Starting phenix.real_space_refine on Tue Mar 19 11:38:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/03_2024/3jd4_6633_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/03_2024/3jd4_6633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/03_2024/3jd4_6633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/03_2024/3jd4_6633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/03_2024/3jd4_6633_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd4_6633/03_2024/3jd4_6633_updated.pdb" } resolution = 3.4 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= 0.005 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 42 5.49 5 S 114 5.16 5 C 15060 2.51 5 N 4194 2.21 5 O 4644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24054 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3889 Classifications: {'peptide': 497} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 475} Chain: "B" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3889 Classifications: {'peptide': 497} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 475} Chain: "C" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3889 Classifications: {'peptide': 497} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 475} Chain: "D" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3889 Classifications: {'peptide': 497} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 475} Chain: "E" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3889 Classifications: {'peptide': 497} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 475} Chain: "F" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3889 Classifications: {'peptide': 497} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 475} Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'GTP': 1, 'NAI': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 12.96, per 1000 atoms: 0.54 Number of scatterers: 24054 At special positions: 0 Unit cell: (114.12, 129.421, 165.123, 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 114 16.00 P 42 15.00 O 4644 8.00 N 4194 7.00 C 15060 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 - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 9.47 Conformation dependent library (CDL) restraints added in 4.1 seconds 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5412 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 22 sheets defined 49.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.615A pdb=" N ILE A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.998A pdb=" N SER A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 117 removed outlier: 4.091A pdb=" N ALA A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 155 removed outlier: 3.526A pdb=" N LYS A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.569A pdb=" N TRP A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 214 through 227 Processing helix chain 'A' and resid 230 through 236 removed outlier: 4.201A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 288 through 297 removed outlier: 3.558A pdb=" N PHE A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 333 through 338 Proline residue: A 337 - end of helix No H-bonds generated for 'chain 'A' and resid 333 through 338' Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.859A pdb=" N LYS A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 387 removed outlier: 4.376A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLY A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 420 removed outlier: 3.648A pdb=" N PHE A 399 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYS A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR A 401 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 402 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG A 403 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU A 410 " --> pdb=" O TYR A 407 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET A 411 " --> pdb=" O HIS A 408 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 413 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 418 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.752A pdb=" N ASP A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 439' Processing helix chain 'A' and resid 445 through 470 removed outlier: 3.645A pdb=" N VAL A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 454 " --> pdb=" O HIS A 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 461 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 495 removed outlier: 3.531A pdb=" N ARG A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.615A pdb=" N ILE B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 53 removed outlier: 3.998A pdb=" N SER B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 117 removed outlier: 4.091A pdb=" N ALA B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 116 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 155 removed outlier: 3.525A pdb=" N LYS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.570A pdb=" N TRP B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 230 through 236 removed outlier: 4.201A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 288 through 297 removed outlier: 3.558A pdb=" N PHE B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 333 through 338 Proline residue: B 337 - end of helix No H-bonds generated for 'chain 'B' and resid 333 through 338' Processing helix chain 'B' and resid 354 through 362 removed outlier: 3.858A pdb=" N LYS B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 387 removed outlier: 4.376A pdb=" N ALA B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY B 376 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 378 " --> pdb=" O ASN B 374 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 420 removed outlier: 3.648A pdb=" N PHE B 399 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYS B 400 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR B 401 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 402 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG B 403 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU B 410 " --> pdb=" O TYR B 407 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET B 411 " --> pdb=" O HIS B 408 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 413 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 418 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 434 through 439 removed outlier: 3.752A pdb=" N ASP B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 434 through 439' Processing helix chain 'B' and resid 445 through 470 removed outlier: 3.645A pdb=" N VAL B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA B 461 " --> pdb=" O MET B 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 470 " --> pdb=" O ARG B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 removed outlier: 3.531A pdb=" N ARG B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 492 " --> pdb=" O LYS B 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.615A pdb=" N ILE C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 53 removed outlier: 3.998A pdb=" N SER C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 117 removed outlier: 4.091A pdb=" N ALA C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 116 " --> pdb=" O THR C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 155 removed outlier: 3.526A pdb=" N LYS C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 186 removed outlier: 3.570A pdb=" N TRP C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 214 through 227 Processing helix chain 'C' and resid 230 through 236 removed outlier: 4.201A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 264 Processing helix chain 'C' and resid 288 through 297 removed outlier: 3.558A pdb=" N PHE C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 333 through 338 Proline residue: C 337 - end of helix No H-bonds generated for 'chain 'C' and resid 333 through 338' Processing helix chain 'C' and resid 354 through 362 removed outlier: 3.858A pdb=" N LYS C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 387 removed outlier: 4.377A pdb=" N ALA C 375 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY C 376 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL C 378 " --> pdb=" O ASN C 374 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 420 removed outlier: 3.649A pdb=" N PHE C 399 " --> pdb=" O ARG C 396 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS C 400 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR C 401 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 402 " --> pdb=" O PHE C 399 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG C 403 " --> pdb=" O LYS C 400 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU C 410 " --> pdb=" O TYR C 407 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET C 411 " --> pdb=" O HIS C 408 