Starting phenix.real_space_refine on Sun Feb 18 19:08:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mim_23856/02_2024/7mim_23856_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mim_23856/02_2024/7mim_23856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mim_23856/02_2024/7mim_23856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mim_23856/02_2024/7mim_23856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mim_23856/02_2024/7mim_23856_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mim_23856/02_2024/7mim_23856_updated.pdb" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 36 5.49 5 S 124 5.16 5 Na 4 4.78 5 C 15064 2.51 5 N 3476 2.21 5 O 4024 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 122": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ARG 567": "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 "A ARG 757": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B ARG 567": "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 "B ARG 757": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C ARG 567": "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 "C ARG 757": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 509": "NH1" <-> "NH2" Residue "D ARG 567": "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" Residue "D ARG 757": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22728 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "B" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "C" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "D" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5213 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "A" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 471 Unusual residues: {' NA': 3, 'POV': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 469 Unusual residues: {' NA': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 11.55, per 1000 atoms: 0.51 Number of scatterers: 22728 At special positions: 0 Unit cell: (129.285, 129.285, 132.6, 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 124 16.00 P 36 15.00 Na 4 11.00 O 4024 8.00 N 3476 7.00 C 15064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 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: 7.87 Conformation dependent library (CDL) restraints added in 3.9 seconds 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4904 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 4 sheets defined 54.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.00 Creating SS restraints... Processing helix chain 'A' and resid 119 through 129 removed outlier: 3.570A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 removed outlier: 3.514A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.516A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.519A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.682A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.568A pdb=" N ALA A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 237 removed outlier: 3.522A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 3.798A pdb=" N ALA A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 299 through 305 removed outlier: 3.502A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.537A pdb=" N ILE A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 351 removed outlier: 3.558A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.709A pdb=" N ARG A 371 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N SER A 372 " --> pdb=" O PRO A 369 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.568A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 4.242A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 460 removed outlier: 3.783A pdb=" N PHE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 507 removed outlier: 3.927A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (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 541 removed outlier: 3.882A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 566 removed outlier: 3.519A pdb=" N LEU A 551 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL A 552 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 553 " --> pdb=" O CYS A 550 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA A 556 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 557 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP A 559 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET A 562 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 563 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 565 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 removed outlier: 3.626A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 576 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 606 removed outlier: 3.561A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 removed outlier: 4.071A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 665 removed outlier: 3.686A pdb=" N LEU A 655 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 686 removed outlier: 4.269A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 704 removed outlier: 3.513A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (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 119 through 129 removed outlier: 3.570A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 removed outlier: 3.514A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.517A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 removed outlier: 3.519A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.682A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 218 through 224 removed outlier: 3.569A pdb=" N ALA B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 237 removed outlier: 3.522A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 3.798A pdb=" N ALA B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 299 through 305 removed outlier: 3.502A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.537A pdb=" N ILE B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.559A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.708A pdb=" N ARG B 371 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N SER B 372 " --> pdb=" O PRO B 369 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.568A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 435 removed outlier: 4.242A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 460 removed outlier: 3.784A pdb=" N PHE B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 507 removed outlier: 3.927A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (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 541 removed outlier: 3.882A pdb=" N PHE B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 566 removed outlier: 3.519A pdb=" N LEU B 551 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL B 552 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B 553 " --> pdb=" O CYS B 550 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA B 556 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 557 " --> pdb=" O ALA B 554 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TRP B 559 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET B 562 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 563 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR B 565 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 585 removed outlier: 3.626A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B 576 " --> pdb=" O MET B 572 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 606 removed outlier: 3.562A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 removed outlier: 4.071A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 665 removed outlier: 3.685A pdb=" N LEU B 655 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 686 removed outlier: 4.269A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 704 removed outlier: 