHE 0.024 0.002 PHE H 329 TYR 0.018 0.002 TYR D 417 ARG 0.018 0.001 ARG J 69 *********************** 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 663 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 518 time to evaluate : 5.562 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: A 107 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6387 (m-30) REVERT: A 129 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6985 (tm-30) REVERT: A 188 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6515 (tm-30) REVERT: A 344 ASN cc_start: 0.7704 (m110) cc_final: 0.7439 (m-40) REVERT: A 449 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8199 (mt) REVERT: A 531 SER cc_start: 0.8527 (m) cc_final: 0.8256 (p) REVERT: A 549 MET cc_start: 0.8505 (tpt) cc_final: 0.8260 (mmm) REVERT: C 64 ASP cc_start: 0.7326 (m-30) cc_final: 0.7081 (m-30) REVERT: C 229 MET cc_start: -0.0345 (tmm) cc_final: -0.3189 (ptm) REVERT: C 448 MET cc_start: 0.7675 (ttm) cc_final: 0.7209 (ttt) REVERT: E 288 ARG cc_start: 0.6651 (mtm-85) cc_final: 0.6359 (mtm-85) REVERT: E 350 MET cc_start: 0.7291 (tmm) cc_final: 0.6777 (tmm) REVERT: E 466 MET cc_start: 0.8236 (tpp) cc_final: 0.7979 (tpt) REVERT: E 666 MET cc_start: 0.5341 (ttt) cc_final: 0.3518 (mmp) REVERT: E 699 MET cc_start: 0.4760 (mtp) cc_final: 0.4325 (ptp) REVERT: F 83 ASP cc_start: 0.7395 (t0) cc_final: 0.6824 (t0) REVERT: G 549 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6693 (tpt) REVERT: H 142 CYS cc_start: 0.7811 (m) cc_final: 0.7186 (m) REVERT: I 124 MET cc_start: 0.7721 (pmm) cc_final: 0.6940 (mtt) REVERT: I 191 THR cc_start: 0.4591 (OUTLIER) cc_final: 0.4285 (p) REVERT: I 448 MET cc_start: 0.7496 (tpp) cc_final: 0.6924 (tpt) REVERT: I 699 MET cc_start: 0.5848 (mpp) cc_final: 0.5360 (mpp) REVERT: J 98 ASP cc_start: 0.7955 (m-30) cc_final: 0.7259 (t0) REVERT: J 331 GLU cc_start: 0.7228 (tt0) cc_final: 0.6981 (tt0) REVERT: K 97 ASP cc_start: 0.8040 (m-30) cc_final: 0.7347 (t0) REVERT: K 217 MET cc_start: -0.4775 (ttt) cc_final: -0.5567 (ptm) REVERT: K 350 MET cc_start: 0.8264 (tmm) cc_final: 0.7708 (tmm) REVERT: K 459 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.5979 (tmt90) REVERT: K 549 MET cc_start: 0.8528 (tpp) cc_final: 0.8194 (mmt) REVERT: K 693 MET cc_start: 0.6372 (ttt) cc_final: 0.6146 (tpt) REVERT: K 695 MET cc_start: 0.7152 (tmm) cc_final: 0.6520 (tmm) REVERT: L 316 MET cc_start: 0.6809 (ttm) cc_final: 0.6561 (ttm) REVERT: L 423 THR cc_start: 0.8200 (p) cc_final: 0.7869 (t) outliers start: 145 outliers final: 91 residues processed: 619 average time/residue: 0.5746 time to fit residues: 610.7689 Evaluate side-chains 566 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 470 time to evaluate : 5.857 ------------------------------------------------------------------------------- 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 356 VAL Chi-restraints excluded: chain A residue 370 VAL 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 A residue 645 GLU Chi-restraints excluded: chain A residue 669 VAL 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 145 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 354 LEU 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 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 124 MET Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 453 ILE 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 669 VAL 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 595 THR Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 607 VAL 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 451 THR Chi-restraints excluded: chain H residue 537 ILE Chi-restraints excluded: chain I residue 67 LEU 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 443 ILE 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 264 ASP Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 164 ILE Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 369 LEU 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 