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 413 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 418 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'C' and resid 434 through 439 removed outlier: 3.752A pdb=" N ASP C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 434 through 439' Processing helix chain 'C' and resid 445 through 470 removed outlier: 3.645A pdb=" N VAL C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 454 " --> pdb=" O HIS C 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA C 461 " --> pdb=" O MET C 457 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS C 470 " --> pdb=" O ARG C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 495 removed outlier: 3.532A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 492 " --> pdb=" O LYS C 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.614A pdb=" N ILE D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 53 removed outlier: 3.998A pdb=" N SER D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 117 removed outlier: 4.091A pdb=" N ALA D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 155 removed outlier: 3.526A pdb=" N LYS D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 186 removed outlier: 3.569A pdb=" N TRP D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 214 through 227 Processing helix chain 'D' and resid 230 through 236 removed outlier: 4.201A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 288 through 297 removed outlier: 3.557A pdb=" N PHE D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 354 through 362 removed outlier: 3.859A pdb=" N LYS D 358 " --> pdb=" O PRO D 354 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 387 removed outlier: 4.376A pdb=" N ALA D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY D 376 " --> pdb=" O TYR D 372 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL D 378 " --> pdb=" O ASN D 374 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE D 383 " --> pdb=" O THR D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 420 removed outlier: 3.648A pdb=" N PHE D 399 " --> pdb=" O ARG D 396 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYS D 400 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR D 401 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU D 402 " --> pdb=" O PHE D 399 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG D 403 " --> pdb=" O LYS D 400 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN D 406 " --> pdb=" O ARG D 403 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU D 410 " --> pdb=" O TYR D 407 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET D 411 " --> pdb=" O HIS D 408 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL D 413 " --> pdb=" O LEU D 410 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU D 418 " --> pdb=" O GLU D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 424 No H-bonds generated for 'chain 'D' and resid 422 through 424' Processing helix chain 'D' and resid 434 through 439 removed outlier: 3.752A pdb=" N ASP D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG D 439 " --> pdb=" O GLU D 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 434 through 439' Processing helix chain 'D' and resid 445 through 470 removed outlier: 3.645A pdb=" N VAL D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA D 461 " --> pdb=" O MET D 457 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS D 470 " --> pdb=" O ARG D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 495 removed outlier: 3.530A pdb=" N ARG D 491 " --> pdb=" O GLU D 487 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 492 " --> pdb=" O LYS D 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 29 removed outlier: 3.614A pdb=" N ILE E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 53 removed outlier: 3.998A pdb=" N SER E 47 " --> pdb=" O ASN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 117 removed outlier: 4.092A pdb=" N ALA E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 116 " --> pdb=" O THR E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 155 removed outlier: 3.525A pdb=" N LYS E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 186 removed outlier: 3.569A pdb=" N TRP E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 214 through 227 Processing helix chain 'E' and resid 230 through 236 removed outlier: 4.200A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 264 Processing helix chain 'E' and resid 288 through 297 removed outlier: 3.558A pdb=" N PHE E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 316 No H-bonds generated for 'chain 'E' and resid 314 through 316' Processing helix chain 'E' and resid 333 through 338 Proline residue: E 337 - end of helix No H-bonds generated for 'chain 'E' and resid 333 through 338' Processing helix chain 'E' and resid 354 through 362 removed outlier: 3.859A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 387 removed outlier: 4.375A pdb=" N ALA E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY E 376 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY E 377 " --> pdb=" O LEU E 373 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL E 378 " --> pdb=" O ASN E 374 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE E 383 " --> pdb=" O THR E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 420 removed outlier: 3.648A pdb=" N PHE E 399 " --> pdb=" O ARG E 396 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS E 400 " --> pdb=" O LEU E 397 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR E 401 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU E 402 " --> pdb=" O PHE E 399 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG E 403 " --> pdb=" O LYS E 400 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU E 410 " --> pdb=" O TYR E 407 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET E 411 " --> pdb=" O HIS E 408 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL E 413 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU E 418 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 424 No H-bonds generated for 'chain 'E' and resid 422 through 424' Processing helix chain 'E' and resid 434 through 439 removed outlier: 3.753A pdb=" N ASP E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG E 439 " --> pdb=" O GLU E 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 434 through 439' Processing helix chain 'E' and resid 445 through 470 removed outlier: 3.645A pdb=" N VAL E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA E 454 " --> pdb=" O HIS E 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA E 461 " --> pdb=" O MET E 457 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS E 470 " --> pdb=" O ARG E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 495 removed outlier: 3.530A pdb=" N ARG E 491 " --> pdb=" O GLU E 487 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 29 removed outlier: 3.615A pdb=" N ILE F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 53 removed outlier: 3.998A pdb=" N SER F 47 " --> pdb=" O ASN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 117 removed outlier: 4.092A pdb=" N ALA F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA F 116 " --> pdb=" O THR F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 155 removed outlier: 3.526A pdb=" N LYS F 155 " --> pdb=" O GLU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 186 removed outlier: 3.570A pdb=" N TRP F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 214 through 227 Processing helix chain 'F' and resid 230 through 236 removed outlier: 4.201A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 264 Processing helix chain 'F' and resid 288 through 297 removed outlier: 3.558A pdb=" N PHE F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' Processing helix chain 'F' and resid 333 through 338 Proline residue: F 337 - end of helix No H-bonds generated for 'chain 'F' and resid 333 through 338' Processing helix chain 'F' and resid 354 through 362 removed outlier: 3.859A pdb=" N LYS F 358 " --> pdb=" O PRO F 354 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE F 359 " --> pdb=" O GLU F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 387 removed outlier: 4.376A pdb=" N ALA F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY F 376 " --> pdb=" O TYR F 372 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLY F 377 " --> pdb=" O LEU F 373 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL F 378 " --> pdb=" O ASN F 374 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE F 383 " --> pdb=" O THR F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 420 removed outlier: 3.649A pdb=" N PHE F 399 " --> pdb=" O ARG F 396 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LYS F 400 " --> pdb=" O LEU F 397 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR F 401 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU F 402 " --> pdb=" O PHE F 399 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG F 403 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU F 410 " --> pdb=" O TYR F 407 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET F 411 " --> pdb=" O HIS F 408 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL F 413 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 418 " --> pdb=" O GLU F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 424 No H-bonds generated for 'chain 'F' and resid 422 through 424' Processing helix chain 'F' and resid 434 through 439 removed outlier: 3.752A pdb=" N ASP F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG F 439 " --> pdb=" O GLU F 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 434 through 439' Processing helix chain 'F' and resid 445 through 470 removed outlier: 3.644A pdb=" N VAL F 449 " --> pdb=" O GLU F 445 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA F 454 " --> pdb=" O HIS F 450 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA F 461 " --> pdb=" O MET F 457 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS F 470 " --> pdb=" O ARG F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 495 removed outlier: 3.531A pdb=" N ARG F 491 " --> pdb=" O GLU F 487 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL F 492 " --> pdb=" O LYS F 488 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 57 through 60 removed outlier: 4.407A pdb=" N GLY A 92 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 272 through 274 removed outlier: 4.494A pdb=" N SER A 279 " --> pdb=" O TYR A 310 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 308 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 321 through 324 removed outlier: 6.523A pdb=" N ILE A 343 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA A 345 " --> pdb=" O PRO A 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 57 through 60 Processing sheet with id= E, first strand: chain 'B' and resid 89 through 92 Processing sheet with id= F, first strand: chain 'B' and resid 272 through 274 removed outlier: 4.494A pdb=" N SER B 279 " --> pdb=" O TYR B 310 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 308 " --> pdb=" O TRP B 281 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 321 through 324 removed outlier: 6.524A pdb=" N ILE B 343 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA B 345 " --> pdb=" O PRO B 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= I, first strand: chain 'C' and resid 89 through 92 Processing sheet with id= J, first strand: chain 'C' and resid 272 through 274 removed outlier: 4.495A pdb=" N SER C 279 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 308 " --> pdb=" O TRP C 281 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 321 through 324 removed outlier: 6.523A pdb=" N ILE C 343 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA C 345 " --> pdb=" O PRO C 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= M, first strand: chain 'D' and resid 89 through 92 Processing sheet with id= N, first strand: chain 'D' and resid 272 through 274 removed outlier: 4.494A pdb=" N SER D 279 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 308 " --> pdb=" O TRP D 281 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 321 through 324 removed outlier: 6.523A pdb=" N ILE D 343 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA D 345 " --> pdb=" O PRO D 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= Q, first strand: chain 'E' and resid 89 through 92 Processing sheet with id= R, first strand: chain 'E' and resid 272 through 274 removed outlier: 4.494A pdb=" N SER E 279 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS E 308 " --> pdb=" O TRP E 281 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 321 through 324 removed outlier: 6.523A pdb=" N ILE E 343 " --> pdb=" O LEU E 322 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA E 345 " --> pdb=" O PRO E 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'F' and resid 57 through 60 removed outlier: 4.408A pdb=" N GLY F 92 " --> pdb=" O ALA F 125 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 272 through 274 removed outlier: 4.494A pdb=" N SER F 279 " --> pdb=" O TYR F 310 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS F 308 " --> pdb=" O TRP F 281 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 321 through 324 removed outlier: 6.524A pdb=" N ILE F 343 " --> pdb=" O LEU F 322 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA F 345 " --> pdb=" O PRO F 324 " (cutoff:3.500A) No H-bonds generated for sheet with id= V 912 hydrogen bonds defined for protein. 2478 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: 7.15 Time building geometry restraints manager: 10.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7511 1.33 - 1.45: 3456 1.45 - 1.57: 13375 1.57 - 1.68: 78 1.68 - 1.80: 192 Bond restraints: 24612 Sorted by residual: bond pdb=" C4A NAI A 601 " pdb=" C5A NAI A 601 " ideal model delta sigma weight residual 1.386 1.466 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" N PRO F 429 " pdb=" CD PRO F 429 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.60e+01 bond pdb=" C4A NAI B 602 " pdb=" C5A NAI B 602 " ideal model delta sigma weight residual 1.386 1.466 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C4A NAI C 602 " pdb=" C5A NAI C 602 " ideal model delta sigma weight residual 1.386 1.466 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C4A NAI E 602 " pdb=" C5A NAI E 602 " ideal model delta sigma weight residual 1.386 1.466 -0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 24607 not shown) Histogram of bond angle deviations from ideal: 98.66 - 106.79: 849 106.79 - 114.93: 14871 114.93 - 123.06: 16450 123.06 - 131.19: 1096 131.19 - 139.32: 118 Bond angle restraints: 33384 Sorted by residual: angle pdb=" C ILE A 428 " pdb=" N PRO A 429 " pdb=" CA PRO A 429 " ideal model delta sigma weight residual 119.84 114.17 5.67 1.25e+00 6.40e-01 2.06e+01 angle pdb=" C ILE C 428 " pdb=" N PRO C 429 " pdb=" CA PRO C 429 " ideal model delta sigma weight residual 119.84 114.19 5.65 1.25e+00 6.40e-01 2.04e+01 angle pdb=" C ILE E 428 " pdb=" N PRO E 429 " pdb=" CA PRO E 429 " ideal model delta sigma weight residual 119.84 114.20 5.64 1.25e+00 6.40e-01 2.04e+01 angle pdb=" C ILE B 428 " pdb=" N PRO B 429 " pdb=" CA PRO B 429 " ideal model delta sigma weight residual 119.84 114.20 5.64 1.25e+00 6.40e-01 2.03e+01 angle pdb=" C ILE F 428 " pdb=" N PRO F 429 " pdb=" CA PRO F 429 " ideal model delta sigma weight residual 119.84 114.21 5.63 1.25e+00 6.40e-01 2.03e+01 ... (remaining 33379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.47: 14779 33.47 - 66.95: 293 66.95 - 100.42: 12 100.42 - 133.89: 6 133.89 - 167.37: 6 Dihedral angle restraints: 15096 sinusoidal: 6600 harmonic: 8496 Sorted by residual: dihedral pdb=" C8 GTP D 602 " pdb=" C1' GTP D 602 " pdb=" N9 GTP D 602 " pdb=" O4' GTP D 602 " ideal model delta sinusoidal sigma weight residual 104.59 -62.77 167.37 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C8 GTP F 603 " pdb=" C1' GTP F 603 " pdb=" N9 GTP F 603 " pdb=" O4' GTP F 603 " ideal model delta sinusoidal sigma weight residual 104.59 -62.72 167.32 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C8 GTP C 603 " pdb=" C1' GTP C 603 " pdb=" N9 GTP C 603 " pdb=" O4' GTP C 603 " ideal model delta sinusoidal sigma weight residual 104.59 -62.72 167.31 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 15093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2508 0.049 - 0.097: 930 0.097 - 0.146: 135 0.146 - 0.195: 31 0.195 - 0.244: 14 Chirality restraints: 3618 Sorted by residual: chirality pdb=" C1B NAI E 602 " pdb=" C2B NAI E 602 " pdb=" N9A NAI E 602 " pdb=" O4B NAI E 602 " both_signs ideal model delta sigma weight residual False 2.31 2.55 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1B NAI D 601 " pdb=" C2B NAI D 601 " pdb=" N9A NAI D 601 " pdb=" O4B NAI D 601 " both_signs ideal model delta sigma weight residual False 2.31 2.55 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1B NAI B 602 " pdb=" C2B NAI B 602 " pdb=" N9A NAI B 602 " pdb=" O4B NAI B 602 " both_signs ideal model delta sigma weight residual False 2.31 2.55 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 3615 not shown) Planarity restraints: 4242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 282 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO D 283 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 283 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 283 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 282 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO F 283 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 283 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 283 