Starting phenix.real_space_refine on Mon Mar 18 17:33:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugg_26488/03_2024/7ugg_26488_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugg_26488/03_2024/7ugg_26488.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugg_26488/03_2024/7ugg_26488_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugg_26488/03_2024/7ugg_26488_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugg_26488/03_2024/7ugg_26488_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugg_26488/03_2024/7ugg_26488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugg_26488/03_2024/7ugg_26488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugg_26488/03_2024/7ugg_26488_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugg_26488/03_2024/7ugg_26488_updated.pdb" } resolution = 3.16 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= 0.023 sd= 0.102 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 116 5.16 5 Na 2 4.78 5 C 14260 2.51 5 N 3348 2.21 5 O 3920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ARG 716": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 509": "NH1" <-> "NH2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Residue "D PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21670 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5053 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 15, 'TRANS': 604} Chain breaks: 2 Chain: "B" Number of atoms: 5053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5053 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 15, 'TRANS': 604} Chain breaks: 2 Chain: "C" Number of atoms: 5053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5053 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 15, 'TRANS': 604} Chain breaks: 2 Chain: "D" Number of atoms: 5053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5053 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 15, 'TRANS': 604} Chain breaks: 2 Chain: "A" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 355 Unusual residues: {' NA': 1, 'N8R': 2, 'POV': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 333 Unusual residues: {'N8R': 1, 'POV': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 312 Unusual residues: {'POV': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 334 Unusual residues: {' NA': 1, 'N8R': 1, 'POV': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Time building chain proxies: 11.48, per 1000 atoms: 0.53 Number of scatterers: 21670 At special positions: 0 Unit cell: (147.06, 147.06, 122.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 24 15.00 Na 2 11.00 O 3920 8.00 N 3348 7.00 C 14260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.42 Conformation dependent library (CDL) restraints added in 3.4 seconds 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4744 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 4 sheets defined 53.9% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.574A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 removed outlier: 3.583A pdb=" N ARG A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N CYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 removed outlier: 3.917A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.644A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.636A pdb=" N ALA A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 299 through 305 removed outlier: 3.748A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 4.022A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 351 removed outlier: 3.626A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.705A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 423 through 435 removed outlier: 4.153A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 434 " --> pdb=" O HIS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 460 removed outlier: 3.551A pdb=" N PHE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 507 removed outlier: 3.676A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 516 No H-bonds generated for 'chain 'A' and resid 513 through 516' Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 527 through 540 removed outlier: 3.764A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 568 removed outlier: 3.743A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N MET A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N THR A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ARG A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLY A 568 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 585 removed outlier: 3.757A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 605 removed outlier: 3.787A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 627 No H-bonds generated for 'chain 'A' and resid 624 through 627' Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.830A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 646 No H-bonds generated for 'chain 'A' and resid 643 through 646' Processing helix chain 'A' and resid 656 through 666 removed outlier: 3.655A pdb=" N TYR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 684 removed outlier: 3.889A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 703 removed outlier: 3.927A pdb=" N GLN A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 