Starting phenix.real_space_refine on Fri Mar 15 18:26:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6feq_4246/03_2024/6feq_4246_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6feq_4246/03_2024/6feq_4246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6feq_4246/03_2024/6feq_4246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6feq_4246/03_2024/6feq_4246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6feq_4246/03_2024/6feq_4246_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6feq_4246/03_2024/6feq_4246_updated.pdb" } resolution = 3.6 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= 0.016 sd= 0.107 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 8006 2.51 5 N 2040 2.21 5 O 2283 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12397 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 18, 'TRANS': 547} Chain breaks: 3 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 73 Unusual residues: {'D6T': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.09, per 1000 atoms: 0.57 Number of scatterers: 12397 At special positions: 0 Unit cell: (102.24, 96.915, 145.905, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2283 8.00 N 2040 7.00 C 8006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.02 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.05 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 596 " " NAG B1001 " - " ASN B 596 " Time building additional restraints: 4.47 Conformation dependent library (CDL) restraints added in 2.1 seconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 12 sheets defined 39.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 136 through 147 removed outlier: 3.666A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.673A pdb=" N GLU A 159 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.745A pdb=" N LYS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 234 removed outlier: 3.517A pdb=" N ASN A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.683A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.302A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.744A pdb=" N ILE A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.629A pdb=" N ILE A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 removed outlier: 3.592A pdb=" N GLU A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.547A pdb=" N TRP A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 396 through 412 Processing helix chain 'A' and resid 422 through 450 removed outlier: 3.582A pdb=" N PHE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 442 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N SER A 443 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ALA A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.664A pdb=" N HIS A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 478 through 497 removed outlier: 3.545A pdb=" N ARG A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 3.656A pdb=" N TYR A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 528 removed outlier: 3.601A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 548 removed outlier: 3.507A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 573 through 585 removed outlier: 3.595A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 removed outlier: 3.581A pdb=" N LYS A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 649 removed outlier: 3.561A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 136 through 147 removed outlier: 3.602A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 168 Processing helix chain 'B' and resid 188 through 199 removed outlier: 3.721A pdb=" N LYS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 234 removed outlier: 3.595A pdb=" N ASN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.811A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.847A pdb=" N PHE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 299 removed outlier: 3.573A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.615A pdb=" N GLU B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 353 removed outlier: 3.594A pdb=" N GLU B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 390 removed outlier: 3.525A pdb=" N TRP B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 412 Processing helix chain 'B' and resid 422 through 450 removed outlier: 