Starting phenix.real_space_refine on Tue Apr 9 11:51:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ujn_26567/04_2024/7ujn_26567_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ujn_26567/04_2024/7ujn_26567.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ujn_26567/04_2024/7ujn_26567_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ujn_26567/04_2024/7ujn_26567_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ujn_26567/04_2024/7ujn_26567_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ujn_26567/04_2024/7ujn_26567.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ujn_26567/04_2024/7ujn_26567.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ujn_26567/04_2024/7ujn_26567_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ujn_26567/04_2024/7ujn_26567_updated.pdb" } resolution = 2.89 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= -0.000 sd= 0.004 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 36 5.49 5 S 92 5.16 5 C 10288 2.51 5 N 2816 2.21 5 O 3040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 234": "OE1" <-> "OE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C GLU 459": "OE1" <-> "OE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D GLU 459": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16272 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3975 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 24, 'TRANS': 462} Chain: "B" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3975 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 24, 'TRANS': 462} Chain: "C" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3975 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 24, 'TRANS': 462} Chain: "D" Number of atoms: 3975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3975 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 24, 'TRANS': 462} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'T8T': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'T8T': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'T8T': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'T8T': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.45, per 1000 atoms: 0.52 Number of scatterers: 16272 At special positions: 0 Unit cell: (110.04, 91.56, 118.44, 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 92 16.00 P 36 15.00 O 3040 8.00 N 2816 7.00 C 10288 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.20 Conformation dependent library (CDL) restraints added in 2.8 seconds 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 111 helices and 12 sheets defined 49.9% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 139 through 146 removed outlier: 4.784A pdb=" N LEU A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG A 145 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR A 146 " --> pdb=" O GLN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 164 through 185 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 193 through 206 Processing helix chain 'A' and resid 216 through 219 No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 233 through 248 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 261 through 273 removed outlier: 4.210A pdb=" N CYS A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 299 removed outlier: 5.234A pdb=" N PHE A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 353 through 372 removed outlier: 4.023A pdb=" N VAL A 356 " --> pdb=" O ASP A 353 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY A 357 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 396 removed outlier: 5.012A pdb=" N ASP A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TYR A 396 " --> pdb=" O LYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 421 removed outlier: 4.399A pdb=" N LYS A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 removed outlier: 3.603A pdb=" N LEU A 431 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 removed outlier: 4.719A pdb=" N ASP A 440 " --> pdb=" O LYS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 559 through 575 Processing helix chain 'B' and resid 130 through 136 Processing helix chain 'B' and resid 139 through 146 removed outlier: 4.785A pdb=" N LEU B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR B 146 " --> pdb=" O GLN B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 Processing helix chain 'B' and resid 164 through 185 Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 193 through 206 Processing helix chain 'B' and resid 216 through 219 No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 261 through 273 removed outlier: 4.211A pdb=" N CYS B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 5.233A pdb=" N PHE B 296 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B 298 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B 299 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 353 through 372 removed outlier: 4.024A pdb=" N VAL B 356 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY B 357 " --> pdb=" O LYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 396 removed outlier: 5.014A pdb=" N ASP B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N TYR B 396 " --> pdb=" O LYS B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.397A pdb=" N LYS B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 431 removed outlier: 3.603A pdb=" N LEU B 431 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 449 removed outlier: 4.717A pdb=" N ASP B 440 " --> pdb=" O LYS B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 472 No H-bonds generated for 'chain 'B' and resid 470 through 472' Processing helix chain 'B' and resid 476 through 481 Processing helix chain 'B' and resid 495 through 497 No H-bonds generated for 'chain 'B' and resid 495 through 497' Processing helix chain 'B' and resid 514 through 517 Processing helix chain 'B' and resid 534 through 536 No H-bonds generated for 'chain 'B' and resid 534 through 536' Processing helix chain 'B' and resid 559 through 575 Processing helix chain 'B' and resid 589 through 594 Proline residue: B 593 - end of helix No H-bonds generated for 'chain 'B' and resid 589 