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 119 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 347 MET Chi-restraints excluded: chain L residue 390 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 209 optimal weight: 0.9990 chunk 559 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 364 optimal weight: 0.7980 chunk 153 optimal weight: 0.5980 chunk 622 optimal weight: 0.8980 chunk 516 optimal weight: 1.9990 chunk 288 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 326 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN B 446 HIS E 371 GLN H 483 GLN I 169 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 51362 Z= 0.173 Angle : 0.562 13.730 69523 Z= 0.291 Chirality : 0.044 0.190 7874 Planarity : 0.004 0.076 9037 Dihedral : 6.418 76.626 7453 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.97 % Favored : 96.88 % Rotamer: Outliers : 1.74 % Allowed : 12.80 % Favored : 85.46 % 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: 0.61 (0.11), residues: 6497 helix: 1.02 (0.11), residues: 2359 sheet: 0.73 (0.14), residues: 1331 loop : -0.17 (0.12), residues: 2807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 559 HIS 0.010 0.001 HIS I 169 PHE 0.021 0.001 PHE I 345 TYR 0.014 0.001 TYR E 473 ARG 0.007 0.000 ARG A 154 *********************** 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 626 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 532 time to evaluate : 4.799 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 129 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6957 (tm-30) REVERT: A 188 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6413 (tm-30) REVERT: A 344 ASN cc_start: 0.7686 (m110) cc_final: 0.7439 (m-40) REVERT: A 449 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8202 (mt) REVERT: A 531 SER cc_start: 0.8418 (m) cc_final: 0.8186 (p) REVERT: C 64 ASP cc_start: 0.7313 (m-30) cc_final: 0.7073 (m-30) REVERT: C 229 MET cc_start: -0.0491 (tmm) cc_final: -0.3221 (ptm) REVERT: C 231 ILE cc_start: 0.6192 (mm) cc_final: 0.5506 (mt) REVERT: C 448 MET cc_start: 0.7602 (ttm) cc_final: 0.7196 (ttt) REVERT: C 695 MET cc_start: 0.5248 (tpp) cc_final: 0.4668 (ttp) REVERT: E 124 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6653 (pmm) REVERT: E 288 ARG cc_start: 0.6739 (mtm-85) cc_final: 0.6476 (mtm-85) REVERT: E 350 MET cc_start: 0.7152 (tmm) cc_final: 0.6622 (tmm) REVERT: E 466 MET cc_start: 0.8285 (tpp) cc_final: 0.8032 (tpt) REVERT: E 666 MET cc_start: 0.5434 (ttt) cc_final: 0.4080 (mmp) REVERT: E 699 MET cc_start: 0.4890 (mtp) cc_final: 0.4356 (ptp) REVERT: F 83 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6748 (t0) REVERT: G 577 ASN cc_start: 0.7492 (t0) cc_final: 0.7251 (t0) REVERT: H 142 CYS cc_start: 0.7628 (m) cc_final: 0.6962 (m) REVERT: I 124 MET cc_start: 0.7632 (pmm) cc_final: 0.6884 (mtt) REVERT: I 191 THR cc_start: 0.4372 (OUTLIER) cc_final: 0.3924 (p) REVERT: I 448 MET cc_start: 0.7478 (tpp) cc_final: 0.6968 (tpt) REVERT: I 531 SER cc_start: 0.8103 (t) cc_final: 0.7570 (p) REVERT: I 693 MET cc_start: 0.7003 (mpp) cc_final: 0.6604 (mtm) REVERT: I 699 MET cc_start: 0.5868 (mpp) cc_final: 0.5342 (mpp) REVERT: J 98 ASP cc_start: 0.7901 (m-30) cc_final: 0.7272 (t70) REVERT: J 145 MET cc_start: 0.8420 (mmm) cc_final: 0.8163 (mtp) REVERT: J 331 GLU cc_start: 0.7249 (tt0) cc_final: 0.7014 (tt0) REVERT: K 97 ASP cc_start: 0.8081 (m-30) cc_final: 0.7329 (t0) REVERT: K 174 MET cc_start: 0.7240 (mmm) cc_final: 0.6689 (mmm) REVERT: K 217 MET cc_start: -0.4512 (ttt) cc_final: -0.5352 (ptm) REVERT: K 350 MET cc_start: 0.8286 (tmm) cc_final: 0.7679 (tmm) REVERT: K 459 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.5922 (tmt90) REVERT: K 538 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8651 (mt) REVERT: K 695 MET cc_start: 0.7078 (tmm) cc_final: 0.5897 (tmm) REVERT: L 423 THR cc_start: 0.8137 (p) cc_final: 0.7842 (t) outliers start: 94 outliers final: 66 residues processed: 597 average time/residue: 0.5413 time to fit residues: 554.3313 Evaluate side-chains 551 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 479 time to evaluate : 4.