3.513A pdb=" N PHE B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL B 442 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ALA B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 450 " --> pdb=" O GLU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'B' and resid 466 through 476 removed outlier: 3.513A pdb=" N LEU B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 497 Proline residue: B 485 - end of helix removed outlier: 3.574A pdb=" N VAL B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 528 removed outlier: 3.758A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.836A pdb=" N ILE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 552 " --> pdb=" O MET B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 560 No H-bonds generated for 'chain 'B' and resid 558 through 560' Processing helix chain 'B' and resid 566 through 570 removed outlier: 3.520A pdb=" N GLN B 569 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 566 through 570' Processing helix chain 'B' and resid 573 through 583 removed outlier: 3.631A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 616 removed outlier: 3.561A pdb=" N LYS B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 649 removed outlier: 3.631A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'A' and resid 68 through 71 removed outlier: 3.524A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.140A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE A 238 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE A 78 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE A 240 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 241 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 68 through 71 Processing sheet with id= D, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.005A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE B 238 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ILE B 78 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE B 240 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N GLY B 80 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER B 241 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 19 through 24 Processing sheet with id= F, first strand: chain 'C' and resid 85 through 90 removed outlier: 5.928A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 6 through 8 removed outlier: 3.520A pdb=" N CYS D 22 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.802A pdb=" N LYS D 45 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 41 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TRP D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR D 108 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 19 through 24 Processing sheet with id= J, first strand: chain 'E' and resid 85 through 90 removed outlier: 5.928A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 6 through 8 removed outlier: 3.519A pdb=" N CYS F 22 " --> pdb=" O PHE F 79 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 58 through 60 removed outlier: 3.802A pdb=" N LYS F 45 " --> pdb=" O PHE F 41 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE F 41 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP F 37 " --> pdb=" O MET F 49 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TRP F 35 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR F 108 " --> pdb=" O THR F 98 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1335 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: 3.54 Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1939 1.31 - 1.44: 3587 1.44 - 1.56: 7041 1.56 - 1.69: 4 1.69 - 1.82: 106 Bond restraints: 12677 Sorted by residual: bond pdb=" C27 D6T A1002 " pdb=" C31 D6T A1002 " ideal model delta sigma weight residual 1.400 1.618 -0.218 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C28 D6T A1002 " pdb=" C34 D6T A1002 " ideal model delta sigma weight residual 1.400 1.615 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C32 D6T A1002 " pdb=" C33 D6T A1002 " ideal model delta sigma weight residual 1.411 1.241 0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" C19 D6T A1002 " pdb=" C20 D6T A1002 " ideal model delta sigma weight residual 1.386 1.550 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" C18 D6T A1002 " pdb=" C23 D6T A1002 " ideal model delta sigma