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 282 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 283 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.028 5.00e-02 4.00e+02 ... (remaining 4239 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1174 2.71 - 3.25: 26475 3.25 - 3.80: 39019 3.80 - 4.35: 53457 4.35 - 4.90: 86124 Nonbonded interactions: 206249 Sorted by model distance: nonbonded pdb=" O HIS D 195 " pdb=" NZ LYS D 201 " model vdw 2.157 2.520 nonbonded pdb=" O HIS C 195 " pdb=" NZ LYS C 201 " model vdw 2.157 2.520 nonbonded pdb=" O HIS A 195 " pdb=" NZ LYS A 201 " model vdw 2.157 2.520 nonbonded pdb=" O HIS B 195 " pdb=" NZ LYS B 201 " model vdw 2.157 2.520 nonbonded pdb=" O HIS E 195 " pdb=" NZ LYS E 201 " model vdw 2.158 2.520 ... (remaining 206244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 501 or resid 601)) selection = (chain 'B' and (resid 5 through 501 or resid 602)) selection = (chain 'C' and (resid 5 through 501 or resid 601)) selection = (chain 'D' and (resid 5 through 501 or resid 601)) selection = (chain 'E' and (resid 5 through 501 or resid 602)) selection = (chain 'F' and (resid 5 through 501 or resid 601)) } 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: 1.390 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: 0.020 Extract box with map and model: 5.260 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 63.270 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 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 : 0.009 0.080 24612 Z= 0.587 Angle : 0.963 14.319 33384 Z= 0.498 Chirality : 0.052 0.244 3618 Planarity : 0.004 0.051 4242 Dihedral : 12.302 167.367 9684 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.84 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.82 (0.12), residues: 2970 helix: -3.67 (0.08), residues: 1320 sheet: -3.54 (0.22), residues: 312 loop : -2.42 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 178 HIS 0.010 0.002 HIS E 450 PHE 0.034 0.003 PHE C 122 TYR 0.033 0.003 TYR A 78 ARG 0.005 0.001 ARG F 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 542 time to evaluate : 2.729 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: A 6 ASP cc_start: 0.8401 (t0) cc_final: 0.7931 (m-30) REVERT: A 33 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7929 (mtmt) REVERT: A 72 TRP cc_start: 0.8354 (m100) cc_final: 0.8147 (m100) REVERT: A 84 GLN cc_start: 0.8320 (mm-40) cc_final: 0.8073 (mm-40) REVERT: A 181 ASP cc_start: 0.8449 (t70) cc_final: 0.7995 (t0) REVERT: A 308 LYS cc_start: 0.7902 (pttt) cc_final: 0.7414 (mttp) REVERT: B 6 ASP cc_start: 0.8394 (t0) cc_final: 0.7865 (m-30) REVERT: B 33 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7871 (mtmt) REVERT: B 72 TRP cc_start: 0.8365 (m100) cc_final: 0.8084 (m100) REVERT: B 84 GLN cc_start: 0.8301 (mm-40) cc_final: 0.8059 (mm-40) REVERT: B 181 ASP cc_start: 0.8531 (t70) cc_final: 0.8037 (t0) REVERT: B 308 LYS cc_start: 0.8002 (pttt) cc_final: 0.7518 (mttp) REVERT: C 6 ASP cc_start: 0.8424 (t0) cc_final: 0.7900 (m-30) REVERT: C 72 TRP cc_start: 0.8371 (m100) cc_final: 0.8043 (m100) REVERT: C 181 ASP cc_start: 0.8463 (t70) cc_final: 0.7995 (t0) REVERT: C 292 GLU cc_start: 0.8434 (tt0) cc_final: 0.7976 (tm-30) REVERT: C 308 LYS cc_start: 0.7915 (pttt) cc_final: 0.7436 (mttp) REVERT: C 372 TYR cc_start: 0.8003 (t80) cc_final: 0.7674 (t80) REVERT: D 6 ASP cc_start: 0.8395 (t0) cc_final: 0.7892 (m-30) REVERT: D 33 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7957 (mtmt) REVERT: D 72 TRP cc_start: 0.8354 (m100) cc_final: 0.8107 (m100) REVERT: D 84 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8086 (mm-40) REVERT: D 181 ASP cc_start: 0.8470 (t70) cc_final: 0.8018 (t0) REVERT: D 308 LYS cc_start: 0.7913 (pttt) cc_final: 0.7442 (mttp) REVERT: E 6 ASP cc_start: 0.8388 (t0) cc_final: 0.7857 (m-30) REVERT: E 33 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7874 (mtmt) REVERT: E 72 TRP cc_start: 0.8356 (m100) cc_final: 0.8077 (m100) REVERT: E 84 GLN cc_start: 0.8303 (mm-40) cc_final: 0.8055 (mm-40) REVERT: E 181 ASP cc_start: 0.8533 (t70) cc_final: 0.8043 (t0) REVERT: E 308 LYS cc_start: 0.8011 (pttt) cc_final: 0.7533 (mttp) REVERT: F 6 ASP cc_start: 0.8423 (t0) cc_final: 0.7897 (m-30) REVERT: F 72 TRP cc_start: 0.8369 (m100) cc_final: 0.8044 (m100) REVERT: F 181 ASP cc_start: 0.8463 (t70) cc_final: 0.7991 (t0) REVERT: F 292 GLU cc_start: 0.8430 (tt0) cc_final: 0.7974 (tm-30) REVERT: F 308 LYS cc_start: 0.7915 (pttt) cc_final: 0.7439 (mttp) REVERT: F 372 TYR cc_start: 0.7999 (t80) cc_final: 0.7670 (t80) outliers start: 0 outliers final: 0 residues processed: 542 average time/residue: 0.4153 time to fit residues: 330.2551 Evaluate side-chains 299 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 7.9990 chunk 222 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 140 optimal weight: 50.0000 chunk 171 optimal weight: 6.9990 chunk 266 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 HIS ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 HIS ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 ASN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 24612 Z= 0.362 Angle : 0.676 10.457 33384 Z= 0.342 Chirality : 0.047 0.193 3618 Planarity : 0.005 0.043 4242 Dihedral : 13.735 163.701 4080 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.44 % Allowed : 7.47 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.53 (0.14), residues: 2970 helix: -1.41 (0.12), residues: 1332 sheet: -2.73 (0.25), residues: 312 loop : -1.53 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 178 HIS 0.008 0.002 HIS E 450 PHE 0.022 0.002 PHE A 16 TYR 0.023 0.002 TYR C 78 ARG 0.004 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 358 time to evaluate : 2.453 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 6 ASP cc_start: 0.8326 (t0) cc_final: 0.7783 (m-30) REVERT: A 33 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7875 (mtmt) REVERT: A 81 GLN cc_start: 0.8068 (mt0) cc_final: 0.7845 (mt0) REVERT: A 84 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7973 (mm-40) REVERT: A 181 ASP cc_start: 0.8468 (t70) cc_final: 0.8067 (t0) REVERT: A 308 LYS cc_start: 0.7822 (pttt) cc_final: 0.7362 (mttp) REVERT: A 495 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7876 (mt-10) REVERT: B 6 ASP cc_start: 0.8296 (t0) cc_final: 0.7743 (m-30) REVERT: B 33 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7903 (mtmt) REVERT: B 72 TRP cc_start: 0.8334 (m100) cc_final: 0.8066 (m100) REVERT: B 84 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7974 (mm-40) REVERT: B 163 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7956 (m-30) REVERT: B 181 ASP cc_start: 0.8489 (t70) cc_final: 0.8098 (t0) REVERT: B 308 LYS cc_start: 0.7963 (pttt) cc_final: 0.7499 (mttp) REVERT: C 6 ASP cc_start: 0.8332 (t0) cc_final: 0.7770 (m-30) REVERT: C 72 TRP cc_start: 0.8352 (m100) cc_final: 0.8045 (m100) REVERT: C 81 GLN cc_start: 0.8161 (mt0) cc_final: 0.7954 (mt0) REVERT: C 181 ASP cc_start: 0.8501 (t70) cc_final: 0.8056 (t0) REVERT: C 308 LYS cc_start: 0.7864 (pttt) cc_final: 0.7384 (mttp) REVERT: C 372 TYR cc_start: 0.7978 (t80) cc_final: 0.7629 (t80) REVERT: C 457 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7574 (mtm) REVERT: C 495 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8030 (mt-10) REVERT: D 6 ASP cc_start: 0.8306 (t0) cc_final: 0.7765 (m-30) REVERT: D 33 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7877 (mtmt) REVERT: D 72 TRP cc_start: 0.8322 (m100) cc_final: 0.8119 (m100) REVERT: D 181 ASP cc_start: 0.8476 (t70) cc_final: 0.8074 (t0) REVERT: D 308 LYS cc_start: 0.7812 (pttt) cc_final: 0.7370 (mttp) REVERT: D 495 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7862 (mt-10) REVERT: E 6 ASP cc_start: 0.8293 (t0) cc_final: 0.7742 (m-30) REVERT: E 33 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7904 (mtmt) REVERT: E 72 TRP cc_start: 0.8330 (m100) cc_final: 0.8099 (m100) REVERT: E 181 ASP cc_start: 0.8496 (t70) cc_final: 0.8105 (t0) REVERT: E 308 LYS cc_start: 0.7954 (pttt) cc_final: 0.7495 (mttp) REVERT: F 6 ASP cc_start: 0.8329 (t0) cc_final: 0.7774 (m-30) REVERT: F 72 TRP cc_start: 0.8357 (m100) cc_final: 0.8045 (m100) REVERT: F 81 GLN cc_start: 0.8152 (mt0) cc_final: 0.7951 (mt0) REVERT: F 181 ASP cc_start: 0.8501 (t70) cc_final: 0.8052 (t0) REVERT: F 308 LYS cc_start: 0.7864 (pttt) cc_final: 0.7386 (mttp) REVERT: F 372 TYR cc_start: 0.7981 (t80) cc_final: 0.7632 (t80) REVERT: F 457 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7569 (mtm) REVERT: F 495 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8027 (mt-10) outliers start: 61 outliers final: 45 residues processed: 402 average time/residue: 0.3562 time to fit residues: 223.2868 Evaluate side-chains 312 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 264 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 457 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 222 optimal weight: 3.9990 chunk 181 optimal weight: 30.0000 chunk 73 optimal weight: 5.9990 chunk 267 optimal weight: 1.9990 chunk 288 optimal weight: 9.9990 chunk 238 optimal weight: 30.0000 chunk 265 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 214 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 HIS ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 HIS ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN E 221 HIS ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 HIS ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24612 Z= 0.319 Angle : 0.614 9.642 33384 Z= 0.310 Chirality : 0.045 0.157 3618 Planarity : 0.004 0.045 4242 Dihedral : 12.978 161.112 4080 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.16 % Allowed : 8.67 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 2970 helix: 0.01 (0.14), residues: 1302 sheet: -2.11 (0.26), residues: 282 loop : -0.95 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 72 HIS 0.007 0.002 HIS F 450 PHE 0.019 0.002 PHE D 122 TYR 0.018 0.002 TYR F 78 ARG 0.004 0.000 ARG E 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 314 time to evaluate : 2.