through 594' Processing helix chain 'C' and resid 130 through 136 Processing helix chain 'C' and resid 139 through 146 removed outlier: 4.783A pdb=" N LEU C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG C 145 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR C 146 " --> pdb=" O GLN C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 155 Processing helix chain 'C' and resid 164 through 185 Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 193 through 206 Processing helix chain 'C' and resid 216 through 219 No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 233 through 248 Processing helix chain 'C' and resid 251 through 256 Processing helix chain 'C' and resid 261 through 273 removed outlier: 4.211A pdb=" N CYS C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 299 removed outlier: 5.233A pdb=" N PHE C 296 " --> pdb=" O ASN C 293 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR C 298 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU C 299 " --> pdb=" O PHE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 353 through 372 removed outlier: 4.015A pdb=" N VAL C 356 " --> pdb=" O ASP C 353 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY C 357 " --> pdb=" O LYS C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 396 removed outlier: 5.010A pdb=" N ASP C 395 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TYR C 396 " --> pdb=" O LYS C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 421 removed outlier: 4.398A pdb=" N LYS C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 431 removed outlier: 3.602A pdb=" N LEU C 431 " --> pdb=" O LEU C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 449 removed outlier: 4.719A pdb=" N ASP C 440 " --> pdb=" O LYS C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 472 No H-bonds generated for 'chain 'C' and resid 470 through 472' Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'C' and resid 495 through 497 No H-bonds generated for 'chain 'C' and resid 495 through 497' Processing helix chain 'C' and resid 514 through 517 Processing helix chain 'C' and resid 534 through 536 No H-bonds generated for 'chain 'C' and resid 534 through 536' Processing helix chain 'C' and resid 559 through 575 Processing helix chain 'C' and resid 592 through 594 No H-bonds generated for 'chain 'C' and resid 592 through 594' Processing helix chain 'D' and resid 130 through 136 Processing helix chain 'D' and resid 139 through 146 removed outlier: 4.783A pdb=" N LEU D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG D 145 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR D 146 " --> pdb=" O GLN D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 155 Processing helix chain 'D' and resid 164 through 185 Processing helix chain 'D' and resid 187 through 189 No H-bonds generated for 'chain 'D' and resid 187 through 189' Processing helix chain 'D' and resid 193 through 206 Processing helix chain 'D' and resid 216 through 219 No H-bonds generated for 'chain 'D' and resid 216 through 219' Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 261 through 273 removed outlier: 4.198A pdb=" N CYS D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 299 removed outlier: 5.233A pdb=" N PHE D 296 " --> pdb=" O ASN D 293 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR D 298 " --> pdb=" O SER D 295 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU D 299 " --> pdb=" O PHE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 353 through 372 removed outlier: 4.023A pdb=" N VAL D 356 " --> pdb=" O ASP D 353 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY D 357 " --> pdb=" O LYS D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 396 removed outlier: 5.009A pdb=" N ASP D 395 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TYR D 396 " --> pdb=" O LYS D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 404 No H-bonds generated for 'chain 'D' and resid 402 through 404' Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 421 removed outlier: 4.399A pdb=" N LYS D 421 " --> pdb=" O GLU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 431 removed outlier: 3.602A pdb=" N LEU D 431 " --> pdb=" O LEU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 449 removed outlier: 4.719A pdb=" N ASP D 440 " --> pdb=" O LYS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 472 No H-bonds generated for 'chain 'D' and resid 470 through 472' Processing helix chain 'D' and resid 476 through 481 Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'D' and resid 514 through 517 Processing helix chain 'D' and resid 534 through 536 No H-bonds generated for 'chain 'D' and resid 534 through 536' Processing helix chain 'D' and resid 559 through 575 Processing helix chain 'D' and resid 592 through 594 No H-bonds generated for 'chain 'D' and resid 592 through 594' Processing sheet with id= A, first strand: chain 'A' and resid 116 through 120 Processing sheet with id= B, first strand: chain 'A' and resid 338 through 343 Processing sheet with id= C, first strand: chain 'A' and resid 498 through 505 removed outlier: 3.529A pdb=" N ILE A 550 " --> pdb=" O THR A 460 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 458 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N CYS A 554 " --> pdb=" O TYR A 456 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TYR A 456 " --> pdb=" O CYS A 554 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 116 through 120 Processing sheet with id= E, first strand: chain 'B' and resid 338 through 343 Processing sheet with id= F, first strand: chain 'B' and resid 498 through 505 removed outlier: 3.518A pdb=" N ILE B 550 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 458 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N CYS B 554 " --> pdb=" O TYR B 456 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N TYR B 456 " --> pdb=" O CYS B 554 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 116 through 120 Processing sheet with id= H, first strand: chain 'C' and resid 338 through 343 Processing sheet with id= I, first strand: chain 'C' and resid 498 through 505 removed