weight residual 1.388 1.542 -0.154 2.00e-02 2.50e+03 5.95e+01 ... (remaining 12672 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.32: 217 105.32 - 112.50: 6487 112.50 - 119.68: 4348 119.68 - 126.86: 5977 126.86 - 134.03: 149 Bond angle restraints: 17178 Sorted by residual: angle pdb=" C29 D6T A1002 " pdb=" C30 D6T A1002 " pdb=" N6 D6T A1002 " ideal model delta sigma weight residual 110.04 129.48 -19.44 3.00e+00 1.11e-01 4.20e+01 angle pdb=" C SER B 572 " pdb=" N ILE B 573 " pdb=" CA ILE B 573 " ideal model delta sigma weight residual 120.33 125.16 -4.83 8.00e-01 1.56e+00 3.65e+01 angle pdb=" C27 D6T A1002 " pdb=" C26 D6T A1002 " pdb=" N6 D6T A1002 " ideal model delta sigma weight residual 112.58 129.64 -17.06 3.00e+00 1.11e-01 3.23e+01 angle pdb=" CA LEU A 64 " pdb=" CB LEU A 64 " pdb=" CG LEU A 64 " ideal model delta sigma weight residual 116.30 131.90 -15.60 3.50e+00 8.16e-02 1.99e+01 angle pdb=" C ILE B 63 " pdb=" N LEU B 64 " pdb=" CA LEU B 64 " ideal model delta sigma weight residual 121.54 129.82 -8.28 1.91e+00 2.74e-01 1.88e+01 ... (remaining 17173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7176 17.75 - 35.51: 213 35.51 - 53.26: 57 53.26 - 71.01: 11 71.01 - 88.77: 15 Dihedral angle restraints: 7472 sinusoidal: 2936 harmonic: 4536 Sorted by residual: dihedral pdb=" CA PHE A 414 " pdb=" C PHE A 414 " pdb=" N GLY A 415 " pdb=" CA GLY A 415 " ideal model delta harmonic sigma weight residual -180.00 -137.37 -42.63 0 5.00e+00 4.00e-02 7.27e+01 dihedral pdb=" CA PHE B 414 " pdb=" C PHE B 414 " pdb=" N GLY B 415 " pdb=" CA GLY B 415 " ideal model delta harmonic sigma weight residual -180.00 -137.92 -42.08 0 5.00e+00 4.00e-02 7.08e+01 dihedral pdb=" CB CYS A 603 " pdb=" SG CYS A 603 " pdb=" SG CYS B 603 " pdb=" CB CYS B 603 " ideal model delta sinusoidal sigma weight residual -86.00 -19.98 -66.02 1 1.00e+01 1.00e-02 5.70e+01 ... (remaining 7469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1297 0.052 - 0.104: 532 0.104 - 0.156: 102 0.156 - 0.209: 18 0.209 - 0.261: 5 Chirality restraints: 1954 Sorted by residual: chirality pdb=" CG LEU A 565 " pdb=" CB LEU A 565 " pdb=" CD1 LEU A 565 " pdb=" CD2 LEU A 565 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA THR C 94 " pdb=" N THR C 94 " pdb=" C THR C 94 " pdb=" CB THR C 94 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA THR E 94 " pdb=" N THR E 94 " pdb=" C THR E 94 " pdb=" CB THR E 94 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1951 not shown) Planarity restraints: 2143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 63 " -0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ILE B 63 " 0.075 2.00e-02 2.50e+03 pdb=" O ILE B 63 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU B 64 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 63 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C ILE A 63 " 0.073 2.00e-02 2.50e+03 pdb=" O ILE A 63 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU A 64 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 87 " -0.040 5.00e-02 4.00e+02 6.12e-02 5.98e+00 pdb=" N PRO F 88 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " -0.034 5.00e-02 4.00e+02 ... (remaining 2140 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3512 2.80 - 3.32: 11112 3.32 - 3.85: 19932 3.85 - 4.37: 23388 4.37 - 4.90: 39995 Nonbonded interactions: 97939 Sorted by model distance: nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.271 2.440 nonbonded pdb=" OG SER E 63 " pdb=" OG SER E 74 " model vdw 2.276 2.440 nonbonded pdb=" OG SER C 63 " pdb=" OG SER C 74 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.277 2.440 nonbonded pdb=" O SER B 486 " pdb=" OG1 THR B 490 " model vdw 2.281 2.440 ... (remaining 97934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 654 or resid 1001)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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 group one per residue 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: 0.660 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.440 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 34.070 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 : 0.011 0.218 12677 Z= 0.717 Angle : 1.047 19.441 17178 Z= 0.548 Chirality : 0.057 0.261 1954 Planarity : 0.006 0.061 2141 Dihedral : 11.017 88.766 4555 