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8284 (t0) cc_final: 0.7726 (m-30) REVERT: A 33 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7854 (mtmt) REVERT: A 84 GLN cc_start: 0.8266 (mm-40) cc_final: 0.8023 (mp10) REVERT: A 90 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8609 (tttm) REVERT: A 181 ASP cc_start: 0.8454 (t70) cc_final: 0.8060 (t0) REVERT: A 308 LYS cc_start: 0.7836 (pttt) cc_final: 0.7366 (mttp) REVERT: A 372 TYR cc_start: 0.7930 (t80) cc_final: 0.7687 (t80) REVERT: A 495 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7848 (mt-10) REVERT: B 6 ASP cc_start: 0.8288 (t0) cc_final: 0.7692 (m-30) REVERT: B 14 GLU cc_start: 0.7903 (pt0) cc_final: 0.7463 (pt0) REVERT: B 33 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7844 (mtmt) REVERT: B 72 TRP cc_start: 0.8337 (m100) cc_final: 0.8128 (m100) REVERT: B 163 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: B 181 ASP cc_start: 0.8462 (t70) cc_final: 0.8094 (t0) REVERT: B 308 LYS cc_start: 0.7954 (pttt) cc_final: 0.7500 (mttp) REVERT: C 6 ASP cc_start: 0.8288 (t0) cc_final: 0.7688 (m-30) REVERT: C 72 TRP cc_start: 0.8363 (m100) cc_final: 0.8098 (m100) REVERT: C 181 ASP cc_start: 0.8472 (t70) cc_final: 0.8051 (t0) REVERT: C 308 LYS cc_start: 0.7907 (pttt) cc_final: 0.7444 (mttp) REVERT: C 372 TYR cc_start: 0.7997 (t80) cc_final: 0.7487 (t80) REVERT: C 457 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7537 (mtm) REVERT: C 495 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8061 (mt-10) REVERT: D 6 ASP cc_start: 0.8275 (t0) cc_final: 0.7716 (m-30) REVERT: D 33 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7856 (mtmt) REVERT: D 181 ASP cc_start: 0.8468 (t70) cc_final: 0.8078 (t0) REVERT: D 308 LYS cc_start: 0.7823 (pttt) cc_final: 0.7377 (mttp) REVERT: D 372 TYR cc_start: 0.7927 (t80) cc_final: 0.7689 (t80) REVERT: D 495 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7847 (mt-10) REVERT: E 6 ASP cc_start: 0.8287 (t0) cc_final: 0.7685 (m-30) REVERT: E 14 GLU cc_start: 0.7903 (pt0) cc_final: 0.7467 (pt0) REVERT: E 33 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7844 (mtmt) REVERT: E 72 TRP cc_start: 0.8336 (m100) cc_final: 0.8113 (m100) REVERT: E 84 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7818 (mp10) REVERT: E 163 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7915 (m-30) REVERT: E 181 ASP cc_start: 0.8466 (t70) cc_final: 0.8104 (t0) REVERT: E 308 LYS cc_start: 0.7959 (pttt) cc_final: 0.7509 (mttp) REVERT: F 6 ASP cc_start: 0.8277 (t0) cc_final: 0.7680 (m-30) REVERT: F 72 TRP cc_start: 0.8367 (m100) cc_final: 0.8101 (m100) REVERT: F 90 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8506 (tttm) REVERT: F 181 ASP cc_start: 0.8460 (t70) cc_final: 0.8040 (t0) REVERT: F 308 LYS cc_start: 0.7910 (pttt) cc_final: 0.7450 (mttp) REVERT: F 372 TYR cc_start: 0.7995 (t80) cc_final: 0.7495 (t80) REVERT: F 457 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7535 (mtm) outliers start: 79 outliers final: 50 residues processed: 370 average time/residue: 0.3506 time to fit residues: 203.2789 Evaluate side-chains 326 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 270 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 405 SER Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 457 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 268 optimal weight: 30.0000 chunk 284 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 254 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 221 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS C 81 GLN C 84 GLN ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS D 221 HIS ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 HIS F 81 GLN F 84 GLN ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24612 Z= 0.340 Angle : 0.610 9.830 33384 Z= 0.306 Chirality : 0.045 0.155 3618 Planarity : 0.004 0.047 4242 Dihedral : 12.635 158.670 4080 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.64 % Allowed : 9.87 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.16), residues: 2970 helix: 0.32 (0.14), residues: 1326 sheet: -1.90 (0.22), residues: 420 loop : -0.59 (0.20), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 72 HIS 0.007 0.002 HIS F 450 PHE 0.018 0.002 PHE D 122 TYR 0.016 0.002 TYR F 78 ARG 0.004 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 290 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.8276 (t0) cc_final: 0.7755 (m-30) REVERT: A 33 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7831 (mtmt) REVERT: A 81 GLN cc_start: 0.8114 (mt0) cc_final: 0.7815 (mt0) REVERT: A 84 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8025 (mp10) REVERT: A 90 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8644 (tttm) REVERT: A 163 ASP cc_start: 0.8267 (m-30) cc_final: 0.7622 (m-30) REVERT: A 169 MET cc_start: 0.8761 (ttm) cc_final: 0.8520 (mtm) REVERT: A 181 ASP cc_start: 0.8466 (t70) cc_final: 0.8057 (t0) REVERT: A 308 LYS cc_start: 0.7850 (pttt) cc_final: 0.7399 (mttp) REVERT: A 495 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7755 (mt-10) REVERT: B 6 ASP cc_start: 0.8270 (t0) cc_final: 0.7703 (m-30) REVERT: B 14 GLU cc_start: 0.7977 (pt0) cc_final: 0.7559 (pt0) REVERT: B 33 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7858 (mtmt) REVERT: B 72 TRP cc_start: 0.8346 (m100) cc_final: 0.8110 (m100) REVERT: B 163 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7968 (m-30) REVERT: B 181 ASP cc_start: 0.8480 (t70) cc_final: 0.8092 (t0) REVERT: B 308 LYS cc_start: 0.7945 (pttt) cc_final: 0.7499 (mttp) REVERT: C 6 ASP cc_start: 0.8288 (t0) cc_final: 0.7710 (m-30) REVERT: C 72 TRP cc_start: 0.8353 (m100) cc_final: 0.7650 (m100) REVERT: C 81 GLN cc_start: 0.8244 (mt0) cc_final: 0.7909 (mt0) REVERT: C 84 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7865 (mp10) REVERT: C 140 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: C 163 ASP cc_start: 0.8301 (m-30) cc_final: 0.7766 (m-30) REVERT: C 308 LYS cc_start: 0.7903 (pttt) cc_final: 0.7436 (mttp) REVERT: C 372 TYR cc_start: 0.8185 (t80) cc_final: 0.7980 (t80) REVERT: C 457 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7615 (mtm) REVERT: D 6 ASP cc_start: 0.8259 (t0) cc_final: 0.7751 (m-30) REVERT: D 33 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7840 (mtmt) REVERT: D 163 ASP cc_start: 0.8305 (m-30) cc_final: 0.8097 (m-30) REVERT: D 181 ASP cc_start: 0.8463 (t70) cc_final: 0.8061 (t0) REVERT: D 308 LYS cc_start: 0.7872 (pttt) cc_final: 0.7426 (mttp) REVERT: D 372 TYR cc_start: 0.8047 (t80) cc_final: 0.7833 (t80) REVERT: D 495 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7749 (mt-10) REVERT: E 6 ASP cc_start: 0.8266 (t0) cc_final: 0.7696 (m-30) REVERT: E 14 GLU cc_start: 0.7979 (pt0) cc_final: 0.7556 (pt0) REVERT: E 33 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7854 (mtmt) REVERT: E 72 TRP cc_start: 0.8338 (m100) cc_final: 0.8136 (m100) REVERT: E 84 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7909 (mp10) REVERT: E 163 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7974 (m-30) REVERT: E 181 ASP cc_start: 0.8478 (t70) cc_final: 0.8104 (t0) REVERT: E 308 LYS cc_start: 0.7937 (pttt) cc_final: 0.7491 (mttp) REVERT: F 6 ASP cc_start: 0.8297 (t0) cc_final: 0.7732 (m-30) REVERT: F 72 TRP cc_start: 0.8355 (m100) cc_final: 0.7653 (m100) REVERT: F 81 GLN cc_start: 0.8236 (mt0) cc_final: 0.7886 (mt0) REVERT: F 84 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7884 (mp10) REVERT: F 90 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8540 (tttm) REVERT: F 140 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: F 163 ASP cc_start: 0.8286 (m-30) cc_final: 