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 PHE 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 630 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 219 ASP 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 216 VAL 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 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 133 LEU Chi-restraints excluded: chain D residue 144 ILE 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 124 MET Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 431 VAL 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 580 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 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 549 MET 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 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 443 ILE Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain K residue 90 VAL 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 505 SER Chi-restraints excluded: chain K residue 538 LEU Chi-restraints excluded: chain K residue 603 LEU Chi-restraints excluded: chain K residue 671 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 347 MET Chi-restraints excluded: chain L residue 516 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 599 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 354 optimal weight: 0.0870 chunk 454 optimal weight: 7.9990 chunk 352 optimal weight: 5.9990 chunk 523 optimal weight: 2.9990 chunk 347 optimal weight: 0.9990 chunk 619 optimal weight: 3.9990 chunk 387 optimal weight: 0.3980 chunk 377 optimal weight: 0.0370 chunk 286 optimal weight: 7.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS B 446 HIS C 371 GLN F 100 ASN I 169 HIS ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 51362 Z= 0.174 Angle : 0.557 13.682 69523 Z= 0.288 Chirality : 0.044 0.226 7874 Planarity : 0.004 0.075 9037 Dihedral : 6.369 79.277 7453 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.84 % Rotamer: Outliers : 1.98 % Allowed : 13.30 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.11), residues: 6497 helix: 1.13 (0.11), residues: 2323 sheet: 0.74 (0.14), residues: 1295 loop : -0.17 (0.12), residues: 2879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 559 HIS 0.008 0.001 HIS E 358 PHE 0.025 0.001 PHE L 274 TYR 0.021 0.001 TYR H 336 ARG 0.014 0.000 ARG H 69 *********************** 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 616 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 509 time to evaluate : 4.271 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: A 107 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6369 (m-30) REVERT: A 188 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6381 (tm-30) REVERT: A 344 ASN cc_start: 0.7665 (m110) cc_final: 0.7417 (m-40) REVERT: A 449 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8197 (mt) REVERT: A 531 SER cc_start: 0.8404 (m) cc_final: 0.8163 (p) REVERT: C 64 ASP cc_start: 0.7314 (m-30) cc_final: 0.7094 (m-30) REVERT: C 229 MET cc_start: -0.0626 (tmm) cc_final: -0.3247 (ptm) REVERT: C 231 ILE cc_start: 0.6054 (mm) cc_final: 0.5438 (mt) REVERT: C 695 MET cc_start: 0.5277 (tpp) cc_final: 0.4684 (ttp) REVERT: E 124 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6721 (pmm) REVERT: E 288 ARG cc_start: 0.6763 (mtm-85) cc_final: 0.6296 (mtm-85) REVERT: E 350 MET cc_start: 0.7088 (tmm) cc_final: 0.6619 (tmm) REVERT: E 466 MET cc_start: 0.8316 (tpp) cc_final: 0.8069 (tpt) REVERT: E 666 MET cc_start: 0.5333 (ttt) cc_final: 0.3779 (mmp) REVERT: E 699 MET cc_start: 0.4883 (mtp) cc_final: 0.4460 (ptp) REVERT: F 83 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.6726 (t0) REVERT: G 549 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6296 (tpt) REVERT: G 577 ASN cc_start: 0.7443 (t0) cc_final: 0.7077 (t0) REVERT: H 142 CYS cc_start: 0.7645 (m) cc_final: 0.6961 (m) REVERT: I 124 MET cc_start: 0.7538 (pmm) cc_final: 0.7143 (mtt) REVERT: I 169 HIS cc_start: 0.6724 (OUTLIER) cc_final: 0.6215 (t-90) REVERT: I 191 THR cc_start: 0.4613 (OUTLIER) cc_final: 0.4063 (p) REVERT: I 448 MET cc_start: 0.7494 (tpp) cc_final: 0.7160 (tpt) REVERT: I 531 SER cc_start: 0.8064 (t) cc_final: 0.7511 (p) REVERT: I 693 MET cc_start: 0.7079 (mpp) cc_final: 0.6611 (mpp) REVERT: J 98 ASP cc_start: 0.7953 (m-30) cc_final: 0.7298 (t0) REVERT: J 145 MET cc_start: 0.8409 (mmm) cc_final: 0.8152 (mtp) REVERT: J 331 GLU cc_start: 0.7268 (tt0) cc_final: 0.7023 (tt0) REVERT: K 97 ASP cc_start: 0.8099 (m-30) cc_final: 0.7385 (t0) REVERT: K 174 MET cc_start: 0.7134 (mmm) cc_final: 0.6668 (mmm) REVERT: K 217 MET cc_start: -0.4622 (ttt) cc_final: -0.5428 (ptm) REVERT: K 350 MET cc_start: 0.8230 (tmm) cc_final: 0.7578 (tmm) REVERT: L 423 THR cc_start: 0.8091 (p) cc_final: 0.7810 (t) outliers start: 107 outliers final: 82 residues processed: 582 average time/residue: 0.4892 time to fit residues: 493.0368 Evaluate side-chains 562 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 473 time to evaluate : 4.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 290 CYS Chi-restraints excluded: chain A residue 308 LEU 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 453 ILE Chi-restraints excluded: chain A residue 499 ILE 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 B residue 451 THR Chi-restraints excluded: chain C residue 89 THR 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 396 VAL 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 133 LEU Chi-restraints excluded: chain D residue 144 ILE 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 429 VAL Chi-restraints excluded: chain E residue 431 VAL 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 580 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 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 549 MET 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 309 GLU Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 451 THR 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 169 HIS 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 642 LEU Chi-restraints excluded: chain I residue 650 MET Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 432 ASP Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 538 LEU Chi-restraints excluded: chain K residue 671 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 347 MET Chi-restraints excluded: chain L residue 516 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 643 random chunks: chunk 383 optimal weight: 8.9990 chunk 247 optimal weight: 3.9990 chunk 370 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 394 optimal weight: 9.9990 chunk 422 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 487 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 HIS D 41 ASN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN D 528 GLN E 293 GLN G 647 ASN I 169 HIS ** I 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 ASN ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 279 HIS L 88 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 51362 Z= 0.251 Angle : 0.595 14.209 69523 Z= 0.307 Chirality : 0.045 0.266 7874 Planarity : 0.004 0.073 9037 Dihedral : 6.366 79.904 7449 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 2.31 % Allowed : 13.34 % Favored : 84.35 % 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: 0.55 (0.11), residues: 6497 helix: 1.04 (0.11), residues: 2323 sheet: 0.67 (0.14), residues: 1331 loop : -0.26 (0.12), residues: 2843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 559 HIS 0.037 0.001 HIS I 169 PHE 0.030 0.002 PHE L 274 TYR 0.020 0.001 TYR J 176 ARG 0.010 0.000 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 602 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 477 time to evaluate : 5.719 