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.15 % Allowed : 3.48 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.16), residues: 1558 helix: -3.35 (0.11), residues: 602 sheet: -1.64 (0.30), residues: 252 loop : -2.54 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP F 109 HIS 0.015 0.003 HIS B 583 PHE 0.030 0.003 PHE E 98 TYR 0.024 0.003 TYR F 51 ARG 0.009 0.001 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 247 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.9090 (mttt) cc_final: 0.8515 (tptm) REVERT: A 243 HIS cc_start: 0.9213 (t70) cc_final: 0.8905 (t-170) REVERT: A 344 GLU cc_start: 0.8980 (tp30) cc_final: 0.8342 (tp30) REVERT: A 391 ASN cc_start: 0.9041 (t160) cc_final: 0.8704 (t0) REVERT: A 523 MET cc_start: 0.9291 (ttt) cc_final: 0.8959 (ttp) REVERT: B 172 LYS cc_start: 0.8989 (mttt) cc_final: 0.8407 (tmtt) REVERT: B 226 LEU cc_start: 0.8912 (mt) cc_final: 0.8557 (tp) REVERT: B 336 TYR cc_start: 0.9002 (t80) cc_final: 0.8777 (t80) REVERT: B 343 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8699 (mttp) REVERT: B 391 ASN cc_start: 0.9206 (t160) cc_final: 0.8629 (m-40) REVERT: B 393 GLN cc_start: 0.6098 (mm-40) cc_final: 0.5758 (tp40) REVERT: B 515 MET cc_start: 0.9399 (mmm) cc_final: 0.9098 (mmp) REVERT: C 79 GLN cc_start: 0.8351 (mm110) cc_final: 0.8026 (mm110) REVERT: C 82 ASP cc_start: 0.8154 (m-30) cc_final: 0.7646 (m-30) REVERT: C 90 GLN cc_start: 0.8504 (pp30) cc_final: 0.7819 (pp30) REVERT: E 15 LEU cc_start: 0.9088 (mp) cc_final: 0.8803 (tt) REVERT: E 79 GLN cc_start: 0.9167 (mm110) cc_final: 0.8676 (mm110) REVERT: E 82 ASP cc_start: 0.8270 (m-30) cc_final: 0.7763 (m-30) REVERT: E 94 THR cc_start: 0.8703 (p) cc_final: 0.8498 (t) REVERT: F 53 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8444 (t0) REVERT: F 100 TYR cc_start: 0.8226 (t80) cc_final: 0.7985 (t80) outliers start: 2 outliers final: 0 residues processed: 249 average time/residue: 0.2779 time to fit residues: 95.7754 Evaluate side-chains 125 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 0.0170 chunk 120 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 ASN A 109 ASN A 116 ASN A 222 ASN A 375 HIS A 391 ASN A 425 ASN A 436 ASN A 437 GLN A 583 HIS B 41 ASN B 68 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS B 391 ASN B 425 ASN B 437 GLN B 457 HIS B 583 HIS C 6 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN F 40 GLN F 53 ASN F 77 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12677 Z= 0.170 Angle : 0.672 11.506 17178 Z= 0.333 Chirality : 0.042 0.184 1954 Planarity : 0.004 0.056 2141 Dihedral : 8.501 85.719 1769 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.48 % Allowed : 8.00 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.19), residues: 1558 helix: -0.65 (0.18), residues: 630 sheet: -1.25 (0.30), residues: 268 loop : -1.96 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 564 HIS 0.005 0.001 HIS A 243 PHE 0.016 0.002 PHE A 277 TYR 0.018 0.001 TYR B 336 ARG 0.008 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 1.493 Fit side-chains revert: symmetry clash REVERT: A 172 LYS cc_start: 0.9089 (mttt) cc_final: 0.8498 (tptm) REVERT: A 182 PHE cc_start: 0.8234 (m-80) cc_final: 0.7524 (t80) REVERT: A 344 GLU cc_start: 0.8964 (tp30) cc_final: 0.8348 (tp30) REVERT: A 345 THR cc_start: 0.9005 (m) cc_final: 0.8797 (p) REVERT: A 391 ASN cc_start: 0.9056 (t0) cc_final: 0.8678 (t0) REVERT: B 164 VAL cc_start: 0.9463 (t) cc_final: 0.9239 (p) REVERT: B 172 LYS cc_start: 0.8955 (mttt) cc_final: 0.8384 (tmtt) REVERT: B 226 LEU cc_start: 0.9040 (mt) cc_final: 0.8722 (tp) REVERT: B 351 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.6975 (pm20) REVERT: B 393 GLN cc_start: 0.5817 (mm-40) cc_final: 0.5509 (tp40) REVERT: B 515 MET cc_start: 0.9244 (mmm) cc_final: 0.8968 (mmt) REVERT: C 55 GLU cc_start: 0.8395 (tp30) cc_final: 0.8070 (tp30) REVERT: C 79 GLN cc_start: 0.8298 (mm110) cc_final: 0.8009 (mm110) REVERT: E 79 GLN cc_start: 0.9039 (mm110) cc_final: 0.8618 (mm-40) REVERT: E 82 ASP cc_start: 0.7989 (m-30) cc_final: 0.7624 (m-30) REVERT: F 55 ASP cc_start: 0.8756 (p0) cc_final: 0.8257 (p0) outliers start: 20 outliers final: 7 residues processed: 191 average time/residue: 0.2366 time to fit residues: 66.3767 Evaluate side-chains 123 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 