0.7766 (m-30) REVERT: F 291 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8793 (tt) REVERT: F 308 LYS cc_start: 0.7905 (pttt) cc_final: 0.7438 (mttp) REVERT: F 457 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7611 (mtm) REVERT: F 495 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8007 (mt-10) outliers start: 91 outliers final: 67 residues processed: 358 average time/residue: 0.3643 time to fit residues: 205.2397 Evaluate side-chains 352 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 276 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 399 PHE Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 457 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 211 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 255 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN F 84 GLN ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 24612 Z= 0.234 Angle : 0.552 9.253 33384 Z= 0.276 Chirality : 0.043 0.152 3618 Planarity : 0.004 0.048 4242 Dihedral : 12.144 156.460 4080 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.00 % Allowed : 10.91 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.16 (0.16), residues: 2970 helix: 0.78 (0.15), residues: 1290 sheet: -1.14 (0.25), residues: 348 loop : -0.60 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 72 HIS 0.005 0.001 HIS C 258 PHE 0.014 0.002 PHE C 9 TYR 0.013 0.001 TYR F 372 ARG 0.003 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 285 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7764 (mtmt) REVERT: A 81 GLN cc_start: 0.8164 (mt0) cc_final: 0.7699 (mt0) REVERT: A 84 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8050 (mp10) REVERT: A 90 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8531 (tttm) REVERT: A 163 ASP cc_start: 0.8191 (m-30) cc_final: 0.7446 (m-30) REVERT: A 308 LYS cc_start: 0.7853 (pttt) cc_final: 0.7476 (mttp) REVERT: A 495 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7737 (mt-10) REVERT: B 6 ASP cc_start: 0.8149 (t0) cc_final: 0.7600 (m-30) REVERT: B 14 GLU cc_start: 0.7956 (pt0) cc_final: 0.7605 (pt0) REVERT: B 33 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7828 (mtmt) REVERT: B 72 TRP cc_start: 0.8322 (m100) cc_final: 0.8111 (m100) REVERT: B 163 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7939 (m-30) REVERT: B 181 ASP cc_start: 0.8397 (t70) cc_final: 0.8023 (t0) REVERT: B 308 LYS cc_start: 0.7912 (pttt) cc_final: 0.7528 (mttp) REVERT: C 6 ASP cc_start: 0.8182 (t0) cc_final: 0.7597 (m-30) REVERT: C 72 TRP cc_start: 0.8305 (m100) cc_final: 0.7914 (m100) REVERT: C 84 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7935 (mp10) REVERT: C 140 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: C 163 ASP cc_start: 0.8246 (m-30) cc_final: 0.7948 (m-30) REVERT: C 308 LYS cc_start: 0.7849 (pttt) cc_final: 0.7476 (mttp) REVERT: C 372 TYR cc_start: 0.8109 (t80) cc_final: 0.7894 (t80) REVERT: C 384 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8378 (tt0) REVERT: C 457 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7477 (mtm) REVERT: C 495 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7947 (mt-10) REVERT: D 33 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7804 (mtmt) REVERT: D 81 GLN cc_start: 0.8096 (mt0) cc_final: 0.7640 (mt0) REVERT: D 84 GLN cc_start: 0.8339 (mm-40) cc_final: 0.7895 (mp10) REVERT: D 163 ASP cc_start: 0.8207 (m-30) cc_final: 0.7483 (m-30) REVERT: D 308 LYS cc_start: 0.7839 (pttt) cc_final: 0.7479 (mttp) REVERT: D 495 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7878 (mt-10) REVERT: E 6 ASP cc_start: 0.8148 (t0) cc_final: 0.7597 (m-30) REVERT: E 14 GLU cc_start: 0.7954 (pt0) cc_final: 0.7605 (pt0) REVERT: E 33 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7831 (mtmt) REVERT: E 72 TRP cc_start: 0.8320 (m100) cc_final: 0.8112 (m100) REVERT: E 81 GLN cc_start: 0.8288 (mt0) cc_final: 0.7633 (mt0) REVERT: E 84 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7905 (mp10) REVERT: E 163 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7490 (m-30) REVERT: E 181 ASP cc_start: 0.8400 (t70) cc_final: 0.8024 (t0) REVERT: E 308 LYS cc_start: 0.7911 (pttt) cc_final: 0.7525 (mttp) REVERT: F 6 ASP cc_start: 0.8174 (t0) cc_final: 0.7596 (m-30) REVERT: F 72 TRP cc_start: 0.8302 (m100) cc_final: 0.7871 (m100) REVERT: F 84 GLN cc_start: 0.8183 (mm110) cc_final: 0.7944 (mp10) REVERT: F 90 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8619 (tttm) REVERT: F 140 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7731 (mt-10) REVERT: F 291 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8739 (tt) REVERT: F 308 LYS cc_start: 0.7854 (pttt) cc_final: 0.7480 (mttp) REVERT: F 372 TYR cc_start: 0.7898 (t80) cc_final: 0.7543 (t80) REVERT: F 384 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: F 457 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7403 (mtm) REVERT: F 495 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7937 (mt-10) outliers start: 75 outliers final: 56 residues processed: 338 average time/residue: 0.3377 time to fit residues: 182.3452 Evaluate side-chains 332 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 265 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 399 PHE Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 457 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 10.0000 chunk 255 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 236 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 23 optimal weight: 30.0000 chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN F 84 GLN ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24612 Z= 0.187 Angle : 0.527 7.826 33384 Z= 0.264 Chirality : 0.042 0.157 3618 Planarity : 0.004 0.047 4242 Dihedral : 11.766 154.266 4080 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.80 % Allowed : 11.71 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.02 (0.16), residues: 2970 helix: 0.90 (0.14), residues: 1332 sheet: -1.47 (0.24), residues: 378 loop : -0.40 (0.19), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 72 HIS 0.004 0.001 HIS C 258 PHE 0.016 0.001 PHE F 9 TYR 0.012 0.001 TYR F 372 ARG 0.004 0.000 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 308 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7763 (mtmt) REVERT: A 81 GLN cc_start: 0.8167 (mt0) cc_final: 0.7628 (mt0) REVERT: A 84 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8040 (mp10) REVERT: A 163 ASP cc_start: 0.8186 (m-30) cc_final: 0.7410 (m-30) REVERT: A 308 LYS cc_start: 0.7799 (pttt) cc_final: 0.7517 (mttp) REVERT: A 495 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7847 (mt-10) REVERT: B 6 ASP cc_start: 0.8156 (t0) cc_final: 0.7715 (m-30) REVERT: B 14 GLU cc_start: 0.7975 (pt0) cc_final: 0.7640 (pt0) REVERT: B 33 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7821 (mtmt) REVERT: B 81 GLN cc_start: 0.8289 (mt0) cc_final: 0.7571 (mt0) REVERT: B 163 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: B 181 ASP cc_start: 0.8352 (t70) cc_final: 0.7989 (t0) REVERT: B 308 LYS cc_start: 0.7890 (pttt) cc_final: 0.7584 (mttp) REVERT: C 6 ASP cc_start: 0.8091 (t0) cc_final: 0.7657 (m-30) REVERT: C 72 TRP cc_start: 0.8303 (m100) cc_final: 0.7893 (m100) REVERT: C 81 GLN cc_start: 0.8044 (mt0) cc_final: 0.7648 (mt0) REVERT: C 137 THR cc_start: 0.8675 (m) cc_final: 0.8099 (p) REVERT: C 140 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7358 (mt-10) REVERT: C 163 ASP cc_start: 0.8200 (m-30) cc_final: 0.7751 (m-30) REVERT: C 308 LYS cc_start: 0.7821 (pttt) cc_final: 0.7485 (mttp) REVERT: C 372 TYR cc_start: 0.8071 (t80) cc_final: 0.7867 (t80) REVERT: C 457 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7414 (mtm) REVERT: C 495 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7667 (mt-10) REVERT: D 33 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7757 (mtmt) REVERT: D 81 GLN cc_start: 0.8145 (mt0) cc_final: 0.7658 (mt0) REVERT: D 84 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7864 (mp10) REVERT: D 163 ASP cc_start: 0.8220 (m-30) cc_final: 0.7505 (m-30) REVERT: D 308 LYS cc_start: 0.7796 (pttt) cc_final: 0.7534 (mttp) REVERT: D 495 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7847 (mt-10) REVERT: E 14 GLU cc_start: 0.7970 (pt0) cc_final: 0.7638 (pt0) REVERT: E 33 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7825 (mtmt) REVERT: E 72 TRP cc_start: 0.8302 (m100) cc_final: 0.8091 (m100) REVERT: E 81 GLN cc_start: 0.8271 (mt0) cc_final: 0.7576 (mt0) REVERT: E 84 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7944 (mp10) REVERT: E 163 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: E 181 ASP cc_start: 0.8351 (t70) cc_final: 0.7987 (t0) REVERT: E 308 LYS cc_start: 0.7880 (pttt) cc_final: 0.7577 (mttp) REVERT: F 6 ASP cc_start: 0.8111 (t0) cc_final: 0.7681 (m-30) REVERT: F 72 TRP cc_start: 0.8305 (m100) cc_final: 0.7900 (m100) REVERT: F 84 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7886 (mp10) REVERT: F 140 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: F 308 LYS cc_start: 0.7816 (pttt) cc_final: 0.7484 (mttp) REVERT: F 372 TYR cc_start: 0.8039 (t80) cc_final: 0.7632 (t80) REVERT: F 457 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7372 (mtm) REVERT: F 495 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7887 (mt-10) outliers start: 70 outliers final: 47 residues processed: 363 average time/residue: 0.3529 time to fit residues: 201.9971 Evaluate side-chains 318 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 265 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 399 PHE Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain F residue 12 MET Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 457 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 239 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 chunk 283 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 172 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24612 Z= 0.198 Angle : 0.540 11.023 33384 Z= 0.268 Chirality : 0.043 0.157 3618 Planarity : 0.004 0.048 4242 Dihedral : 11.141 152.203 4080 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.24 % Allowed : 12.23 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.19 (0.16), residues: 2970 helix: 1.04 (0.14), residues: 1344 sheet: -1.25 (0.25), residues: 378 loop : -0.31 (0.20), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 72 HIS 0.005 0.001 HIS A 450 PHE 0.014 0.001 PHE C 9 TYR 0.011 0.001 TYR F 372 ARG 0.003 0.000 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 270 time to evaluate : 2.468 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7735 (mtmt) REVERT: A 81 GLN cc_start: 0.8197 (mt0) cc_final: 0.7619 (mt0) REVERT: A 84 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8087 (mp10) REVERT: A 90 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8517 (tttm) REVERT: A 163 ASP cc_start: 0.8236 (m-30) cc_final: 0.7467 (m-30) REVERT: A 308 LYS cc_start: 0.7812 (pttt) cc_final: 0.7534 (mttp) REVERT: A 495 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7872 (mt-10) REVERT: B 14 GLU cc_start: 0.8003 (pt0) cc_final: 0.7730 (pt0) REVERT: B 33 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7797 (mtmt) REVERT: B 72 TRP cc_start: 0.8313 (m100) cc_final: 0.7926 (m100) REVERT: B 81 GLN cc_start: 0.8277 (mt0) cc_final: 0.7521 (mt0) REVERT: B 163 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: B 181 ASP cc_start: 0.8329 (t70) cc_final: 0.7916 (t0) REVERT: B 308 LYS cc_start: 0.7896 (pttt) cc_final: 0.7604 (mttp) REVERT: C 6 ASP cc_start: 0.8091 (t0) cc_final: 0.7665 (m-30) REVERT: C 72 TRP cc_start: 0.8309 (m100) cc_final: 0.7909 (m100) REVERT: C 137 THR cc_start: 0.8657 (m) cc_final: 0.8120 (p) REVERT: C 140 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7376 (mt-10) REVERT: C 308 LYS cc_start: 0.7873 (pttt) cc_final: 0.7579 (mttp) REVERT: C 372 TYR cc_start: 0.8091 (t80) cc_final: 0.7888 (t80) REVERT: C 384 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: C 457 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7435 (mtm) REVERT: C 495 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7641 (mt-10) REVERT: D 33 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7735 (mtmt) REVERT: D 81 GLN cc_start: 0.8192 (mt0) cc_final: 0.7651 (mt0) REVERT: D 84 GLN cc_start: 0.8380 (mm-40) cc_final: 0.7932 (mp10) REVERT: D 163 ASP cc_start: 0.8248 (m-30) cc_final: 0.7555 (m-30) REVERT: D 308 LYS cc_start: 0.7806 (pttt) cc_final: 0.7564 (mttp) REVERT: D 495 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7857 (mt-10) REVERT: E 14 GLU cc_start: 0.7997 (pt0) cc_final: 0.7726 (pt0) REVERT: E 33 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7800 (mtmt) REVERT: E 81 GLN cc_start: 0.8288 (mt0) cc_final: 0.7586 (mt0) REVERT: E 84 GLN cc_start: 0.8324 (mm-40) cc_final: 0.7938 (mp10) REVERT: E 163 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: E 181 ASP cc_start: 0.8331 (t70) cc_final: 0.7913 (t0) REVERT: E 308 LYS cc_start: 0.7886 (pttt) cc_final: 0.7595 (mttp) REVERT: F 6 ASP cc_start: 0.8088 (t0) cc_final: 0.7702 (m-30) REVERT: F 72 TRP cc_start: 0.8323 (m100) cc_final: 0.7930 (m100) REVERT: F 137 THR cc_start: 0.8673 (m) cc_final: 0.8156 (p) REVERT: F 140 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7397 (mt-10) REVERT: F 308 LYS cc_start: 0.7860 (pttt) cc_final: 0.7582 (mttp) REVERT: F 372 TYR cc_start: 0.8108 (t80) cc_final: 0.7708 (t80) REVERT: F 384 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: F 457 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7386 (mtm) REVERT: F 495 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7636 (mt-10) outliers start: 81 outliers final: 55 residues processed: 330 average time/residue: 0.3541 time to fit residues: 185.4849 Evaluate side-chains 321 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 257 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain F residue 12 MET Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 457 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 54 optimal weight: 0.0370 chunk 180 optimal weight: 8.9990 chunk 193 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 222 optimal weight: 20.0000 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24612 Z= 0.215 Angle : 0.546 10.761 33384 Z= 0.270 Chirality : 0.042 0.157 3618 Planarity : 0.004 0.047 4242 Dihedral : 10.826 150.173 4080 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.96 % Allowed : 12.35 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.23 (0.16), residues: 2970 helix: 1.07 (0.14), residues: 1356 sheet: -1.12 (0.26), residues: 378 loop : -0.32 (0.20), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 72 HIS 0.005 0.001 HIS A 450 PHE 0.012 0.001 PHE E 148 TYR 0.011 0.001 TYR F 372 ARG 0.003 0.000 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 269 time to evaluate : 2.599 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8240 (mt0) cc_final: 0.7616 (mt0) REVERT: A 84 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8110 (mp10) REVERT: A 90 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8538 (tttm) REVERT: A 163 ASP cc_start: 0.8244 (m-30) cc_final: 0.7515 (m-30) REVERT: A 308 LYS cc_start: 0.7825 (pttt) cc_final: 0.7545 (mttp) REVERT: A 372 TYR cc_start: 0.7724 (t80) cc_final: 0.7509 (t80) REVERT: B 33 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7778 (mtmt) REVERT: B 66 ARG cc_start: 0.8823 (ttm-80) cc_final: 0.8614 (ttm-80) REVERT: B 72 TRP cc_start: 0.8366 (m100) cc_final: 0.7954 (m100) REVERT: B 81 GLN cc_start: 0.8285 (mt0) cc_final: 0.7507 (mt0) REVERT: B 163 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: B 308 LYS cc_start: 0.7895 (pttt) cc_final: 0.7631 (mttp) REVERT: C 6 ASP cc_start: 0.8098 (t0) cc_final: 0.7676 (m-30) REVERT: C 72 TRP cc_start: 0.8315 (m100) cc_final: 0.7954 (m100) REVERT: C 137 THR cc_start: 0.8658 (m) cc_final: 0.8104 (p) REVERT: C 140 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: C 308 LYS cc_start: 0.7884 (pttt) cc_final: 0.7585 (mttp) REVERT: C 372 TYR cc_start: 0.8103 (t80) cc_final: 0.7902 (t80) REVERT: C 384 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8367 (tt0) REVERT: C 457 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7447 (mtm) REVERT: C 495 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7868 (mt-10) REVERT: D 81 GLN cc_start: 0.8219 (mt0) cc_final: 0.7594 (mt0) REVERT: D 163 ASP cc_start: 0.8267 (m-30) cc_final: 0.7577 (m-30) REVERT: D 308 LYS cc_start: 0.7804 (pttt) cc_final: 0.7592 (mttp) REVERT: E 33 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7789 (mtmt) REVERT: E 72 TRP cc_start: 0.8333 (m100) cc_final: 0.7873 (m100) REVERT: E 81 GLN cc_start: 0.8304 (mt0) cc_final: 0.7614 (mt0) REVERT: E 84 GLN cc_start: 0.8351 (mm-40) cc_final: 0.7969 (mp10) REVERT: E 163 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: E 308 LYS cc_start: 0.7901 (pttt) cc_final: 0.7633 (mttp) REVERT: F 6 ASP cc_start: 0.8122 (t0) cc_final: 0.7729 (m-30) REVERT: F 72 TRP cc_start: 0.8325 (m100) cc_final: 0.7944 (m100) REVERT: F 137 THR cc_start: 0.8668 (m) cc_final: 0.8116 (p) REVERT: F 140 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: F 308 LYS cc_start: 0.7856 (pttt) cc_final: 0.7584 (mttp) REVERT: F 372 TYR cc_start: 0.8185 (t80) cc_final: 0.7811 (t80) REVERT: F 384 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: F 457 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7440 (mtm) REVERT: F 495 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7859 (mt-10) outliers start: 74 outliers final: 59 residues processed: 328 average time/residue: 0.3410 time to fit residues: 177.8338 Evaluate side-chains 319 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 251 