outlier: 3.537A pdb=" N ILE C 550 " --> pdb=" O THR C 460 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY C 458 " --> pdb=" O VAL C 552 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N CYS C 554 " --> pdb=" O TYR C 456 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TYR C 456 " --> pdb=" O CYS C 554 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 116 through 120 Processing sheet with id= K, first strand: chain 'D' and resid 338 through 343 Processing sheet with id= L, first strand: chain 'D' and resid 498 through 505 removed outlier: 3.530A pdb=" N ILE D 550 " --> pdb=" O THR D 460 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY D 458 " --> pdb=" O VAL D 552 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N CYS D 554 " --> pdb=" O TYR D 456 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N TYR D 456 " --> pdb=" O CYS D 554 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1380 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: 5.18 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 5368 1.36 - 1.50: 4270 1.50 - 1.63: 6906 1.63 - 1.77: 0 1.77 - 1.90: 132 Bond restraints: 16676 Sorted by residual: bond pdb=" PA T8T A 702 " pdb=" S1A T8T A 702 " ideal model delta sigma weight residual 2.160 1.898 0.262 2.00e-02 2.50e+03 1.72e+02 bond pdb=" PA T8T C 702 " pdb=" S1A T8T C 702 " ideal model delta sigma weight residual 2.160 1.898 0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" PA T8T D 702 " pdb=" S1A T8T D 702 " ideal model delta sigma weight residual 2.160 1.898 0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" PA T8T B 701 " pdb=" S1A T8T B 701 " ideal model delta sigma weight residual 2.160 1.898 0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" PA T8T A 703 " pdb=" S1A T8T A 703 " ideal model delta sigma weight residual 2.160 1.900 0.260 2.00e-02 2.50e+03 1.70e+02 ... (remaining 16671 not shown) Histogram of bond angle deviations from ideal: 98.89 - 106.04: 512 106.04 - 113.19: 8838 113.19 - 120.34: 6436 120.34 - 127.48: 6584 127.48 - 134.63: 246 Bond angle restraints: 22616 Sorted by residual: angle pdb=" C1' T8T B 703 " pdb=" N9 T8T B 703 " pdb=" C8 T8T B 703 " ideal model delta sigma weight residual 91.41 128.28 -36.87 3.00e+00 1.11e-01 1.51e+02 angle pdb=" C1' T8T C 701 " pdb=" N9 T8T C 701 " pdb=" C8 T8T C 701 " ideal model delta sigma weight residual 91.41 128.28 -36.87 3.00e+00 1.11e-01 1.51e+02 angle pdb=" C1' T8T A 703 " pdb=" N9 T8T A 703 " pdb=" C8 T8T A 703 " ideal model delta sigma weight residual 91.41 128.28 -36.87 3.00e+00 1.11e-01 1.51e+02 angle pdb=" C1' T8T D 701 " pdb=" N9 T8T D 701 " pdb=" C8 T8T D 701 " ideal model delta sigma weight residual 91.41 128.27 -36.86 3.00e+00 1.11e-01 1.51e+02 angle pdb=" C1' T8T B 702 " pdb=" N9 T8T B 702 " pdb=" C8 T8T B 702 " ideal model delta sigma weight residual 91.41 127.43 -36.02 3.00e+00 1.11e-01 1.44e+02 ... (remaining 22611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.10: 9487 26.10 - 52.20: 410 52.20 - 78.31: 59 78.31 - 104.41: 28 104.41 - 130.51: 4 Dihedral angle restraints: 9988 sinusoidal: 4288 harmonic: 5700 Sorted by residual: dihedral pdb=" C4' T8T C 703 " pdb=" C5' T8T C 703 " pdb=" O5' T8T C 703 " pdb=" PA T8T C 703 " ideal model delta sinusoidal sigma weight residual 154.74 -74.75 -130.51 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C4' T8T D 703 " pdb=" C5' T8T D 703 " pdb=" O5' T8T D 703 " pdb=" PA T8T D 703 " ideal model delta sinusoidal sigma weight residual 154.74 -74.77 -130.49 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C4' T8T A 701 " pdb=" C5' T8T A 701 " pdb=" O5' T8T A 701 " pdb=" PA T8T A 701 " ideal model delta sinusoidal sigma weight residual 154.74 -74.79 -130.47 1 3.00e+01 1.11e-03 1.76e+01 ... (remaining 9985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2083 0.069 - 0.137: 286 0.137 - 0.206: 7 0.206 - 0.274: 0 0.274 - 0.343: 12 Chirality restraints: 2388 Sorted by residual: chirality pdb=" PA T8T D 703 " pdb=" O2A T8T D 703 " pdb=" O3A T8T D 703 " pdb=" O5' T8T D 703 " both_signs ideal model delta sigma weight residual True 3.08 3.42 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" PA T8T C 703 " pdb=" O2A T8T C 703 " pdb=" O3A T8T C 703 " pdb=" O5' T8T C 703 " both_signs ideal model delta sigma weight residual True 3.08 3.42 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" PA T8T B 702 " pdb=" O2A T8T B 702 " pdb=" O3A T8T B 702 " pdb=" O5' T8T B 702 " both_signs ideal model delta sigma weight residual True 3.08 3.42 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 2385 not shown) Planarity restraints: 2872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' T8T B 702 " -0.026 2.00e-02 2.50e+03 1.08e-02 3.53e+00 pdb=" C2 T8T B 702 " 0.005 2.00e-02 2.50e+03 pdb=" C4 T8T B 702 " 0.011 2.00e-02 2.50e+03 pdb=" C5 T8T B 702 " 0.006 2.00e-02 2.50e+03 pdb=" C6 T8T B 702 " -0.003 2.00e-02 2.50e+03 pdb=" C8 T8T B 702 " 0.006 2.00e-02 2.50e+03 pdb=" N1 T8T B 702 " -0.002 2.00e-02 2.50e+03 pdb=" N2 T8T B 702 " -0.005 2.00e-02 2.50e+03 pdb=" N3 T8T B 702 " 0.013 2.00e-02 2.50e+03 pdb=" N7 T8T B 702 " 0.005 2.00e-02 2.50e+03 pdb=" N9 T8T B 702 " 0.006 2.00e-02 2.50e+03 pdb=" O6 T8T B 702 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' T8T A 701 " -0.026 2.00e-02 2.50e+03 1.07e-02 3.43e+00 pdb=" C2 T8T A 701 " 0.005 2.00e-02 2.50e+03 pdb=" C4 T8T A 701 " 0.011 2.00e-02 2.50e+03 pdb=" C5 T8T A 701 " 0.006 2.00e-02 2.50e+03 pdb=" C6 T8T A 701 " -0.003 2.00e-02 2.50e+03 pdb=" C8 T8T A 701 " 0.006 2.00e-02 2.50e+03 pdb=" N1 T8T A 701 " -0.003 2.00e-02 2.50e+03 pdb=" N2 T8T A 701 " -0.005 2.00e-02 2.50e+03 pdb=" N3 T8T A 701 " 0.013 2.00e-02 2.50e+03 pdb=" N7 T8T A 701 " 0.005 2.00e-02 2.50e+03 pdb=" N9 T8T A 701 " 0.006 2.00e-02 2.50e+03 pdb=" O6 T8T A 701 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' T8T D 703 " 0.026 2.00e-02 2.50e+03 1.07e-02 3.43e+00 pdb=" C2 T8T D 703 " -0.005 2.00e-02 2.50e+03 pdb=" C4 T8T D 703 " -0.011 2.00e-02 2.50e+03 pdb=" C5 T8T D 703 " -0.006 2.00e-02 2.50e+03 pdb=" C6 T8T D 703 " 0.003 2.00e-02 2.50e+03 pdb=" C8 T8T D 703 " -0.006 2.00e-02 2.50e+03 pdb=" N1 