112 optimal weight: 0.2980 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN A 243 HIS A 457 HIS ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12677 Z= 0.269 Angle : 0.666 13.181 17178 Z= 0.328 Chirality : 0.042 0.166 1954 Planarity : 0.004 0.051 2141 Dihedral : 8.027 87.063 1767 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.89 % Allowed : 10.00 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1558 helix: 0.37 (0.20), residues: 642 sheet: -1.00 (0.30), residues: 264 loop : -1.80 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 92 HIS 0.007 0.001 HIS A 243 PHE 0.018 0.002 PHE F 79 TYR 0.018 0.002 TYR A 336 ARG 0.007 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 124 time to evaluate : 1.571 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8303 (mmm) cc_final: 0.8006 (mmm) REVERT: A 172 LYS cc_start: 0.9084 (mttt) cc_final: 0.8516 (tptm) REVERT: A 182 PHE cc_start: 0.8329 (m-80) cc_final: 0.7456 (t80) REVERT: A 265 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7493 (mtm) REVERT: A 274 LEU cc_start: 0.8423 (tp) cc_final: 0.8178 (pp) REVERT: A 344 GLU cc_start: 0.8988 (tp30) cc_final: 0.8356 (tp30) REVERT: A 345 THR cc_start: 0.9014 (m) cc_final: 0.8795 (p) REVERT: A 391 ASN cc_start: 0.9075 (t0) cc_final: 0.8689 (t0) REVERT: B 172 LYS cc_start: 0.9016 (mttt) cc_final: 0.8457 (tmtt) REVERT: B 226 LEU cc_start: 0.9121 (mt) cc_final: 0.8752 (tp) REVERT: B 351 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.6846 (pp30) REVERT: B 393 GLN cc_start: 0.5852 (mm-40) cc_final: 0.5542 (tp40) REVERT: B 515 MET cc_start: 0.9292 (mmm) cc_final: 0.9005 (mmt) REVERT: C 55 GLU cc_start: 0.8466 (tp30) cc_final: 0.8131 (tp30) REVERT: E 79 GLN cc_start: 0.9054 (mm110) cc_final: 0.8613 (mm-40) REVERT: E 82 ASP cc_start: 0.7977 (m-30) cc_final: 0.7579 (m-30) REVERT: F 55 ASP cc_start: 0.8726 (p0) cc_final: 0.8247 (p0) outliers start: 39 outliers final: 22 residues processed: 155 average time/residue: 0.1966 time to fit residues: 47.2457 Evaluate side-chains 134 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 81 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 0.3980 chunk 105 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 0.0770 chunk 94 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 12677 Z= 0.139 Angle : 0.584 11.491 17178 Z= 0.284 Chirality : 0.040 0.167 1954 Planarity : 0.003 0.048 2141 Dihedral : 7.552 84.843 1767 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.30 % Allowed : 10.59 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.21), residues: 1558 helix: 1.05 (0.21), residues: 634 sheet: -0.76 (0.31), residues: 262 loop : -1.50 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 564 HIS 0.001 0.000 HIS A 267 PHE 0.010 0.001 PHE A 266 TYR 0.015 0.001 TYR D 33 ARG 0.003 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 1.469 Fit side-chains REVERT: A 71 MET cc_start: 0.8326 (mmm) cc_final: 0.8035 (mmm) REVERT: A 172 LYS cc_start: 0.9062 (mttt) cc_final: 0.8507 (tptm) REVERT: A 182 PHE cc_start: 0.8329 (m-80) cc_final: 0.7417 (t80) REVERT: A 265 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7364 (mtm) REVERT: A 274 LEU cc_start: 0.8448 (tp) cc_final: 0.8222 (pp) REVERT: A 344 GLU cc_start: 0.9009 (tp30) cc_final: 0.8310 (tp30) REVERT: A 345 THR cc_start: 0.9008 (m) cc_final: 0.8799 (p) REVERT: A 391 ASN cc_start: 0.9109 (t0) cc_final: 0.8686 (t0) REVERT: A 479 LEU cc_start: 0.8403 (tp) cc_final: 0.8198 (tp) REVERT: B 172 LYS cc_start: 0.9006 (mttt) cc_final: 0.8443 (tmtt) REVERT: B 226 LEU cc_start: 0.9080 (mt) cc_final: 0.8748 (tp) REVERT: B 351 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.6983 (pp30) REVERT: B 393 GLN cc_start: 0.5940 (mm-40) cc_final: 0.5539 (tp40) REVERT: B 515 MET cc_start: 0.9278 (mmm) cc_final: 0.9018 (mmt) REVERT: C 55 GLU cc_start: 0.8405 (tp30) cc_final: 0.8066 (tp30) REVERT: E 79 GLN cc_start: 0.9011 (mm110) cc_final: 0.8583 (mm-40) REVERT: E 82 ASP cc_start: 0.7880 (m-30) cc_final: 0.7448 (m-30) REVERT: F 55 ASP cc_start: 0.8746 (p0) cc_final: 0.8273 (p0) outliers start: 31 outliers final: 14 residues processed: 156 average time/residue: 0.1875 time to fit residues: 46.4593 Evaluate side-chains 127 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 2 optimal weight: 0.0070 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 133 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 overall best weight: 2.