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: A 107 ASP cc_start: 0.7020 (OUTLIER) cc_final: 0.6345 (m-30) REVERT: A 449 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8286 (mt) REVERT: A 531 SER cc_start: 0.8495 (m) cc_final: 0.8227 (p) REVERT: C 64 ASP cc_start: 0.7361 (m-30) cc_final: 0.7120 (m-30) REVERT: C 229 MET cc_start: -0.0608 (tmm) cc_final: -0.3142 (ptm) REVERT: C 231 ILE cc_start: 0.6251 (mm) cc_final: 0.5728 (mt) REVERT: C 448 MET cc_start: 0.7336 (ttm) cc_final: 0.6895 (ttt) REVERT: C 695 MET cc_start: 0.4906 (tpp) cc_final: 0.4439 (ttp) REVERT: E 124 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6777 (pmm) REVERT: E 350 MET cc_start: 0.7161 (tmm) cc_final: 0.6684 (tmm) REVERT: E 466 MET cc_start: 0.8318 (tpp) cc_final: 0.8069 (tpt) REVERT: E 666 MET cc_start: 0.5291 (ttt) cc_final: 0.3750 (mmp) REVERT: E 699 MET cc_start: 0.4829 (OUTLIER) cc_final: 0.4419 (ptp) REVERT: F 83 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.6933 (t0) REVERT: G 549 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6216 (tpt) REVERT: G 577 ASN cc_start: 0.7433 (t0) cc_final: 0.7163 (t0) REVERT: H 142 CYS cc_start: 0.7776 (m) cc_final: 0.7173 (m) REVERT: I 124 MET cc_start: 0.7791 (pmm) cc_final: 0.7158 (mtt) REVERT: I 127 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7857 (mt) REVERT: I 191 THR cc_start: 0.4965 (OUTLIER) cc_final: 0.4557 (p) REVERT: I 345 PHE cc_start: 0.5513 (OUTLIER) cc_final: 0.4492 (m-80) REVERT: I 448 MET cc_start: 0.7524 (tpp) cc_final: 0.7248 (tpt) REVERT: I 531 SER cc_start: 0.8210 (t) cc_final: 0.7741 (p) REVERT: I 666 MET cc_start: 0.5492 (mtp) cc_final: 0.4877 (mmm) REVERT: I 693 MET cc_start: 0.7173 (mpp) cc_final: 0.6801 (mpp) REVERT: J 98 ASP cc_start: 0.7946 (m-30) cc_final: 0.7412 (t70) REVERT: J 145 MET cc_start: 0.8458 (mmm) cc_final: 0.8245 (mtp) REVERT: K 97 ASP cc_start: 0.8131 (m-30) cc_final: 0.7490 (t0) REVERT: K 217 MET cc_start: -0.4651 (ttt) cc_final: -0.5430 (ptm) REVERT: K 350 MET cc_start: 0.8135 (tmm) cc_final: 0.7462 (tmm) REVERT: K 399 ARG cc_start: 0.6612 (mtp85) cc_final: 0.6294 (mtp85) REVERT: K 549 MET cc_start: 0.8112 (tpp) cc_final: 0.7809 (mtp) REVERT: L 423 THR cc_start: 0.8206 (p) cc_final: 0.7919 (t) outliers start: 125 outliers final: 89 residues processed: 564 average time/residue: 0.5765 time to fit residues: 561.7266 Evaluate side-chains 553 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 455 time to evaluate : 5.761 ------------------------------------------------------------------------------- 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 449 ILE Chi-restraints excluded: chain A residue 453 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 A residue 642 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 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 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 274 VAL Chi-restraints excluded: chain C residue 345 PHE 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 655 THR Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 144 ILE 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 281 ASN Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 566 HIS 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 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 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 580 VAL 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 G residue 653 LYS 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 H residue 451 THR Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 127 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 642 LEU Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 274 VAL 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 538 LEU Chi-restraints excluded: chain K residue 575 SER Chi-restraints excluded: chain K residue 616 CYS Chi-restraints excluded: chain K residue 671 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 347 MET 