T8T D 703 " 0.003 2.00e-02 2.50e+03 pdb=" N2 T8T D 703 " 0.005 2.00e-02 2.50e+03 pdb=" N3 T8T D 703 " -0.013 2.00e-02 2.50e+03 pdb=" N7 T8T D 703 " -0.005 2.00e-02 2.50e+03 pdb=" N9 T8T D 703 " -0.006 2.00e-02 2.50e+03 pdb=" O6 T8T D 703 " 0.014 2.00e-02 2.50e+03 ... (remaining 2869 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 632 2.72 - 3.27: 16338 3.27 - 3.81: 26672 3.81 - 4.36: 34970 4.36 - 4.90: 58133 Nonbonded interactions: 136745 Sorted by model distance: nonbonded pdb=" OD2 ASP B 319 " pdb=" OH TYR B 374 " model vdw 2.175 2.440 nonbonded pdb=" OD2 ASP A 319 " pdb=" OH TYR A 374 " model vdw 2.176 2.440 nonbonded pdb=" OD2 ASP C 319 " pdb=" OH TYR C 374 " model vdw 2.193 2.440 nonbonded pdb=" OD2 ASP D 319 " pdb=" OH TYR D 374 " model vdw 2.193 2.440 nonbonded pdb=" NZ LYS A 185 " pdb=" O ALA A 338 " model vdw 2.260 2.520 ... (remaining 136740 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.590 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: 8.460 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 44.700 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.130 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:18.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 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 : 0.015 0.262 16676 Z= 0.980 Angle : 1.447 36.868 22616 Z= 0.536 Chirality : 0.050 0.343 2388 Planarity : 0.004 0.034 2872 Dihedral : 15.363 130.508 6324 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1940 helix: 1.10 (0.18), residues: 884 sheet: -0.24 (0.57), residues: 100 loop : -0.14 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 285 HIS 0.003 0.001 HIS D 321 PHE 0.012 0.001 PHE C 165 TYR 0.012 0.001 TYR C 315 ARG 0.002 0.000 ARG C 305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7538 (mt-10) REVERT: A 367 ASN cc_start: 0.7728 (t0) cc_final: 0.7481 (t0) REVERT: A 496 GLU cc_start: 0.7686 (tp30) cc_final: 0.7148 (tt0) REVERT: A 556 LYS cc_start: 0.5610 (mtpt) cc_final: 0.5354 (mtmt) REVERT: B 299 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7542 (mt-10) REVERT: B 367 ASN cc_start: 0.7727 (t0) cc_final: 0.7501 (t0) REVERT: B 496 GLU cc_start: 0.7647 (tp30) cc_final: 0.7143 (tt0) REVERT: B 556 LYS cc_start: 0.5593 (mtpt) cc_final: 0.5359 (mtmt) REVERT: C 299 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7535 (mt-10) REVERT: C 326 GLN cc_start: 0.7334 (mm110) cc_final: 0.6646 (mp10) REVERT: C 367 ASN cc_start: 0.7728 (t0) cc_final: 0.7480 (t0) REVERT: C 496 GLU cc_start: 0.7636 (tp30) cc_final: 0.7138 (tt0) REVERT: D 299 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7538 (mt-10) REVERT: D 326 GLN cc_start: 0.7336 (mm110) cc_final: 0.6656 (mp10) REVERT: D 367 ASN cc_start: 0.7726 (t0) cc_final: 0.7480 (t0) REVERT: D 496 GLU cc_start: 0.7669 (tp30) cc_final: 0.7160 (tt0) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 1.9259 time to fit residues: 477.3139 Evaluate side-chains 159 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 174 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN B 119 ASN B 271 GLN B 452 ASN C 119 ASN C 326 GLN C 452 ASN D 119 ASN D 326 GLN D 452 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16676 Z= 0.182 Angle : 0.579 8.232 22616 Z= 0.287 Chirality : 0.046 0.295 2388 Planarity : 0.006 0.114 2872 Dihedral : 10.993 119.088 2276 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.14 % Allowed : 6.64 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1940 helix: 0.95 (0.18), residues: 888 sheet: 0.14 (0.47), residues: 140 loop : -0.24 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 285 HIS 0.004 0.001 HIS B 321 PHE 0.013 0.002 PHE C 213 TYR 0.035 0.002 TYR D 315 ARG 0.008 0.000 ARG C 451 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 163 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6784 (ptm) REVERT: A 299 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7561 (mt-10) REVERT: A 367 ASN cc_start: 0.7220 (t0) cc_final: 0.6993 (t0) REVERT: A 496 GLU cc_start: 0.7701 (tp30) cc_final: 0.7144 (tt0) REVERT: A 531 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7227 (mmt180) REVERT: B 299 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7570 (mt-10) REVERT: B 367 ASN cc_start: 0.7312 (t0) cc_final: 0.7090 (t0) REVERT: B 496 GLU cc_start: 0.7709 (tp30) cc_final: 0.7149 (tt0) REVERT: B 531 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7226 (mmt180) REVERT: C 299 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7569 (mt-10) REVERT: C 326 GLN cc_start: 0.7445 (mm-40) cc_final: 0.6781 (mp10) REVERT: C 367 ASN cc_start: 0.7227 (t0) cc_final: 0.6996 (t0) REVERT: C 496 GLU cc_start: 0.7695 (tp30) cc_final: 0.7129 (tt0) REVERT: C 531 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7232 (mmt180) REVERT: D 299 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7566 (mt-10) REVERT: D 326 GLN cc_start: 0.7448 (mm-40) cc_final: 0.6786 (mp10) REVERT: D 367 ASN cc_start: 0.7218 (t0) cc_final: 0.6988 (t0) REVERT: D 496 GLU cc_start: 0.7697 (tp30) cc_final: 0.7137 (tt0) REVERT: D 531 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7227 (mmt180) outliers start: 37 outliers final: 8 residues processed: 184 average time/residue: 2.1140 time to fit residues: 416.5528 Evaluate side-chains 165 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 531 ARG Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 531 ARG Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 531 ARG Chi-restraints excluded: chain D residue 535 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.4980 chunk 54 optimal weight: 8.9990 chunk 145 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 16676 Z= 0.168 Angle : 0.568 11.809 22616 Z= 0.276 Chirality : 0.045 0.258 2388 Planarity : 0.005 0.092 2872 Dihedral : 10.722 115.246 2276 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.21 % Allowed : 9.64 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1940 helix: 0.76 (0.18), residues: 884 sheet: 0.19 (0.48), residues: 140 loop : -0.16 (0.22), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 285 HIS 0.005 0.001 HIS C 215 PHE 0.010 0.001 PHE D 213 TYR 