712 No H-bonds generated for 'chain 'A' and resid 709 through 712' Processing helix chain 'B' and resid 120 through 129 removed outlier: 3.575A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 removed outlier: 3.583A pdb=" N ARG B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N CYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 161 removed outlier: 3.918A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 removed outlier: 3.645A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 193 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.636A pdb=" N ALA B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 299 through 305 removed outlier: 3.747A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 4.022A pdb=" N ASP B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.627A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.705A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 423 through 435 removed outlier: 4.154A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 434 " --> pdb=" O HIS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 460 removed outlier: 3.550A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 507 removed outlier: 3.675A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 516 No H-bonds generated for 'chain 'B' and resid 513 through 516' Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 527 through 540 removed outlier: 3.764A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 568 removed outlier: 3.743A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N THR B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ARG B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLY B 568 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 585 removed outlier: 3.757A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 605 removed outlier: 3.788A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 627 No H-bonds generated for 'chain 'B' and resid 624 through 627' Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.830A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 646 No H-bonds generated for 'chain 'B' and resid 643 through 646' Processing helix chain 'B' and resid 656 through 666 removed outlier: 3.655A pdb=" N TYR B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 684 removed outlier: 3.888A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 703 removed outlier: 3.927A pdb=" N GLN B 695 " --> pdb=" O ILE B 691 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 702 " --> pdb=" O ARG B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 712 No H-bonds generated for 'chain 'B' and resid 709 through 712' Processing helix chain 'C' and resid 120 through 129 removed outlier: 3.575A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.583A pdb=" N ARG C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N CYS C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 161 removed outlier: 3.918A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 removed outlier: 3.645A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 193 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 229 through 237 removed outlier: 3.635A pdb=" N ALA C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 257 No H-bonds generated for 'chain 'C' and resid 255 through 257' Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 275 through 282 Processing helix chain 'C' and resid 299 through 305 removed outlier: 3.748A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 4.022A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 351 removed outlier: 3.627A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.705A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 423 through 435 removed outlier: 4.153A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 434 " --> pdb=" O HIS C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 460 removed outlier: 3.550A pdb=" N PHE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 447 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 507 removed outlier: 3.675A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 498 " --> pdb=" O ALA C 494 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 516 No H-bonds generated for 'chain 'C' and resid 513 through 516' Processing helix chain 'C' and resid 521 through 525 Processing helix chain 'C' and resid 527 through 540 removed outlier: 3.764A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 568 removed outlier: 3.743A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N MET C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ARG C 567 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY C 568 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 585 removed outlier: 3.756A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 605 removed outlier: 3.787A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 627 No H-bonds generated for 'chain 'C' and resid 624 through 627' Processing helix chain 'C' and resid 630 through 637 removed outlier: 3.830A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 646 No H-bonds generated for 'chain 'C' and resid 643 through 646' Processing helix chain 'C' and resid 656 through 666 removed outlier: 3.655A pdb=" N TYR C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 