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 405 SER Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 399 PHE Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 457 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 2.9990 chunk 271 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 chunk 264 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 81 optimal weight: 30.0000 chunk 238 optimal weight: 30.0000 chunk 249 optimal weight: 7.9990 chunk 263 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS ** E 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24612 Z= 0.169 Angle : 0.525 8.779 33384 Z= 0.260 Chirality : 0.042 0.151 3618 Planarity : 0.004 0.046 4242 Dihedral : 10.502 147.617 4080 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.68 % Allowed : 12.75 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.43 (0.16), residues: 2970 helix: 1.27 (0.14), residues: 1344 sheet: -0.92 (0.26), residues: 378 loop : -0.30 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 72 HIS 0.005 0.001 HIS A 450 PHE 0.012 0.001 PHE E 148 TYR 0.011 0.001 TYR F 372 ARG 0.003 0.000 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 278 time to evaluate : 2.536 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8213 (mt0) cc_final: 0.7592 (mt0) REVERT: A 84 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8077 (mp10) REVERT: A 90 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8500 (tttm) REVERT: A 163 ASP cc_start: 0.8226 (m-30) cc_final: 0.7497 (m-30) REVERT: A 308 LYS cc_start: 0.7801 (pttt) cc_final: 0.7601 (mttp) REVERT: B 33 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7777 (mtmt) REVERT: B 66 ARG cc_start: 0.8804 (ttm-80) cc_final: 0.8602 (ttm-80) REVERT: B 72 TRP cc_start: 0.8361 (m100) cc_final: 0.7963 (m100) REVERT: B 81 GLN cc_start: 0.8266 (mt0) cc_final: 0.7520 (mt0) REVERT: B 163 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7445 (m-30) REVERT: B 308 LYS cc_start: 0.7861 (pttt) cc_final: 0.7637 (mttp) REVERT: C 72 TRP cc_start: 0.8309 (m100) cc_final: 0.7972 (m100) REVERT: C 137 THR cc_start: 0.8658 (m) cc_final: 0.8149 (p) REVERT: C 140 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: C 308 LYS cc_start: 0.7860 (pttt) cc_final: 0.7626 (mttp) REVERT: C 384 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8345 (tt0) REVERT: C 491 ARG cc_start: 0.8291 (mtp180) cc_final: 0.7952 (mtm-85) REVERT: C 495 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7871 (mt-10) REVERT: D 81 GLN cc_start: 0.8207 (mt0) cc_final: 0.7617 (mt0) REVERT: D 163 ASP cc_start: 0.8257 (m-30) cc_final: 0.7548 (m-30) REVERT: E 33 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7783 (mtmt) REVERT: E 72 TRP cc_start: 0.8347 (m100) cc_final: 0.7873 (m100) REVERT: E 81 GLN cc_start: 0.8292 (mt0) cc_final: 0.7554 (mt0) REVERT: E 84 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7931 (mp10) REVERT: E 163 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: E 308 LYS cc_start: 0.7856 (pttt) cc_final: 0.7634 (mttp) REVERT: F 6 ASP cc_start: 0.8097 (t0) cc_final: 0.7708 (m-30) REVERT: F 72 TRP cc_start: 0.8321 (m100) cc_final: 0.7936 (m100) REVERT: F 137 THR cc_start: 0.8664 (m) cc_final: 0.8152 (p) REVERT: F 140 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: F 308 LYS cc_start: 0.7831 (pttt) cc_final: 0.7615 (mttp) REVERT: F 372 TYR cc_start: 0.8128 (t80) cc_final: 0.7797 (t80) REVERT: F 384 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8344 (tt0) REVERT: F 457 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7413 (mtm) REVERT: F 491 ARG cc_start: 0.8286 (mtp180) cc_final: 0.7832 (mtm-85) REVERT: F 495 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7650 (mt-10) outliers start: 67 outliers final: 52 residues processed: 330 average time/residue: 0.3558 time to fit residues: 184.8727 Evaluate side-chains 326 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 266 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 399 PHE Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 457 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 10.0000 chunk 279 optimal weight: 30.0000 chunk 170 optimal weight: 0.0070 chunk 132 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 292 optimal weight: 2.9990 chunk 269 optimal weight: 10.0000 chunk 233 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24612 Z= 0.217 Angle : 0.549 9.192 33384 Z= 0.271 Chirality : 0.043 0.215 3618 Planarity : 0.004 0.047 4242 Dihedral : 10.393 146.018 4080 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.44 % Allowed : 13.31 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.44 (0.16), residues: 2970 helix: 1.14 (0.14), residues: 1380 sheet: -0.53 (0.26), residues: 402 loop : -0.30 (0.20), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 72 HIS 0.005 0.001 HIS A 450 PHE 0.025 0.001 PHE C 490 TYR 0.014 0.001 TYR A 372 ARG 0.003 0.000 ARG D 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 265 time to evaluate : 2.657 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8259 (mt0) cc_final: 0.7627 (mt0) REVERT: A 84 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8104 (mp10) REVERT: A 90 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8532 (tttm) REVERT: A 163 ASP cc_start: 0.8257 (m-30) cc_final: 0.7569 (m-30) REVERT: A 308 LYS cc_start: 0.7792 (pttt) cc_final: 0.7570 (mttp) REVERT: B 33 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7776 (mtmt) REVERT: B 66 ARG cc_start: 0.8802 (ttm-80) cc_final: 0.8543 (ttm-80) REVERT: B 72 TRP cc_start: 0.8363 (m100) cc_final: 0.7962 (m100) REVERT: B 81 GLN cc_start: 0.8284 (mt0) cc_final: 0.7487 (mt0) REVERT: B 163 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7435 (m-30) REVERT: B 308 LYS cc_start: 0.7872 (pttt) cc_final: 0.7634 (mttp) REVERT: C 6 ASP cc_start: 0.8069 (t0) cc_final: 0.7640 (m-30) REVERT: C 72 TRP cc_start: 0.8333 (m100) cc_final: 0.7973 (m100) REVERT: C 137 THR cc_start: 0.8658 (m) cc_final: 0.8149 (p) REVERT: C 140 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: C 308 LYS cc_start: 0.7845 (pttt) cc_final: 0.7596 (mttp) REVERT: C 384 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8357 (tt0) REVERT: C 495 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7658 (mt-10) REVERT: D 81 GLN cc_start: 0.8241 (mt0) cc_final: 0.7616 (mt0) REVERT: D 163 ASP cc_start: 0.8245 (m-30) cc_final: 0.7574 (m-30) REVERT: E 33 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7785 (mtmt) REVERT: E 72 TRP cc_start: 0.8359 (m100) cc_final: 0.7905 (m100) REVERT: E 81 GLN cc_start: 0.8302 (mt0) cc_final: 0.7592 (mt0) REVERT: E 84 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7968 (mp10) REVERT: E 163 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: E 308 LYS cc_start: 0.7865 (pttt) cc_final: 0.7632 (mttp) REVERT: F 6 ASP cc_start: 0.8097 (t0) cc_final: 0.7716 (m-30) REVERT: F 72 TRP cc_start: 0.8341 (m100) cc_final: 0.7965 (m100) REVERT: F 140 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: F 308 LYS cc_start: 0.7826 (pttt) cc_final: 0.7592 (mttp) REVERT: F 372 TYR cc_start: 0.8183 (t80) cc_final: 0.7883 (t80) REVERT: F 384 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: F 457 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7487 (mtm) REVERT: F 491 ARG cc_start: 0.8318 (mtp180) cc_final: 0.7968 (mtm-85) REVERT: F 495 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7865 (mt-10) outliers start: 61 outliers final: 50 residues processed: 316 average time/residue: 0.3737 time to fit residues: 187.5675 Evaluate side-chains 316 residues out of total 2502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 258 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 405 SER Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 90 LYS Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 405 SER Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 384 GLU Chi-restraints excluded: chain F residue 457 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 233 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.082972 restraints weight = 45130.671| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.26 r_work: 0.2975 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 24612 Z= 0.330 Angle : 0.612 11.451 33384 Z= 0.303 Chirality : 0.045 0.207 3618 Planarity : 0.004 0.047 4242 Dihedral : 10.504 145.744 4080 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.92 % Allowed : 13.39 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.30 (0.16), residues: 2970 helix: 1.04 (0.14), residues: 1374 sheet: -0.62 (0.26), residues: 402 loop : -0.37 (0.20), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 72 HIS 0.007 0.001 HIS E 450 PHE 0.024 0.002 PHE F 490 TYR 0.030 0.002 TYR A 372 ARG 0.003 0.000 ARG D 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5072.53 seconds wall clock time: 93 minutes 22.36 seconds (5602.36 seconds total)