0.030 0.002 TYR C 315 ARG 0.016 0.001 ARG B 451 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.4450 (OUTLIER) cc_final: 0.3852 (ttt) REVERT: A 299 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7528 (mt-10) REVERT: A 346 GLU cc_start: 0.7315 (pm20) cc_final: 0.6986 (pm20) REVERT: A 367 ASN cc_start: 0.7193 (t0) cc_final: 0.6952 (t0) REVERT: A 496 GLU cc_start: 0.7698 (tp30) cc_final: 0.7113 (tt0) REVERT: B 115 MET cc_start: 0.4465 (OUTLIER) cc_final: 0.3862 (ttt) REVERT: B 216 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6628 (ptt) REVERT: B 299 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7528 (mt-10) REVERT: B 346 GLU cc_start: 0.7312 (pm20) cc_final: 0.6983 (pm20) REVERT: B 367 ASN cc_start: 0.7248 (t0) cc_final: 0.7025 (t0) REVERT: B 496 GLU cc_start: 0.7674 (tp30) cc_final: 0.7101 (tt0) REVERT: C 115 MET cc_start: 0.4463 (OUTLIER) cc_final: 0.3863 (ttt) REVERT: C 216 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6636 (ptt) REVERT: C 299 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7528 (mt-10) REVERT: C 326 GLN cc_start: 0.7530 (mm-40) cc_final: 0.6790 (mp10) REVERT: C 346 GLU cc_start: 0.7333 (pm20) cc_final: 0.7009 (pm20) REVERT: C 367 ASN cc_start: 0.7203 (t0) cc_final: 0.6961 (t0) REVERT: C 496 GLU cc_start: 0.7697 (tp30) cc_final: 0.7122 (tt0) REVERT: D 115 MET cc_start: 0.4472 (OUTLIER) cc_final: 0.3870 (ttt) REVERT: D 216 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6620 (ptt) REVERT: D 299 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7533 (mt-10) REVERT: D 326 GLN cc_start: 0.7532 (mm-40) cc_final: 0.6806 (mp10) REVERT: D 346 GLU cc_start: 0.7318 (pm20) cc_final: 0.6995 (pm20) REVERT: D 367 ASN cc_start: 0.7192 (t0) cc_final: 0.6955 (t0) REVERT: D 496 GLU cc_start: 0.7698 (tp30) cc_final: 0.7121 (tt0) outliers start: 21 outliers final: 8 residues processed: 189 average time/residue: 2.0928 time to fit residues: 423.5104 Evaluate side-chains 169 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 535 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS A 358 ASN A 571 GLN B 167 HIS B 358 ASN C 167 HIS C 358 ASN D 167 HIS D 358 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16676 Z= 0.357 Angle : 0.688 9.461 22616 Z= 0.340 Chirality : 0.050 0.291 2388 Planarity : 0.008 0.153 2872 Dihedral : 11.125 112.984 2276 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.56 % Allowed : 11.14 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 1940 helix: 0.08 (0.18), residues: 888 sheet: 0.05 (0.45), residues: 140 loop : -0.42 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 285 HIS 0.010 0.002 HIS D 215 PHE 0.021 0.003 PHE C 363 TYR 0.035 0.003 TYR C 315 ARG 0.022 0.001 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6416 (ptt) REVERT: A 367 ASN cc_start: 0.7302 (t0) cc_final: 0.7069 (t0) REVERT: A 496 GLU cc_start: 0.7722 (tp30) cc_final: 0.7112 (tt0) REVERT: A 549 LEU cc_start: 0.7315 (pp) cc_final: 0.7099 (pt) REVERT: B 216 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6535 (ptt) REVERT: B 367 ASN cc_start: 0.7326 (t0) cc_final: 0.7088 (t0) REVERT: B 496 GLU cc_start: 0.7727 (tp30) cc_final: 0.7120 (tt0) REVERT: B 549 LEU cc_start: 0.7333 (pp) cc_final: 0.7111 (pt) REVERT: C 216 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6531 (ptt) REVERT: C 326 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7055 (mp10) REVERT: C 367 ASN cc_start: 0.7305 (t0) cc_final: 0.7070 (t0) REVERT: C 496 GLU cc_start: 0.7704 (tp30) cc_final: 0.7108 (tt0) REVERT: C 549 LEU cc_start: 0.7281 (pp) cc_final: 0.7072 (pt) REVERT: D 216 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6487 (ptt) REVERT: D 326 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7073 (mp10) REVERT: D 367 ASN cc_start: 0.7304 (t0) cc_final: 0.7071 (t0) REVERT: D 496 GLU cc_start: 0.7701 (tp30) cc_final: 0.7103 (tt0) REVERT: D 549 LEU cc_start: 0.7290 (pp) cc_final: 0.7080 (pt) outliers start: 27 outliers final: 16 residues processed: 180 average time/residue: 1.9285 time to fit residues: 373.4643 Evaluate side-chains 185 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 165 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 535 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 571 GLN B 326 GLN B 571 GLN C 571 GLN D 571 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16676 Z= 0.315 Angle : 0.649 9.168 22616 Z= 0.321 Chirality : 0.048 0.278 2388 Planarity : 0.006 0.094 2872 Dihedral : 10.853 111.876 2276 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.91 % Allowed : 11.78 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.19), residues: 1940 helix: -0.03 (0.17), residues: 888 sheet: -0.09 (0.45), residues: 140 loop : -0.49 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 285 HIS 0.007 0.002 HIS D 321 PHE 0.020 0.002 PHE A 363 TYR 0.031 0.002 TYR C 315 ARG 0.012 0.001 ARG D 451 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6447 (ptt) REVERT: A 346 GLU cc_start: 0.7264 (pm20) cc_final: 0.6975 (pm20) REVERT: A 367 ASN cc_start: 0.7282 (t0) cc_final: 0.7056 (t0) REVERT: A 496 GLU cc_start: 0.7723 (tp30) cc_final: 0.7099 (pp20) REVERT: A 531 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7469 (mmt180) REVERT: B 115 MET cc_start: 0.4505 (OUTLIER) cc_final: 0.3968 (ttt) REVERT: B 216 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6484 (ptt) REVERT: B 346 GLU cc_start: 0.7259 (pm20) cc_final: 0.6974 (pm20) REVERT: B 367 ASN cc_start: 0.7283 (t0) cc_final: 0.7055 (t0) REVERT: B 496 GLU cc_start: 0.7728 (tp30) cc_final: 0.7108 (pp20) REVERT: B 531 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7491 (mmt180) REVERT: C 115 MET cc_start: 0.4506 (OUTLIER) cc_final: 0.3973 (ttt) REVERT: C 216 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6486 (ptt) REVERT: C 326 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7090 (mp10) REVERT: C 346 GLU cc_start: 0.7266 (pm20) cc_final: 0.6986 (pm20) REVERT: C 367 ASN cc_start: 0.7277 (t0) cc_final: 0.7050 (t0) REVERT: C 496 GLU cc_start: 0.7720 (tp30) cc_final: 0.7105 (tt0) REVERT: C 531 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7490 (mmt180) REVERT: D 115 MET cc_start: 0.4524 (OUTLIER) cc_final: 0.3989 (ttt) REVERT: D 216 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6448 (ptt) REVERT: D 326 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7091 (mp10) REVERT: D 346 GLU cc_start: 0.7268 (pm20) cc_final: 0.6926 (pm20) REVERT: D 367 ASN cc_start: 0.7281 (t0) cc_final: 0.7053 (t0) REVERT: D 496 GLU cc_start: 0.7720 (tp30) cc_final: 0.7101 (tt0) REVERT: D 531 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7488 (mmt180) outliers start: 33 outliers final: 13 residues processed: 190 average time/residue: 2.0627 time to fit residues: 420.5655 Evaluate side-chains 187 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 531 ARG Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 ARG Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 531 ARG Chi-restraints excluded: chain D residue 535 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN B 571 GLN D 571 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16676 Z= 0.225 Angle : 0.585 8.816 22616 Z= 0.293 Chirality : 0.046 0.268 2388 Planarity : 0.007 0.138 2872 Dihedral : 10.673 111.465 2276 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.54 % Allowed : 13.34 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 1940 helix: 0.14 (0.18), residues: 888 sheet: -0.54 (0.45), residues: 148 loop : -0.38 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 285 HIS 0.006 0.001 HIS C 321 PHE 0.016 0.002 PHE B 363 TYR 0.028 0.002 TYR D 315 ARG 0.018 0.001 ARG C 451 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.4501 (OUTLIER) cc_final: 0.3958 (ttt) REVERT: A 315 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.6992 (p90) REVERT: A 346 GLU cc_start: 0.7163 (pm20) cc_final: 0.6836 (pm20) REVERT: A 367 ASN cc_start: 0.7243 (t0) cc_final: 0.7019 (t0) REVERT: A 496 GLU cc_start: 0.7747 (tp30) cc_final: 0.7151 (pp20) REVERT: B 115 MET cc_start: 0.4462 (OUTLIER) cc_final: 0.3925 (ttt) REVERT: B 315 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.6974 (p90) REVERT: B 346 GLU cc_start: 0.7155 (pm20) cc_final: 0.6831 (pm20) REVERT: B 367 ASN cc_start: 0.7240 (t0) cc_final: 0.7022 (t0) REVERT: B 496 GLU cc_start: 0.7761 (tp30) cc_final: 0.7129 (pp20) REVERT: C 115 MET cc_start: 0.4469 (OUTLIER) cc_final: 0.3949 (ttt) REVERT: C 315 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.6993 (p90) REVERT: C 326 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7113 (mp10) REVERT: C 344 ASP cc_start: 0.6623 (t0) cc_final: 0.6391 (t0) REVERT: C 346 GLU cc_start: 0.7168 (pm20) cc_final: 0.6844 (pm20) REVERT: C 367 ASN cc_start: 0.7231 (t0) cc_final: 0.7010 (t0) REVERT: C 496 GLU cc_start: 0.7729 (tp30) cc_final: 0.7098 (tt0) REVERT: D 115 MET cc_start: 0.4466 (OUTLIER) cc_final: 0.3936 (ttt) REVERT: D 315 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.6984 (p90) REVERT: D 326 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7116 (mp10) REVERT: D 346 GLU cc_start: 0.7173 (pm20) cc_final: 0.6850 (pm20) REVERT: D 367 ASN cc_start: 0.7231 (t0) cc_final: 0.7012 (t0) REVERT: D 496 GLU cc_start: 0.7725 (tp30) cc_final: 0.7092 (tt0) outliers start: 44 outliers final: 8 residues processed: 197 average time/residue: 1.8589 time to fit residues: 395.9442 Evaluate side-chains 176 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 160 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 535 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN B 571 GLN D 571 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16676 Z= 0.223 Angle : 0.603 13.050 22616 Z= 0.294 Chirality : 0.046 0.266 2388 Planarity : 0.006 0.100 2872 Dihedral : 10.581 111.384 2276 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.02 % Allowed : 14.67 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.19), residues: 1940 helix: 0.16 (0.18), residues: 888 sheet: -0.53 (0.45), residues: 148 loop : -0.36 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 285 HIS 0.005 0.001 HIS D 321 PHE 0.016 0.002 PHE C 363 TYR 0.030 0.002 TYR B 456 ARG 0.013 0.000 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.4449 (OUTLIER) cc_final: 0.3895 (ttt) REVERT: A 315 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.6983 (p90) REVERT: A 367 ASN cc_start: 0.7228 (t0) cc_final: 0.6984 (t0) REVERT: A 496 GLU cc_start: 0.7749 (tp30) cc_final: 0.7139 (pp20) REVERT: A 549 LEU cc_start: 0.7354 (pp) cc_final: 0.7146 (pt) REVERT: B 115 MET cc_start: 0.4449 (OUTLIER) cc_final: 0.3889 (ttt) REVERT: B 315 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.6966 (p90) REVERT: B 367 ASN cc_start: 0.7248 (t0) cc_final: 0.7010 (t0) REVERT: B 496 GLU cc_start: 0.7750 (tp30) cc_final: 0.7155 (pp20) REVERT: B 549 LEU cc_start: 0.7481 (pp) cc_final: 0.7257 (pt) REVERT: C 115 MET cc_start: 0.4446 (OUTLIER) cc_final: 0.3889 (ttt) REVERT: C 315 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.6982 (p90) REVERT: C 326 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7090 (mp10) REVERT: C 344 ASP cc_start: 0.6626 (t0) cc_final: 0.6332 (t0) REVERT: C 367 ASN cc_start: 0.7212 (t0) cc_final: 0.6971 (t0) REVERT: C 496 GLU cc_start: 0.7702 (tp30) cc_final: 0.7107 (tt0) REVERT: C 549 LEU cc_start: 0.7361 (pp) cc_final: 0.7158 (pt) REVERT: D 115 MET cc_start: 0.4451 (OUTLIER) cc_final: 0.3894 (ttt) REVERT: D 315 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.6974 (p90) REVERT: D 326 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7093 (mp10) REVERT: D 367 ASN cc_start: 0.7227 (t0) cc_final: 0.6987 (t0) REVERT: D 496 GLU cc_start: 0.7699 (tp30) cc_final: 0.7063 (tt0) REVERT: D 549 LEU cc_start: 0.7365 (pp) cc_final: 0.7162 (pt) outliers start: 35 outliers final: 14 residues processed: 186 average time/residue: 1.8807 time to fit residues: 377.7586 Evaluate side-chains 179 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 157 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 535 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 117 optimal weight: 0.0870 chunk 126 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN B 571 GLN C 571 GLN D 571 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16676 