662 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 664 " --> pdb=" O THR C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 684 removed outlier: 3.889A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 703 removed outlier: 3.926A pdb=" N GLN C 695 " --> pdb=" O ILE C 691 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU C 702 " --> pdb=" O ARG C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 712 No H-bonds generated for 'chain 'C' and resid 709 through 712' Processing helix chain 'D' and resid 120 through 129 removed outlier: 3.576A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 147 removed outlier: 3.582A pdb=" N ARG D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 161 removed outlier: 3.917A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 177 removed outlier: 3.645A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 193 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 229 through 237 removed outlier: 3.637A pdb=" N ALA D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 265 through 271 Processing helix chain 'D' and resid 275 through 282 Processing helix chain 'D' and resid 299 through 305 removed outlier: 3.748A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 removed outlier: 4.022A pdb=" N ASP D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 351 removed outlier: 3.626A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.704A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 423 through 435 removed outlier: 4.153A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS D 434 " --> pdb=" O HIS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 460 removed outlier: 3.550A pdb=" N PHE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE D 447 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 507 removed outlier: 3.676A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER D 498 " --> pdb=" O ALA D 494 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 516 No H-bonds generated for 'chain 'D' and resid 513 through 516' Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 527 through 540 removed outlier: 3.763A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 568 removed outlier: 3.743A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N MET D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N THR D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ARG D 567 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY D 568 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 585 removed outlier: 3.756A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 605 removed outlier: 3.788A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 627 No H-bonds generated for 'chain 'D' and resid 624 through 627' Processing helix chain 'D' and resid 630 through 637 removed outlier: 3.830A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 646 No H-bonds generated for 'chain 'D' and resid 643 through 646' Processing helix chain 'D' and resid 656 through 666 removed outlier: 3.655A pdb=" N TYR D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 662 " --> pdb=" O LEU D 658 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 664 " --> pdb=" O THR D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 684 removed outlier: 3.889A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 703 removed outlier: 3.926A pdb=" N GLN D 695 " --> pdb=" O ILE D 691 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 712 No H-bonds generated for 'chain 'D' and resid 709 through 712' Processing sheet with id= A, first strand: chain 'A' and resid 376 through 381 removed outlier: 6.932A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 727 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 724 " --> pdb=" O ASP A 727 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ARG A 729 " --> pdb=" O LYS A 722 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LYS A 722 " --> pdb=" O ARG A 729 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N CYS A 731 " --> pdb=" O LEU A 720 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU A 720 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 376 through 381 removed outlier: 6.932A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP B 727 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 724 " --> pdb=" O ASP B 727 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ARG B 729 " --> pdb=" O LYS B 722 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LYS B 722 " --> pdb=" O ARG B 729 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N CYS B 731 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU B 720 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 376 through 381 removed outlier: 6.933A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP C 727 " --> pdb=" O ALA C 724 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 724 " --> pdb=" O ASP C 727 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ARG C 729 " --> pdb=" O LYS C 722 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LYS C 722 " --> pdb=" O ARG C 729 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N CYS C 731 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU C 720 " --> pdb=" O CYS C 731 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 376 through 381 removed outlier: 6.931A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP D 727 " --> pdb=" O ALA D 724 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA D 724 " --> pdb=" O ASP D 727 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ARG D 729 " --> pdb=" O LYS D 722 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LYS D 722 " --> pdb=" O ARG D 729 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N CYS D 731 " --> pdb=" O LEU D 720 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU D 720 " --> pdb=" O CYS D 731 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1788 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: 6.02 Time building geometry restraints manager: 8.