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12677 Z= 0.265 Angle : 0.628 12.341 17178 Z= 0.307 Chirality : 0.041 0.195 1954 Planarity : 0.004 0.048 2141 Dihedral : 7.630 89.452 1767 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.37 % Allowed : 11.56 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.22), residues: 1558 helix: 1.20 (0.21), residues: 646 sheet: -0.70 (0.31), residues: 262 loop : -1.37 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 379 HIS 0.009 0.001 HIS A 243 PHE 0.017 0.001 PHE F 79 TYR 0.012 0.001 TYR B 463 ARG 0.006 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 1.364 Fit side-chains REVERT: A 71 MET cc_start: 0.8401 (mmm) cc_final: 0.8111 (mmm) REVERT: A 172 LYS cc_start: 0.9080 (mttt) cc_final: 0.8535 (tptm) REVERT: A 182 PHE cc_start: 0.8343 (m-80) cc_final: 0.7465 (t80) REVERT: A 265 MET cc_start: 0.7803 (mtp) cc_final: 0.7483 (mtm) REVERT: A 274 LEU cc_start: 0.8477 (tp) cc_final: 0.8239 (pp) REVERT: A 344 GLU cc_start: 0.9033 (tp30) cc_final: 0.8323 (tp30) REVERT: A 345 THR cc_start: 0.9029 (m) cc_final: 0.8813 (p) REVERT: A 391 ASN cc_start: 0.9107 (t0) cc_final: 0.8695 (t0) REVERT: B 172 LYS cc_start: 0.9048 (mttt) cc_final: 0.8450 (tmtt) REVERT: B 226 LEU cc_start: 0.9127 (mt) cc_final: 0.8778 (tp) REVERT: B 351 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7288 (pm20) REVERT: B 393 GLN cc_start: 0.6235 (mm-40) cc_final: 0.5912 (tp40) REVERT: B 402 THR cc_start: 0.9133 (m) cc_final: 0.8858 (p) REVERT: B 515 MET cc_start: 0.9295 (mmm) cc_final: 0.9023 (mmt) REVERT: C 55 GLU cc_start: 0.8426 (tp30) cc_final: 0.8078 (tp30) REVERT: C 79 GLN cc_start: 0.8808 (mp10) cc_final: 0.8385 (mp10) REVERT: D 47 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7124 (tt0) REVERT: E 11 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7474 (m-80) REVERT: E 79 GLN cc_start: 0.9035 (mm110) cc_final: 0.8572 (mm-40) REVERT: E 82 ASP cc_start: 0.7929 (m-30) cc_final: 0.7459 (m-30) REVERT: F 55 ASP cc_start: 0.8716 (p0) cc_final: 0.8269 (p0) outliers start: 32 outliers final: 18 residues processed: 139 average time/residue: 0.2107 time to fit residues: 45.9396 Evaluate side-chains 129 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 12677 Z= 0.458 Angle : 0.746 12.968 17178 Z= 0.369 Chirality : 0.045 0.206 1954 Planarity : 0.004 0.043 2141 Dihedral : 8.072 86.816 1767 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.26 % Allowed : 11.11 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.22), residues: 1558 helix: 1.06 (0.21), residues: 650 sheet: -0.68 (0.31), residues: 262 loop : -1.38 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 92 HIS 0.007 0.002 HIS A 243 PHE 0.025 0.002 PHE F 79 TYR 0.019 0.002 TYR A 413 ARG 0.007 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 112 time to evaluate : 1.552 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8421 (mmm) cc_final: 0.8133 (mmm) REVERT: A 172 LYS cc_start: 0.9096 (mttt) cc_final: 0.8585 (tptm) REVERT: A 182 PHE cc_start: 0.8384 (m-80) cc_final: 0.7544 (t80) REVERT: A 274 LEU cc_start: 0.8584 (tp) cc_final: 0.8347 (pp) REVERT: A 344 GLU cc_start: 0.8942 (tp30) cc_final: 0.8199 (tp30) REVERT: A 345 THR cc_start: 0.9006 (m) cc_final: 0.8775 (p) REVERT: A 391 ASN cc_start: 0.9127 (t0) cc_final: 0.8735 (t0) REVERT: B 76 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7908 (m-40) REVERT: B 172 LYS cc_start: 0.9106 (mttt) cc_final: 0.8404 (tmtt) REVERT: B 351 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: B 391 ASN cc_start: 0.9196 (t0) cc_final: 0.8822 (m-40) REVERT: B 402 THR cc_start: 0.9139 (m) cc_final: 0.8877 (p) REVERT: B 515 MET cc_start: 0.9304 (mmm) cc_final: 0.9052 (mmt) REVERT: C 79 GLN cc_start: 0.8656 (mp10) cc_final: 0.8409 (mp10) REVERT: D 47 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7266 (tt0) REVERT: E 79 GLN cc_start: 0.9070 (mm110) cc_final: 0.8554 (mm-40) REVERT: E 82 ASP cc_start: 0.7995 (m-30) cc_final: 0.7666 (m-30) REVERT: F 16 GLN cc_start: 0.7815 (tt0) cc_final: 0.7164 (pp30) REVERT: F 55 ASP cc_start: 0.8708 (p0) cc_final: 0.8348 (p0) outliers start: 44 outliers final: 24 residues processed: 146 average