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 563 optimal weight: 4.9990 chunk 593 optimal weight: 6.9990 chunk 541 optimal weight: 9.9990 chunk 577 optimal weight: 0.7980 chunk 347 optimal weight: 0.6980 chunk 251 optimal weight: 8.9990 chunk 453 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 521 optimal weight: 0.0970 chunk 546 optimal weight: 10.0000 chunk 575 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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** G 647 ASN ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 51362 Z= 0.166 Angle : 0.568 13.745 69523 Z= 0.292 Chirality : 0.044 0.308 7874 Planarity : 0.004 0.073 9037 Dihedral : 6.297 82.186 7449 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.08 % Favored : 96.84 % Rotamer: Outliers : 1.91 % Allowed : 13.91 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.11), residues: 6497 helix: 1.14 (0.11), residues: 2323 sheet: 0.79 (0.14), residues: 1331 loop : -0.27 (0.12), residues: 2843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 559 HIS 0.007 0.001 HIS K 358 PHE 0.027 0.001 PHE K 152 TYR 0.019 0.001 TYR J 176 ARG 0.007 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 592 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 489 time to evaluate : 5.428 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: A 107 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6423 (m-30) REVERT: A 449 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8253 (mt) REVERT: A 531 SER cc_start: 0.8408 (m) cc_final: 0.8178 (p) REVERT: C 64 ASP cc_start: 0.7257 (m-30) cc_final: 0.7038 (m-30) REVERT: C 229 MET cc_start: -0.0460 (tmm) cc_final: -0.3025 (ptm) REVERT: C 231 ILE cc_start: 0.6242 (mm) cc_final: 0.5724 (mt) REVERT: C 448 MET cc_start: 0.7295 (ttm) cc_final: 0.6859 (ttt) REVERT: C 695 MET cc_start: 0.4876 (tpp) cc_final: 0.4404 (ttp) REVERT: E 124 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6722 (pmm) REVERT: E 217 MET cc_start: 0.0193 (ttt) cc_final: -0.0308 (ttt) REVERT: E 350 MET cc_start: 0.7157 (tmm) cc_final: 0.6640 (tmm) REVERT: E 466 MET cc_start: 0.8314 (tpp) cc_final: 0.8066 (tpt) REVERT: E 666 MET cc_start: 0.5195 (ttt) cc_final: 0.3659 (mmp) REVERT: E 699 MET cc_start: 0.4901 (OUTLIER) cc_final: 0.4469 (ptp) REVERT: F 83 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.6804 (t0) REVERT: G 560 GLU cc_start: 0.7428 (pt0) cc_final: 0.7164 (pt0) REVERT: G 577 ASN cc_start: 0.7369 (t0) cc_final: 0.7086 (t0) REVERT: H 142 CYS cc_start: 0.7672 (m) cc_final: 0.7010 (m) REVERT: I 124 MET cc_start: 0.7825 (pmm) cc_final: 0.7289 (mtt) REVERT: I 345 PHE cc_start: 0.5519 (OUTLIER) cc_final: 0.4422 (m-80) REVERT: I 448 MET cc_start: 0.7472 (tpp) cc_final: 0.7205 (tpt) REVERT: I 451 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6561 (ptpt) REVERT: I 531 SER cc_start: 0.8038 (t) cc_final: 0.7587 (p) REVERT: I 666 MET cc_start: 0.5422 (mtp) cc_final: 0.4762 (mmm) REVERT: I 693 MET cc_start: 0.7153 (mpp) cc_final: 0.6843 (mpp) REVERT: K 97 ASP cc_start: 0.8038 (m-30) cc_final: 0.7413 (t0) REVERT: K 217 MET cc_start: -0.4580 (ttt) cc_final: -0.5388 (ptm) REVERT: K 350 MET cc_start: 0.8134 (tmm) cc_final: 0.7412 (tmm) REVERT: K 695 MET cc_start: 0.7243 (tmm) cc_final: 0.6921 (tmm) REVERT: L 423 THR cc_start: 0.8164 (p) cc_final: 0.7891 (t) outliers start: 103 outliers final: 83 residues processed: 564 average time/residue: 0.5700 time to fit residues: 552.8671 Evaluate side-chains 549 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 459 time to evaluate : 5.460 ------------------------------------------------------------------------------- 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 449 ILE Chi-restraints excluded: chain A residue 453 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 A residue 642 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 451 THR Chi-restraints excluded: chain C residue 89 THR 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 