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3284 1.30 - 1.43: 5668 1.43 - 1.55: 12639 1.55 - 1.68: 177 1.68 - 1.81: 196 Bond restraints: 21964 Sorted by residual: bond pdb=" C18 N8R A 907 " pdb=" N01 N8R A 907 " ideal model delta sigma weight residual 1.488 1.309 0.179 2.00e-02 2.50e+03 8.02e+01 bond pdb=" C18 N8R D 907 " pdb=" N01 N8R D 907 " ideal model delta sigma weight residual 1.488 1.309 0.179 2.00e-02 2.50e+03 7.97e+01 bond pdb=" C18 N8R B 907 " pdb=" N01 N8R B 907 " ideal model delta sigma weight residual 1.488 1.310 0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" C18 N8R A 905 " pdb=" N01 N8R A 905 " ideal model delta sigma weight residual 1.488 1.311 0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" C14 N8R A 907 " pdb=" N01 N8R A 907 " ideal model delta sigma weight residual 1.488 1.311 0.177 2.00e-02 2.50e+03 7.83e+01 ... (remaining 21959 not shown) Histogram of bond angle deviations from ideal: 97.08 - 104.49: 234 104.49 - 111.89: 10282 111.89 - 119.30: 7870 119.30 - 126.71: 10810 126.71 - 134.12: 288 Bond angle restraints: 29484 Sorted by residual: angle pdb=" N VAL B 248 " pdb=" CA VAL B 248 " pdb=" C VAL B 248 " ideal model delta sigma weight residual 112.96 106.36 6.60 1.00e+00 1.00e+00 4.36e+01 angle pdb=" N VAL D 248 " pdb=" CA VAL D 248 " pdb=" C VAL D 248 " ideal model delta sigma weight residual 112.96 106.36 6.60 1.00e+00 1.00e+00 4.36e+01 angle pdb=" N VAL C 248 " pdb=" CA VAL C 248 " pdb=" C VAL C 248 " ideal model delta sigma weight residual 112.96 106.37 6.59 1.00e+00 1.00e+00 4.34e+01 angle pdb=" N VAL A 248 " pdb=" CA VAL A 248 " pdb=" C VAL A 248 " ideal model delta sigma weight residual 112.96 106.40 6.56 1.00e+00 1.00e+00 4.30e+01 angle pdb=" N GLY A 602 " pdb=" CA GLY A 602 " pdb=" C GLY A 602 " ideal model delta sigma weight residual 112.50 118.44 -5.94 1.16e+00 7.43e-01 2.62e+01 ... (remaining 29479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 12820 35.74 - 71.47: 443 71.47 - 107.21: 61 107.21 - 142.94: 28 142.94 - 178.68: 8 Dihedral angle restraints: 13360 sinusoidal: 6052 harmonic: 7308 Sorted by residual: dihedral pdb=" CA ASP B 315 " pdb=" C ASP B 315 " pdb=" N PHE B 316 " pdb=" CA PHE B 316 " ideal model delta harmonic sigma weight residual 180.00 -139.69 -40.31 0 5.00e+00 4.00e-02 6.50e+01 dihedral pdb=" CA ASP A 315 " pdb=" C ASP A 315 " pdb=" N PHE A 316 " pdb=" CA PHE A 316 " ideal model delta harmonic sigma weight residual -180.00 -139.70 -40.30 0 5.00e+00 4.00e-02 6.50e+01 dihedral pdb=" CA ASP D 315 " pdb=" C ASP D 315 " pdb=" N PHE D 316 " pdb=" CA PHE D 316 " ideal model delta harmonic sigma weight residual -180.00 -139.71 -40.29 0 5.00e+00 4.00e-02 6.49e+01 ... (remaining 13357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2769 0.073 - 0.146: 442 0.146 - 0.218: 17 0.218 - 0.291: 0 0.291 - 0.364: 4 Chirality restraints: 3232 Sorted by residual: chirality pdb=" CG LEU D 475 " pdb=" CB LEU D 475 " pdb=" CD1 LEU D 475 " pdb=" CD2 LEU D 475 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CG LEU B 475 " pdb=" CB LEU B 475 " pdb=" CD1 LEU B 475 " pdb=" CD2 LEU B 475 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CG LEU C 475 " pdb=" CB LEU C 475 " pdb=" CD1 LEU C 475 " pdb=" CD2 LEU C 475 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3229 not shown) Planarity restraints: 3556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 526 " -0.012 2.00e-02 2.50e+03 2.15e-02 8.11e+00 pdb=" CG PHE A 526 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE A 526 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 526 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 526 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 526 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 526 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 526 " -0.012 2.00e-02 2.50e+03 2.15e-02 8.07e+00 pdb=" CG PHE C 526 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE C 526 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE C 526 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE C 526 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE C 526 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 526 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 526 " -0.012 2.00e-02 2.50e+03 2.14e-02 7.98e+00 pdb=" CG PHE D 526 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE D 526 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE D 526 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 526 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE D 526 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 526 " -0.006 2.00e-02 2.50e+03 ... (remaining 3553 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2026 2.73 - 3.27: 19153 3.27 - 3.82: 31741 3.82 - 4.36: 40513 4.36 - 4.90: 69863 Nonbonded interactions: 163296 Sorted by model distance: nonbonded pdb=" OH TYR C 213 " pdb=" O PRO D 753 " model vdw 2.192 2.440 nonbonded pdb=" O PRO A 753 " pdb=" OH TYR D 213 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR A 213 " pdb=" O PRO B 753 " model vdw 2.283 2.440 nonbonded pdb=" OH TYR B 213 " pdb=" O PRO C 753 " model vdw 2.303 2.440 nonbonded pdb=" OH TYR A 321 " pdb=" OE2 GLU A 334 " model vdw 2.304 2.440 ... (remaining 163291 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 118 through 756 or resid 901 through 904 or resid 906)) selection = (chain 'B' and (resid 118 through 756 or resid 901 through 904 or resid 906)) selection = (chain 'C' and (resid 118 through 756 or resid 901 through 904 or resid 906)) selection = (chain 'D' and (resid 118 through 756 or resid 901 through 904 or resid 906)) } 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=0.45 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: 1.860 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: 0.000 Extract box with map and model: 4.450 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 53.210 Find NCS groups from input model: 1.610 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: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 0.012 0.179 21964 Z= 0.734 Angle : 1.437 14.018 29484 Z= 0.702 Chirality : 0.052 0.364 3232 Planarity : 0.007 0.064 3556 Dihedral : 18.840 178.679 8616 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.17 % Favored : 92.51 % Rotamer: Outliers : 0.54 % Allowed : 2.72 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -6.21 (0.11), residues: 2456 helix: -4.58 (0.06), residues: 1448 sheet: -4.46 (0.35), residues: 96 loop : -2.86 (0.17), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 493 HIS 0.008 0.002 HIS B 301 PHE 0.044 0.003 PHE A 526 TYR 0.024 0.004 TYR D 390 ARG 0.008 0.001 ARG A 363 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 411 time to evaluate : 2.126 Fit side-chains REVERT: A 581 LYS cc_start: 0.7722 (mmtt) cc_final: 0.7426 (mptt) REVERT: B 581 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7400 (mptt) REVERT: B 653 LEU cc_start: 0.5801 (tp) cc_final: 0.4930 (mp) REVERT: C 143 GLN cc_start: 0.8493 (tp-100) cc_final: 0.8279 (tp-100) REVERT: C 581 LYS cc_start: 0.7654 (mmtt) cc_final: 0.7327 (mptt) REVERT: C 653 LEU cc_start: 0.5789 (tp) cc_final: 0.5008 (mp) outliers start: 12 outliers final: 0 residues processed: 419 average time/residue: 0.3095 time to fit residues: 202.9023 Evaluate side-chains 257 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 0.0170 chunk 194 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 118 optimal weight: 0.4980 chunk 144 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 overall best weight: 1.2622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 255 GLN A 471 HIS A 477 HIS A 643 ASN A 671 ASN A 745 HIS B 178 ASN B 255 GLN B 477 HIS B 643 ASN B 647 ASN B 671 ASN B 745 HIS C 178 ASN C 255 GLN C 471 HIS C 477 HIS C 647 ASN C 671 ASN C 745 HIS D 143 GLN D 178 ASN D 255 GLN D 477 HIS D 745 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21964 Z= 0.154 Angle : 0.592 8.922 29484 Z= 0.303 Chirality : 0.039 0.146 3232 Planarity : 0.004 0.042 3556 Dihedral : 21.735 154.242 3772 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.36 % Favored : 95.32 % Rotamer: Outliers : 1.63 % Allowed : 7.58 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -4.54 (0.13), residues: 2456 helix: -2.96 (0.10), residues: 1460 sheet: -3.69 (0.35), residues: 88 loop : -2.72 (0.17), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 559 HIS 0.009 0.001 HIS A 471 PHE 0.013 0.001 PHE D 526 TYR 0.012 0.001 TYR D 359 ARG 0.005 0.000 ARG D 716 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 292 time to evaluate : 2.169 Fit side-chains REVERT: A 544 TYR cc_start: 0.6339 (m-80) cc_final: 0.6115 (m-80) REVERT: A 650 TYR cc_start: 0.6010 (OUTLIER) cc_final: 0.5706 (m-80) REVERT: B 544 TYR cc_start: 0.6356 (m-80) cc_final: 0.6100 (m-80) REVERT: B 570 GLN cc_start: 0.7597 (tt0) cc_final: 0.7359 (tt0) REVERT: B 726 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7569 (mm-30) REVERT: C 544 TYR cc_start: 0.6365 (m-80) cc_final: 0.6069 (m-80) REVERT: C 570 GLN cc_start: 0.7505 (tt0) cc_final: 0.7252 (tt0) REVERT: D 544 TYR cc_start: 0.6088 (m-80) cc_final: 0.5836 (m-80) REVERT: D 570 GLN cc_start: 0.7964 (tt0) cc_final: 0.7679 (tt0) REVERT: D 650 TYR cc_start: 0.5743 (OUTLIER) cc_final: 0.5158 (m-10) outliers start: 36 outliers final: 10 residues processed: 320 average time/residue: 0.2968 time to fit residues: 152.0100 Evaluate side-chains 245 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 233 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 650 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 225 optimal weight: 4.9990 chunk 243 optimal weight: 0.0270 chunk 200 optimal weight: 0.6980 chunk 223 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 180 optimal weight: 0.6980 