time/residue: 0.2034 time to fit residues: 46.5983 Evaluate side-chains 132 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 148 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12677 Z= 0.281 Angle : 0.639 13.564 17178 Z= 0.314 Chirality : 0.042 0.231 1954 Planarity : 0.004 0.046 2141 Dihedral : 7.772 84.844 1767 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.81 % Allowed : 11.33 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1558 helix: 1.35 (0.21), residues: 644 sheet: -0.66 (0.30), residues: 272 loop : -1.21 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 92 HIS 0.008 0.001 HIS A 243 PHE 0.016 0.001 PHE F 79 TYR 0.019 0.002 TYR A 336 ARG 0.004 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 121 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.8446 (mmm) cc_final: 0.8148 (mmm) REVERT: A 172 LYS cc_start: 0.9093 (mttt) cc_final: 0.8590 (tptm) REVERT: A 182 PHE cc_start: 0.8264 (m-80) cc_final: 0.7500 (t80) REVERT: A 344 GLU cc_start: 0.8936 (tp30) cc_final: 0.8194 (tp30) REVERT: A 345 THR cc_start: 0.9011 (m) cc_final: 0.8782 (p) REVERT: A 391 ASN cc_start: 0.9128 (t0) cc_final: 0.8729 (t0) REVERT: B 172 LYS cc_start: 0.9112 (mttt) cc_final: 0.8415 (tmtt) REVERT: B 391 ASN cc_start: 0.9188 (t0) cc_final: 0.8831 (m-40) REVERT: B 402 THR cc_start: 0.9150 (m) cc_final: 0.8896 (p) REVERT: B 515 MET cc_start: 0.9290 (mmm) cc_final: 0.9026 (mmt) REVERT: C 79 GLN cc_start: 0.8768 (mp10) cc_final: 0.8507 (mp10) REVERT: D 47 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: E 79 GLN cc_start: 0.8997 (mm110) cc_final: 0.8518 (mm-40) REVERT: E 82 ASP cc_start: 0.7974 (m-30) cc_final: 0.7535 (m-30) REVERT: F 16 GLN cc_start: 0.7787 (tt0) cc_final: 0.7136 (pp30) REVERT: F 55 ASP cc_start: 0.8734 (p0) cc_final: 0.8403 (p0) outliers start: 38 outliers final: 28 residues processed: 150 average time/residue: 0.2279 time to fit residues: 53.3833 Evaluate side-chains 140 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 116 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 GLN ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12677 Z= 0.222 Angle : 0.619 13.680 17178 Z= 0.302 Chirality : 0.041 0.231 1954 Planarity : 0.003 0.047 2141 Dihedral : 7.410 87.716 1767 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.59 % Allowed : 11.70 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1558 helix: 1.48 (0.21), residues: 642 sheet: -0.59 (0.31), residues: 272 loop : -1.10 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 624 HIS 0.010 0.001 HIS A 243 PHE 0.014 0.001 PHE F 79 TYR 0.023 0.001 TYR A 336 ARG 0.003 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 118 time to evaluate : 1.454 Fit side-chains revert: symmetry clash REVERT: A 172 LYS cc_start: 0.9084 (mttt) cc_final: 0.8581 (tptm) REVERT: A 182 PHE cc_start: 0.8276 (m-80) cc_final: 0.7471 (t80) REVERT: A 344 GLU cc_start: 0.8940 (tp30) cc_final: 0.8202 (tp30) REVERT: A 345 THR cc_start: 0.8991 (m) cc_final: 0.8761 (p) REVERT: A 391 ASN cc_start: 0.9110 (t0) cc_final: 0.8698 (t0) REVERT: B 172 LYS cc_start: 0.9108 (mttt) cc_final: 0.8419 (tmtt) REVERT: B 391 ASN cc_start: 0.9179 (t0) cc_final: 0.8823 (m-40) REVERT: B 402 THR cc_start: 0.9154 (m) cc_final: 0.8921 (p) REVERT: B 515 MET cc_start: 0.9254 (mmm) cc_final: 0.9041 (mmp) REVERT: C 79 GLN cc_start: 0.8802 (mp10) cc_final: 0.8523 (mp10) REVERT: D 47 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: E 79 GLN cc_start: 0.8999 (mm110) cc_final: 0.8544 (mm-40) REVERT: E 82 ASP cc_start: 0.7931 (m-30) cc_final: 0.7565 (m-30) REVERT: F 55 ASP cc_start: 0.8731 (p0) cc_final: 0.8335 (p0) outliers start: 35 outliers final: 28 residues processed: 146 average time/residue: 0.2004 time to fit residues: 46.6186 Evaluate side-chains 140 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12677 Z= 0.298 Angle : 0.653 13.668 17178 Z= 0.320 Chirality : 0.043 0.262 1954 Planarity : 0.004 0.047 2141 Dihedral : 7.403 85.125 1767 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.67 % Allowed : 11.78 % Favored : 85.56 % 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: -0.05 (0.22), residues: 1558 helix: 1.30 (0.21), residues: 660 sheet: -0.57 (0.31), residues: 272 loop : -1.20 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 109 HIS 0.008 0.001 HIS A 243 PHE 0.017 