Z= 0.239 Angle : 0.611 12.002 22616 Z= 0.299 Chirality : 0.047 0.269 2388 Planarity : 0.006 0.088 2872 Dihedral : 10.635 111.375 2276 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.42 % Allowed : 14.55 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 1940 helix: 0.00 (0.17), residues: 912 sheet: -0.55 (0.45), residues: 148 loop : -0.34 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 285 HIS 0.006 0.001 HIS D 321 PHE 0.017 0.002 PHE C 363 TYR 0.034 0.002 TYR C 456 ARG 0.012 0.001 ARG C 451 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 161 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.4514 (OUTLIER) cc_final: 0.3918 (ttt) REVERT: A 216 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6423 (ptt) REVERT: A 315 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.6992 (p90) REVERT: A 346 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6578 (pm20) REVERT: A 367 ASN cc_start: 0.7215 (t0) cc_final: 0.6971 (t0) REVERT: A 496 GLU cc_start: 0.7753 (tp30) cc_final: 0.7146 (pp20) REVERT: A 531 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7490 (mmt180) REVERT: A 549 LEU cc_start: 0.7386 (pp) cc_final: 0.7161 (pt) REVERT: B 115 MET cc_start: 0.4505 (OUTLIER) cc_final: 0.3911 (ttt) REVERT: B 216 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6461 (ptt) REVERT: B 315 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.6973 (p90) REVERT: B 346 GLU cc_start: 0.7216 (pm20) cc_final: 0.6929 (pm20) REVERT: B 367 ASN cc_start: 0.7223 (t0) cc_final: 0.6982 (t0) REVERT: B 496 GLU cc_start: 0.7751 (tp30) cc_final: 0.7124 (pp20) REVERT: B 531 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7494 (mmt180) REVERT: B 549 LEU cc_start: 0.7398 (pp) cc_final: 0.7178 (pt) REVERT: C 115 MET cc_start: 0.4415 (OUTLIER) cc_final: 0.3838 (ttt) REVERT: C 216 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6456 (ptt) REVERT: C 315 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.6991 (p90) REVERT: C 326 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7112 (mp10) REVERT: C 346 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6589 (pm20) REVERT: C 367 ASN cc_start: 0.7215 (t0) cc_final: 0.6974 (t0) REVERT: C 496 GLU cc_start: 0.7738 (tp30) cc_final: 0.7132 (pp20) REVERT: C 531 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7489 (mmt180) REVERT: C 549 LEU cc_start: 0.7380 (pp) cc_final: 0.7160 (pt) REVERT: D 115 MET cc_start: 0.4509 (OUTLIER) cc_final: 0.3915 (ttt) REVERT: D 216 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6459 (ptt) REVERT: D 315 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.6983 (p90) REVERT: D 326 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7115 (mp10) REVERT: D 367 ASN cc_start: 0.7212 (t0) cc_final: 0.6971 (t0) REVERT: D 496 GLU cc_start: 0.7734 (tp30) cc_final: 0.7127 (pp20) REVERT: D 531 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7490 (mmt180) REVERT: D 549 LEU cc_start: 0.7392 (pp) cc_final: 0.7170 (pt) outliers start: 42 outliers final: 17 residues processed: 183 average time/residue: 1.9259 time to fit residues: 380.7909 Evaluate side-chains 191 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 531 ARG Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 ARG Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 531 ARG Chi-restraints excluded: chain D residue 535 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.6980 chunk 161 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 155 optimal weight: 0.1980 chunk 163 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 113 optimal weight: 0.0010 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN B 571 GLN C 571 GLN D 571 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16676 Z= 0.134 Angle : 0.539 11.852 22616 Z= 0.265 Chirality : 0.044 0.229 2388 Planarity : 0.005 0.055 2872 Dihedral : 9.985 111.008 2276 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.19 % Allowed : 15.47 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1940 helix: 0.51 (0.18), residues: 884 sheet: -0.52 (0.45), residues: 148 loop : -0.35 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 285 HIS 0.003 0.001 HIS D 215 PHE 0.009 0.001 PHE C 363 TYR 0.027 0.001 TYR B 456 ARG 0.009 0.000 ARG C 470 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 174 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.4566 (OUTLIER) cc_final: 0.3994 (ttt) REVERT: A 180 HIS cc_start: 0.6507 (t-90) cc_final: 0.6117 (m-70) REVERT: A 216 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6337 (ptt) REVERT: A 315 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7124 (p90) REVERT: A 346 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6521 (pm20) REVERT: A 367 ASN cc_start: 0.7108 (t0) cc_final: 0.6895 (t0) REVERT: A 371 ARG cc_start: 0.6752 (ttp-110) cc_final: 0.6532 (ttp80) REVERT: A 489 LEU cc_start: 0.6117 (OUTLIER) cc_final: 0.5865 (mm) REVERT: A 496 GLU cc_start: 0.7796 (tp30) cc_final: 0.7140 (pp20) REVERT: A 549 LEU cc_start: 0.7317 (pp) cc_final: 0.7105 (pt) REVERT: B 115 MET cc_start: 0.4540 (OUTLIER) cc_final: 0.3976 (ttt) REVERT: B 180 HIS cc_start: 0.6512 (t-90) cc_final: 0.6125 (m-70) REVERT: B 216 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6324 (ptt) REVERT: B 346 GLU cc_start: 0.7168 (pm20) cc_final: 0.6867 (pm20) REVERT: B 367 ASN cc_start: 0.7101 (t0) cc_final: 0.6887 (t0) REVERT: B 371 ARG cc_start: 0.6753 (ttp-110) cc_final: 0.6535 (ttp80) REVERT: B 489 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.5721 (mm) REVERT: B 496 GLU cc_start: 0.7764 (tp30) cc_final: 0.7147 (pp20) REVERT: B 549 LEU cc_start: 0.7357 (pp) cc_final: 0.7147 (pt) REVERT: C 115 MET cc_start: 0.4559 (OUTLIER) cc_final: 0.3995 (ttt) REVERT: C 180 HIS cc_start: 0.6509 (t-90) cc_final: 0.6115 (m-70) REVERT: C 216 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6340 (ptt) REVERT: C 326 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7032 (mp10) REVERT: C 346 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6529 (pm20) REVERT: C 367 ASN cc_start: 0.7080 (t0) cc_final: 0.6869 (t0) REVERT: C 371 ARG cc_start: 0.6765 (ttp-110) cc_final: 