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 695 GLN B 227 GLN B 255 GLN B 570 GLN C 227 GLN C 255 GLN C 430 HIS C 471 HIS C 570 GLN D 227 GLN D 255 GLN D 570 GLN D 643 ASN D 695 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21964 Z= 0.124 Angle : 0.536 9.211 29484 Z= 0.271 Chirality : 0.037 0.140 3232 Planarity : 0.003 0.029 3556 Dihedral : 19.626 109.629 3772 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.97 % Favored : 94.71 % Rotamer: Outliers : 1.59 % Allowed : 9.66 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.30 (0.14), residues: 2456 helix: -1.77 (0.12), residues: 1456 sheet: -3.42 (0.37), residues: 88 loop : -2.56 (0.17), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 739 HIS 0.007 0.001 HIS C 430 PHE 0.012 0.001 PHE A 316 TYR 0.012 0.001 TYR D 547 ARG 0.002 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 269 time to evaluate : 2.559 Fit side-chains revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8446 (ttm170) cc_final: 0.8174 (ttp80) REVERT: A 581 LYS cc_start: 0.6993 (mmtt) cc_final: 0.6712 (mptt) REVERT: A 650 TYR cc_start: 0.5677 (OUTLIER) cc_final: 0.5407 (m-80) REVERT: B 211 GLU cc_start: 0.7231 (pm20) cc_final: 0.6990 (pm20) REVERT: B 581 LYS cc_start: 0.7015 (mmtt) cc_final: 0.6696 (mptt) REVERT: B 726 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7551 (mm-30) REVERT: C 211 GLU cc_start: 0.7285 (pm20) cc_final: 0.7009 (pm20) REVERT: D 650 TYR cc_start: 0.5394 (OUTLIER) cc_final: 0.4875 (m-10) REVERT: D 679 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.7058 (mp0) outliers start: 35 outliers final: 18 residues processed: 293 average time/residue: 0.3071 time to fit residues: 144.2054 Evaluate side-chains 253 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 679 GLU Chi-restraints excluded: chain D residue 685 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN B 695 GLN C 255 GLN D 255 GLN D 570 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21964 Z= 0.247 Angle : 0.594 8.628 29484 Z= 0.299 Chirality : 0.040 0.157 3232 Planarity : 0.003 0.032 3556 Dihedral : 19.042 102.510 3772 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.82 % Favored : 93.85 % Rotamer: Outliers : 2.04 % Allowed : 9.85 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.71 (0.15), residues: 2456 helix: -1.20 (0.13), residues: 1452 sheet: -3.27 (0.34), residues: 112 loop : -2.43 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 739 HIS 0.007 0.001 HIS D 301 PHE 0.014 0.001 PHE D 316 TYR 0.021 0.002 TYR C 390 ARG 0.002 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 255 time to evaluate : 2.602 Fit side-chains REVERT: A 122 ARG cc_start: 0.8513 (ttm170) cc_final: 0.8242 (ttp80) REVERT: A 544 TYR cc_start: 0.6213 (m-80) cc_final: 0.5963 (m-80) REVERT: A 581 LYS cc_start: 0.7158 (mmtt) cc_final: 0.6950 (mptt) REVERT: A 650 TYR cc_start: 0.5664 (OUTLIER) cc_final: 0.5182 (m-80) REVERT: B 211 GLU cc_start: 0.7234 (pm20) cc_final: 0.7005 (pm20) REVERT: B 544 TYR cc_start: 0.6157 (m-80) cc_final: 0.5912 (m-80) REVERT: B 650 TYR cc_start: 0.5752 (OUTLIER) cc_final: 0.5237 (m-80) REVERT: B 726 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7575 (mm-30) REVERT: C 211 GLU cc_start: 0.7325 (pm20) cc_final: 0.7054 (pm20) REVERT: C 540 TYR cc_start: 0.8130 (t80) cc_final: 0.7551 (t80) REVERT: C 544 TYR cc_start: 0.6176 (m-80) cc_final: 0.5944 (m-80) REVERT: D 603 VAL cc_start: 0.7456 (t) cc_final: 0.7215 (p) REVERT: D 650 TYR cc_start: 0.5685 (OUTLIER) cc_final: 0.5127 (m-80) outliers start: 45 outliers final: 30 residues processed: 289 average time/residue: 0.3190 time to fit residues: 148.4449 Evaluate side-chains 257 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 224 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 650 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 HIS C 255 GLN C 585 HIS D 255 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21964 Z= 0.347 Angle : 0.653 8.540 29484 Z= 0.329 Chirality : 0.043 0.156 3232 Planarity : 0.004 0.034 3556 Dihedral : 19.194 107.130 3772 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.27 % Favored : 93.44 % Rotamer: Outliers : 2.72 % Allowed : 10.71 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.52 (0.15), residues: 2456 helix: -1.08 (0.13), residues: 1448 sheet: -2.88 (0.39), residues: 108 loop : -2.33 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 692 HIS 0.008 0.001 HIS C 301 PHE 0.015 0.002 PHE A 316 TYR 0.018 0.002 TYR A 451 ARG 0.005 0.000 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 244 time to evaluate : 2.223 Fit side-chains revert: symmetry clash REVERT: A 544 TYR cc_start: 0.6141 (m-80) cc_final: 0.5898 (m-80) REVERT: A 581 LYS cc_start: 0.7266 (mmtt) cc_final: 0.7035 (mptt) REVERT: A 650 TYR cc_start: 0.5877 (OUTLIER) cc_final: 0.5391 (m-80) REVERT: B 122 ARG cc_start: 0.8592 (ttm170) cc_final: 0.8334 (ttp80) REVERT: B 211 GLU cc_start: 0.7305 (pm20) cc_final: 0.7072 (pm20) REVERT: B 539 LEU cc_start: 0.7809 (mt) cc_final: 0.7596 (mt) REVERT: B 544 TYR cc_start: 0.6150 (m-80) cc_final: 0.5939 (m-80) REVERT: B 650 TYR cc_start: 0.6047 (OUTLIER) cc_final: 0.5481 (m-80) REVERT: B 726 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7673 (mm-30) REVERT: C 211 GLU cc_start: 0.7372 (pm20) cc_final: 0.7107 (pm20) REVERT: C 544 TYR cc_start: 0.6283 (m-80) cc_final: 0.6026 (m-80) REVERT: D 544 TYR cc_start: 0.6055 (m-80) cc_final: 0.5812 (m-80) outliers start: 60 outliers final: 46 residues processed: 286 average time/residue: 0.3002 time to fit residues: 137.4505 Evaluate side-chains 281 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 233 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 663 ILE Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 685 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 239 optimal weight: 8.9990 chunk 199 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 19 optimal weight: 0.0040 chunk 79 optimal weight: 0.3980 chunk 125 optimal weight: 1.9990 overall best weight: 1.