545 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 671 VAL Chi-restraints excluded: chain C residue 697 ASN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 144 ILE 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 429 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 566 HIS Chi-restraints excluded: chain E residue 580 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 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 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 580 VAL Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 607 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 H residue 451 THR 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 451 LYS Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 274 VAL 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 538 LEU Chi-restraints excluded: chain K residue 616 CYS Chi-restraints excluded: chain K residue 671 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 347 MET 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 379 optimal weight: 7.9990 chunk 610 optimal weight: 0.4980 chunk 372 optimal weight: 2.9990 chunk 289 optimal weight: 0.7980 chunk 424 optimal weight: 9.9990 chunk 640 optimal weight: 0.5980 chunk 589 optimal weight: 0.1980 chunk 510 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 394 optimal weight: 10.0000 chunk 312 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** C 358 HIS D 528 GLN ** J 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 51362 Z= 0.157 Angle : 0.571 15.635 69523 Z= 0.290 Chirality : 0.044 0.239 7874 Planarity : 0.004 0.076 9037 Dihedral : 6.206 84.702 7449 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.16 % Favored : 96.77 % Rotamer: Outliers : 1.79 % Allowed : 14.00 % Favored : 84.20 % 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: 0.72 (0.11), residues: 6497 helix: 1.24 (0.11), residues: 2318 sheet: 0.84 (0.14), residues: 1331 loop : -0.25 (0.12), residues: 2848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 559 HIS 0.006 0.001 HIS K 358 PHE 0.030 0.001 PHE K 152 TYR 0.021 0.001 TYR D 417 ARG 0.011 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 591 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 494 time to evaluate : 5.501 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: A 107 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6468 (m-30) REVERT: A 304 PRO cc_start: 0.6023 (Cg_exo) cc_final: 0.5694 (Cg_endo) REVERT: A 449 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8243 (mt) REVERT: A 531 SER cc_start: 0.8368 (m) cc_final: 0.8140 (p) REVERT: B 197 MET cc_start: 0.8177 (mmt) cc_final: 0.7790 (mmt) REVERT: C 64 ASP cc_start: 0.7197 (m-30) cc_final: 0.6993 (m-30) REVERT: C 146 LEU cc_start: 0.7127 (tp) cc_final: 0.6774 (mt) REVERT: C 229 MET cc_start: -0.0563 (tmm) cc_final: -0.2982 (ptm) REVERT: C 448 MET cc_start: 0.7276 (ttm) cc_final: 0.6862 (ttt) REVERT: C 695 MET cc_start: 0.4786 (tpp) cc_final: 0.4330 (ttp) REVERT: E 174 MET cc_start: 0.6658 (mmm) cc_final: 0.6238 (mmp) REVERT: E 217 MET cc_start: 0.0108 (ttt) cc_final: -0.0351 (ttt) REVERT: E 350 MET cc_start: 0.7095 (tmm) cc_final: 0.6562 (tmm) REVERT: E 466 MET cc_start: 0.8295 (tpp) cc_final: 0.8041 (tpt) REVERT: E 666 MET cc_start: 0.5115 (ttt) cc_final: 0.3629 (mmp) REVERT: E 699 MET cc_start: 0.4980 (OUTLIER) cc_final: 0.4546 (ptp) REVERT: F 83 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.6809 (t0) REVERT: G 549 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.5657 (tpt) REVERT: G 560 GLU cc_start: 0.7379 (pt0) cc_final: 0.7100 (pt0) REVERT: G 577 ASN cc_start: 0.7326 (t0) cc_final: 0.7070 (t0) REVERT: H 142 CYS cc_start: 0.7647 (m) cc_final: 0.6960 (m) REVERT: I 124 MET cc_start: 0.7810 (pmm) cc_final: 0.7392 (mtt) REVERT: I 336 GLU cc_start: 0.5400 (mt-10) cc_final: 0.5105 (mm-30) REVERT: I 345 PHE cc_start: 0.5358 (OUTLIER) cc_final: 0.4173 (m-80) REVERT: I 448 MET cc_start: 0.7483 (tpp) cc_final: 