0.6553 (ttp80) REVERT: C 496 GLU cc_start: 0.7750 (tp30) cc_final: 0.7150 (tt0) REVERT: C 549 LEU cc_start: 0.7320 (pp) cc_final: 0.7107 (pt) REVERT: D 115 MET cc_start: 0.4545 (OUTLIER) cc_final: 0.3981 (ttt) REVERT: D 180 HIS cc_start: 0.6512 (t-90) cc_final: 0.6118 (m-70) REVERT: D 216 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6344 (ptt) REVERT: D 326 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7068 (mp10) REVERT: D 367 ASN cc_start: 0.7078 (t0) cc_final: 0.6861 (t0) REVERT: D 371 ARG cc_start: 0.6783 (ttp-110) cc_final: 0.6398 (ttp80) REVERT: D 496 GLU cc_start: 0.7747 (tp30) cc_final: 0.7144 (tt0) REVERT: D 531 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7396 (mmt180) REVERT: D 549 LEU cc_start: 0.7324 (pp) cc_final: 0.7115 (pt) outliers start: 38 outliers final: 9 residues processed: 195 average time/residue: 1.9321 time to fit residues: 406.1733 Evaluate side-chains 180 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 346 GLU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 531 ARG Chi-restraints excluded: chain D residue 535 ASN Chi-restraints excluded: chain D residue 575 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 571 GLN B 571 GLN C 571 GLN D 571 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16676 Z= 0.222 Angle : 0.600 11.402 22616 Z= 0.295 Chirality : 0.046 0.256 2388 Planarity : 0.008 0.171 2872 Dihedral : 10.405 111.124 2276 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.79 % Allowed : 15.70 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.19), residues: 1940 helix: 0.24 (0.18), residues: 912 sheet: -0.06 (0.45), residues: 140 loop : -0.48 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 285 HIS 0.005 0.001 HIS C 215 PHE 0.015 0.002 PHE C 363 TYR 0.028 0.002 TYR A 315 ARG 0.021 0.001 ARG A 451 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 162 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.4523 (OUTLIER) cc_final: 0.3921 (ttt) REVERT: A 180 HIS cc_start: 0.6494 (t-90) cc_final: 0.6111 (m-70) REVERT: A 216 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6333 (ptt) REVERT: A 315 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7093 (p90) REVERT: A 367 ASN cc_start: 0.7176 (t0) cc_final: 0.6918 (t0) REVERT: A 489 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5788 (mm) REVERT: A 496 GLU cc_start: 0.7748 (tp30) cc_final: 0.7137 (pp20) REVERT: A 531 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7484 (mmt180) REVERT: A 549 LEU cc_start: 0.7314 (pp) cc_final: 0.7089 (pt) REVERT: B 115 MET cc_start: 0.4515 (OUTLIER) cc_final: 0.3915 (ttt) REVERT: B 180 HIS cc_start: 0.6501 (t-90) cc_final: 0.6123 (m-70) REVERT: B 216 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6371 (ptt) REVERT: B 346 GLU cc_start: 0.7171 (pm20) cc_final: 0.6905 (pm20) REVERT: B 367 ASN cc_start: 0.7189 (t0) cc_final: 0.6923 (t0) REVERT: B 496 GLU cc_start: 0.7766 (tp30) cc_final: 0.7154 (pp20) REVERT: B 531 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7487 (mmt180) REVERT: B 549 LEU cc_start: 0.7328 (pp) cc_final: 0.7114 (pt) REVERT: C 115 MET cc_start: 0.4521 (OUTLIER) cc_final: 0.3917 (ttt) REVERT: C 180 HIS cc_start: 0.6495 (t-90) cc_final: 0.6111 (m-70) REVERT: C 216 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6334 (ptt) REVERT: C 326 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7090 (mp10) REVERT: C 367 ASN cc_start: 0.7182 (t0) cc_final: 0.6918 (t0) REVERT: C 489 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5893 (mm) REVERT: C 496 GLU cc_start: 0.7726 (tp30) cc_final: 0.7135 (tt0) REVERT: C 531 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7485 (mmt180) REVERT: C 549 LEU cc_start: 0.7299 (pp) cc_final: 0.7082 (pt) REVERT: D 115 MET cc_start: 0.4520 (OUTLIER) cc_final: 0.3923 (ttt) REVERT: D 180 HIS cc_start: 0.6501 (t-90) cc_final: 0.6114 (m-70) REVERT: D 216 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6335 (ptt) REVERT: D 326 GLN cc_start: 0.7563 (mm-40) cc_final: 0.6930 (mp10) REVERT: D 367 ASN cc_start: 0.7182 (t0) cc_final: 0.6918 (t0) REVERT: D 489 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5912 (mm) REVERT: D 496 GLU cc_start: 0.7721 (tp30) cc_final: 0.7128 (tt0) REVERT: D 531 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7495 (mmt180) REVERT: D 549 LEU cc_start: 0.7310 (pp) cc_final: 0.7096 (pt) outliers start: 31 outliers final: 9 residues processed: 177 average time/residue: 1.9615 time to fit residues: 374.0701 Evaluate side-chains 182 residues out of total 1732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 531 ARG Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 216 MET Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 535 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 531 ARG Chi-restraints excluded: chain C residue 535 ASN Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 216 MET Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 531 ARG Chi-restraints excluded: chain D residue 535 ASN Chi-restraints excluded: chain D residue 575 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 0.0170 chunk 133 optimal weight: 7.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN B 571 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.172974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135034 restraints weight = 15994.860| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.52 r_work: 0.3600 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16676 Z= 0.171 Angle : 0.573 11.342 22616 Z= 0.282 Chirality : 0.045 0.247 2388 Planarity : 0.009 0.214 2872 Dihedral : 10.362 110.796 2276 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.67 % Allowed : 15.82 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1940 helix: 0.26 (0.18), residues: 928 sheet: -0.49 (0.45), residues: 148 loop : -0.27 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 285 HIS 0.004 0.001 HIS D 321 PHE 0.013 0.001 PHE C 363 TYR 0.026 0.002 TYR A 315 ARG 0.026 0.001 ARG C 451 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7049.82 seconds wall clock time: 127 minutes 13.67 seconds (7633.67 seconds total)