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 GLN D 255 GLN D 585 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 21964 Z= 0.156 Angle : 0.547 10.674 29484 Z= 0.274 Chirality : 0.039 0.154 3232 Planarity : 0.003 0.032 3556 Dihedral : 18.373 103.613 3772 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.05 % Favored : 94.67 % Rotamer: Outliers : 2.09 % Allowed : 12.48 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.85 (0.16), residues: 2456 helix: -0.56 (0.13), residues: 1456 sheet: -2.52 (0.42), residues: 112 loop : -2.04 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 739 HIS 0.004 0.001 HIS D 301 PHE 0.014 0.001 PHE A 316 TYR 0.017 0.001 TYR A 547 ARG 0.004 0.000 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 236 time to evaluate : 2.349 Fit side-chains revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8528 (ttm170) cc_final: 0.8265 (ttp80) REVERT: A 650 TYR cc_start: 0.5395 (OUTLIER) cc_final: 0.4850 (m-80) REVERT: B 650 TYR cc_start: 0.5680 (OUTLIER) cc_final: 0.5159 (m-80) REVERT: B 726 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7673 (mm-30) REVERT: C 211 GLU cc_start: 0.7345 (pm20) cc_final: 0.7114 (pm20) REVERT: C 544 TYR cc_start: 0.6149 (m-80) cc_final: 0.5927 (m-80) outliers start: 46 outliers final: 34 residues processed: 268 average time/residue: 0.2885 time to fit residues: 125.1617 Evaluate side-chains 264 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 228 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 540 TYR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 685 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 110 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS C 255 GLN D 255 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21964 Z= 0.266 Angle : 0.605 10.262 29484 Z= 0.302 Chirality : 0.041 0.158 3232 Planarity : 0.003 0.033 3556 Dihedral : 18.452 105.022 3772 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.31 % Favored : 93.44 % Rotamer: Outliers : 2.63 % Allowed : 12.07 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.82 (0.16), residues: 2456 helix: -0.54 (0.13), residues: 1444 sheet: -2.18 (0.45), residues: 108 loop : -2.05 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 559 HIS 0.007 0.001 HIS C 301 PHE 0.015 0.001 PHE D 316 TYR 0.019 0.002 TYR A 460 ARG 0.003 0.000 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 231 time to evaluate : 1.952 Fit side-chains revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8547 (ttm170) cc_final: 0.8274 (ttp80) REVERT: A 581 LYS cc_start: 0.7180 (mmtt) cc_final: 0.6962 (mptt) REVERT: A 650 TYR cc_start: 0.5501 (OUTLIER) cc_final: 0.5037 (m-80) REVERT: B 122 ARG cc_start: 0.8625 (ttm170) cc_final: 0.8384 (ttp80) REVERT: B 514 GLN cc_start: 0.5324 (tp40) cc_final: 0.4755 (mm110) REVERT: B 650 TYR cc_start: 0.5754 (OUTLIER) cc_final: 0.5258 (m-80) REVERT: B 726 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7687 (mm-30) REVERT: C 122 ARG cc_start: 0.8587 (mtm180) cc_final: 0.8260 (ttp80) REVERT: C 211 GLU cc_start: 0.7336 (pm20) cc_final: 0.7124 (pm20) REVERT: C 544 TYR cc_start: 0.6115 (m-80) cc_final: 0.5864 (m-80) outliers start: 58 outliers final: 46 residues processed: 266 average time/residue: 0.3050 time to fit residues: 130.1507 Evaluate side-chains 275 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 227 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 605 LEU Chi-restraints excluded: chain D residue 685 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 217 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21964 Z= 0.116 Angle : 0.520 11.175 29484 Z= 0.259 Chirality : 0.038 0.153 3232 Planarity : 0.003 0.033 3556 Dihedral : 17.591 101.597 3772 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.97 % Favored : 94.83 % Rotamer: Outliers : 1.91 % Allowed : 13.11 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.28 (0.17), residues: 2456 helix: -0.08 (0.14), residues: 1468 sheet: -2.07 (0.43), residues: 120 loop : -1.91 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 739 HIS 0.003 0.001 HIS D 301 PHE 0.013 0.001 PHE C 316 TYR 0.016 0.001 TYR A 460 ARG 0.004 0.000 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 231 time to evaluate : 2.469 Fit side-chains REVERT: A 122 ARG cc_start: 0.8549 (ttm170) cc_final: 0.8309 (ttp80) REVERT: A 531 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8266 (m) REVERT: A 650 TYR cc_start: 0.5226 (OUTLIER) cc_final: 0.4707 (m-80) REVERT: B 650 TYR cc_start: 0.5421 (OUTLIER) cc_final: 0.4866 (m-80) REVERT: B 726 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7665 (mm-30) REVERT: C 122 ARG cc_start: 0.8600 (mtm180) cc_final: 0.8311 (ttp80) REVERT: C 531 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8364 (m) outliers start: 42 outliers final: 24 residues processed: 258 average time/residue: 0.3142 time to fit residues: 128.8554 Evaluate side-chains 250 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 222 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 605 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 10.0000 chunk 208 optimal weight: 0.0670 chunk 222 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 overall best weight: 2.