0.7205 (tpt) REVERT: I 451 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6539 (ptpt) REVERT: I 531 SER cc_start: 0.8000 (t) cc_final: 0.7543 (p) REVERT: I 693 MET cc_start: 0.7201 (mpp) cc_final: 0.6845 (mpp) REVERT: K 97 ASP cc_start: 0.8031 (m-30) cc_final: 0.7397 (t0) REVERT: K 174 MET cc_start: 0.7170 (mmm) cc_final: 0.6660 (mmm) REVERT: K 217 MET cc_start: -0.4694 (ttt) cc_final: -0.5507 (ptm) REVERT: K 316 MET cc_start: 0.4566 (mmt) cc_final: 0.4232 (mmm) REVERT: K 350 MET cc_start: 0.8167 (tmm) cc_final: 0.7481 (tmm) REVERT: K 466 MET cc_start: 0.7461 (tpp) cc_final: 0.7076 (tpt) REVERT: K 538 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8615 (mt) REVERT: K 695 MET cc_start: 0.7524 (tmm) cc_final: 0.7308 (tmm) REVERT: L 212 ASP cc_start: 0.7641 (t70) cc_final: 0.7069 (t70) REVERT: L 423 THR cc_start: 0.8144 (p) cc_final: 0.7856 (t) outliers start: 97 outliers final: 76 residues processed: 565 average time/residue: 0.5891 time to fit residues: 577.5405 Evaluate side-chains 545 residues out of total 5406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 461 time to evaluate : 5.846 ------------------------------------------------------------------------------- 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 449 ILE Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 566 HIS Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 642 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 451 THR Chi-restraints excluded: chain C residue 89 THR 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 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 671 VAL Chi-restraints excluded: chain D residue 144 ILE 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 429 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 454 THR Chi-restraints excluded: chain E residue 566 HIS Chi-restraints excluded: chain E residue 580 VAL 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 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 549 MET Chi-restraints excluded: chain G residue 580 VAL 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 H residue 451 THR Chi-restraints excluded: chain I residue 74 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 451 LYS Chi-restraints excluded: chain I residue 526 LEU Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 642 LEU Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 501 THR Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 538 LEU Chi-restraints excluded: chain K residue 616 CYS Chi-restraints excluded: chain K residue 671 VAL Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 347 MET 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 405 optimal weight: 6.9990 chunk 543 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 470 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 510 optimal weight: 4.9990 chunk 213 optimal weight: 0.7980 chunk 524 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 481 ASN ** J 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.143477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.106616 restraints weight = 126015.231| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.24 r_work: 0.3453 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 51362 Z= 0.189 Angle : 0.580 14.835 69523 Z= 0.296 Chirality : 0.044 0.219 7874 Planarity : 0.004 0.072 9037 Dihedral : 6.189 85.215 7449 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.69 % Rotamer: Outliers : 1.78 % Allowed : 14.47 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.11), residues: 6497 helix: 1.24 (0.11), residues: 2318 sheet: 0.80 (0.14), residues: 1331 loop : -0.28 (0.12), residues: 2848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 559 HIS 0.007 0.001 HIS K 358 PHE 0.030 0.001 PHE K 152 TYR 0.020 0.001 TYR J 176 ARG 0.010 0.000 ARG A 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13496.02 seconds wall clock time: 253 minutes 42.77 seconds (15222.77 seconds total)