0.001 PHE F 79 TYR 0.023 0.002 TYR A 336 ARG 0.003 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: A 172 LYS cc_start: 0.9084 (mttt) cc_final: 0.8592 (tptm) REVERT: A 182 PHE cc_start: 0.8281 (m-80) cc_final: 0.7528 (t80) REVERT: A 344 GLU cc_start: 0.8915 (tp30) cc_final: 0.8177 (tp30) REVERT: A 345 THR cc_start: 0.8999 (m) cc_final: 0.8777 (p) REVERT: A 391 ASN cc_start: 0.9108 (t0) cc_final: 0.8693 (t0) REVERT: B 172 LYS cc_start: 0.9132 (mttt) cc_final: 0.8395 (tmtt) REVERT: B 348 GLU cc_start: 0.8465 (tp30) cc_final: 0.8212 (tp30) REVERT: B 391 ASN cc_start: 0.9169 (t0) cc_final: 0.8814 (m-40) REVERT: B 402 THR cc_start: 0.9168 (m) cc_final: 0.8905 (p) REVERT: B 515 MET cc_start: 0.9269 (mmm) cc_final: 0.9069 (mmp) REVERT: B 545 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8843 (m-10) REVERT: C 79 GLN cc_start: 0.8796 (mp10) cc_final: 0.8501 (mp10) REVERT: D 47 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: E 79 GLN cc_start: 0.9048 (mm110) cc_final: 0.8521 (mm-40) REVERT: E 82 ASP cc_start: 0.7907 (m-30) cc_final: 0.7468 (m-30) REVERT: F 55 ASP cc_start: 0.8698 (p0) cc_final: 0.8367 (p0) outliers start: 36 outliers final: 27 residues processed: 140 average time/residue: 0.1923 time to fit residues: 42.6675 Evaluate side-chains 138 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12677 Z= 0.254 Angle : 0.653 13.456 17178 Z= 0.315 Chirality : 0.042 0.243 1954 Planarity : 0.003 0.047 2141 Dihedral : 7.246 85.876 1767 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.15 % Allowed : 12.74 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.22), residues: 1558 helix: 1.35 (0.21), residues: 660 sheet: -0.56 (0.31), residues: 272 loop : -1.13 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 624 HIS 0.010 0.001 HIS A 243 PHE 0.015 0.001 PHE F 79 TYR 0.025 0.001 TYR A 336 ARG 0.003 0.000 ARG A 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: A 172 LYS cc_start: 0.9070 (mttt) cc_final: 0.8606 (tptm) REVERT: A 182 PHE cc_start: 0.8329 (m-80) cc_final: 0.7572 (t80) REVERT: A 344 GLU cc_start: 0.8904 (tp30) cc_final: 0.8204 (tp30) REVERT: A 345 THR cc_start: 0.9002 (m) cc_final: 0.8780 (p) REVERT: A 391 ASN cc_start: 0.9108 (t0) cc_final: 0.8684 (t0) REVERT: B 172 LYS cc_start: 0.9134 (mttt) cc_final: 0.8397 (tmtt) REVERT: B 391 ASN cc_start: 0.9161 (t0) cc_final: 0.8809 (m-40) REVERT: B 402 THR cc_start: 0.9184 (m) cc_final: 0.8943 (p) REVERT: B 515 MET cc_start: 0.9267 (mmm) cc_final: 0.9055 (mmp) REVERT: B 545 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8776 (m-10) REVERT: C 79 GLN cc_start: 0.8805 (mp10) cc_final: 0.8510 (mp10) REVERT: D 47 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: E 79 GLN cc_start: 0.9003 (mm110) cc_final: 0.8544 (mm-40) REVERT: E 82 ASP cc_start: 0.7886 (m-30) cc_final: 0.7495 (m-30) REVERT: F 55 ASP cc_start: 0.8720 (p0) cc_final: 0.8388 (p0) outliers start: 29 outliers final: 23 residues processed: 136 average time/residue: 0.1912 time to fit residues: 41.2285 Evaluate side-chains 138 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.0470 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 0.4980 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 107 optimal weight: 0.5980 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.087761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.066701 restraints weight = 33888.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.068970 restraints weight = 16058.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.070400 restraints weight = 9891.912| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12677 Z= 0.155 Angle : 0.613 13.180 17178 Z= 0.296 Chirality : 0.041 0.270 1954 Planarity : 0.003 0.048 2141 Dihedral : 6.786 89.847 1767 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.93 % Allowed : 12.89 % Favored : 85.19 % 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: 0.23 (0.22), residues: 1558 helix: 1.54 (0.21), residues: 656 sheet: -0.39 (0.31), residues: 272 loop : -1.06 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 35 HIS 0.009 0.001 HIS A 243 PHE 0.013 0.001 PHE B 545 TYR 0.024 0.001 TYR A 336 ARG 0.004 0.000 ARG B 230 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2129.56 seconds wall clock time: 39 minutes 41.82 seconds (2381.82 seconds total)