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN D 255 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21964 Z= 0.223 Angle : 0.582 10.709 29484 Z= 0.289 Chirality : 0.041 0.162 3232 Planarity : 0.003 0.033 3556 Dihedral : 17.727 102.623 3772 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.58 % Favored : 94.22 % Rotamer: Outliers : 1.63 % Allowed : 13.38 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.29 (0.17), residues: 2456 helix: -0.05 (0.14), residues: 1420 sheet: -1.76 (0.47), residues: 108 loop : -1.94 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 559 HIS 0.006 0.001 HIS D 301 PHE 0.015 0.001 PHE B 316 TYR 0.021 0.002 TYR C 460 ARG 0.003 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 226 time to evaluate : 2.430 Fit side-chains revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8567 (ttm170) cc_final: 0.8307 (ttp80) REVERT: A 529 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6654 (tt0) REVERT: A 650 TYR cc_start: 0.5458 (OUTLIER) cc_final: 0.4918 (m-80) REVERT: B 650 TYR cc_start: 0.5639 (OUTLIER) cc_final: 0.5125 (m-80) REVERT: B 726 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7673 (mm-30) REVERT: C 122 ARG cc_start: 0.8619 (mtm180) cc_final: 0.8312 (ttp80) REVERT: C 529 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6450 (tt0) outliers start: 36 outliers final: 26 residues processed: 250 average time/residue: 0.2988 time to fit residues: 120.4407 Evaluate side-chains 254 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 224 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 529 GLN Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 605 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 247 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 196 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN D 255 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21964 Z= 0.144 Angle : 0.533 11.237 29484 Z= 0.266 Chirality : 0.038 0.159 3232 Planarity : 0.003 0.032 3556 Dihedral : 17.283 100.253 3772 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.17 % Favored : 94.67 % Rotamer: Outliers : 1.27 % Allowed : 14.02 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.14 (0.17), residues: 2456 helix: 0.10 (0.14), residues: 1444 sheet: -1.78 (0.45), residues: 116 loop : -1.97 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 739 HIS 0.004 0.001 HIS D 301 PHE 0.014 0.001 PHE C 316 TYR 0.020 0.001 TYR C 460 ARG 0.004 0.000 ARG A 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4912 Ramachandran restraints generated. 2456 Oldfield, 0 Emsley, 2456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 226 time to evaluate : 2.415 Fit side-chains REVERT: A 122 ARG cc_start: 0.8562 (ttm170) cc_final: 0.8316 (ttp80) REVERT: A 650 TYR cc_start: 0.5278 (OUTLIER) cc_final: 0.4723 (m-80) REVERT: B 650 TYR cc_start: 0.5514 (OUTLIER) cc_final: 0.4976 (m-80) REVERT: B 726 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7629 (mm-30) REVERT: C 122 ARG cc_start: 0.8633 (mtm180) cc_final: 0.8346 (ttp80) REVERT: C 159 MET cc_start: 0.7987 (mmm) cc_final: 0.7443 (mmm) REVERT: C 540 TYR cc_start: 0.8092 (t80) cc_final: 0.7541 (t80) REVERT: D 255 GLN cc_start: 0.8330 (mm110) cc_final: 0.8028 (mm-40) outliers start: 28 outliers final: 24 residues processed: 243 average time/residue: 0.3058 time to fit residues: 119.8420 Evaluate side-chains 250 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 224 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 605 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 202 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.150224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.108609 restraints weight = 32595.871| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.18 r_work: 0.3197 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21964 Z= 0.164 Angle : 0.544 11.122 29484 Z= 0.270 Chirality : 0.039 0.166 3232 Planarity : 0.003 0.033 3556 Dihedral : 17.188 98.280 3772 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.37 % Favored : 94.46 % Rotamer: Outliers : 1.27 % Allowed : 14.02 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.08 (0.17), residues: 2456 helix: 0.14 (0.14), residues: 1448 sheet: -1.75 (0.45), residues: 116 loop : -1.94 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 559 HIS 0.005 0.001 HIS D 301 PHE 0.015 0.001 PHE A 316 TYR 0.022 0.001 TYR A 460 ARG 0.004 0.000 ARG A 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4384.91 seconds wall clock time: 79 minutes 58.84 seconds (4798.84 seconds total)