3.513A pdb=" N ARG B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (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 119 through 129 removed outlier: 3.570A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.514A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.517A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 removed outlier: 3.519A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.682A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 218 through 224 removed outlier: 3.569A pdb=" N ALA C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 removed outlier: 3.523A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 3.797A pdb=" N ALA C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 282 Processing helix chain 'C' and resid 299 through 305 removed outlier: 3.502A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.537A pdb=" N ILE C 324 " --> pdb=" O MET C 320 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 351 removed outlier: 3.559A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.709A pdb=" N ARG C 371 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER C 372 " --> pdb=" O PRO C 369 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 373 " --> pdb=" O LEU C 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.569A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 435 removed outlier: 4.242A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 460 removed outlier: 3.784A pdb=" N PHE C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 507 removed outlier: 3.927A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (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 541 removed outlier: 3.882A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 566 removed outlier: 3.520A pdb=" N LEU C 551 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL C 552 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 553 " --> pdb=" O CYS C 550 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA C 556 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 557 " --> pdb=" O ALA C 554 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TRP C 559 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET C 562 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 563 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 565 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 585 removed outlier: 3.626A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER C 576 " --> pdb=" O MET C 572 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 606 removed outlier: 3.562A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE C 595 " --> pdb=" O LEU C 591 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 removed outlier: 4.071A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 637 " --> pdb=" O PHE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 665 removed outlier: 3.686A pdb=" N LEU C 655 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 686 removed outlier: 4.269A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 704 removed outlier: 3.513A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (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 119 through 129 removed outlier: 3.570A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 147 removed outlier: 3.514A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 161 removed outlier: 3.516A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 177 removed outlier: 3.518A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 196 removed outlier: 3.682A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 218 through 224 removed outlier: 3.569A pdb=" N ALA D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 237 removed outlier: 3.523A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.798A pdb=" N ALA D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 282 Processing helix chain 'D' and resid 299 through 305 removed outlier: 3.502A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 removed outlier: 3.537A pdb=" N ILE D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 351 removed outlier: 3.559A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.708A pdb=" N ARG D 371 " --> pdb=" O LYS D 368 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N SER D 372 " --> pdb=" O PRO D 369 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU D 373 " --> pdb=" O LEU D 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 373' Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.568A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 435 removed outlier: 4.242A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 460 removed outlier: 3.784A pdb=" N PHE D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 507 removed outlier: 3.926A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (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 541 removed outlier: 3.883A pdb=" N PHE D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE D 538 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 566 removed outlier: 3.520A pdb=" N LEU D 551 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL D 552 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU D 553 " --> pdb=" O CYS D 550 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA D 556 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU D 557 " --> pdb=" O ALA D 554 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP D 559 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET D 562 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 563 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 565 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 585 removed outlier: 3.626A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER D 576 " --> pdb=" O MET D 572 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 606 removed outlier: 3.562A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 595 " --> pdb=" O LEU D 591 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 removed outlier: 4.071A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 637 " --> pdb=" O PHE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 665 removed outlier: 3.686A pdb=" N LEU D 655 " --> pdb=" O PRO D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 686 removed outlier: 4.270A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 704 removed outlier: 3.513A pdb=" N ARG D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (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 731 through 737 removed outlier: 3.578A pdb=" N VAL A 385 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASP A 391 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LYS A 376 " --> pdb=" O ASP A 391 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 731 through 737 removed outlier: 3.578A pdb=" N VAL B 385 " --> pdb=" O TYR B 382 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASP B 391 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LYS B 376 " --> pdb=" O ASP B 391 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 731 through 737 removed outlier: 3.578A pdb=" N VAL C 385 " --> pdb=" O TYR C 382 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASP C 391 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LYS C 376 " --> pdb=" O ASP C 391 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 731 through 737 removed outlier: 3.578A pdb=" N VAL D 385 " --> pdb=" O TYR D 382 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASP D 391 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LYS D 376 " --> pdb=" O ASP D 391 " (cutoff:3.500A) 652 hydrogen bonds defined for protein. 1872 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: 6.24 Time building geometry restraints manager: 8.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3432 1.31 - 1.44: 6004 1.44 - 1.56: 13432 1.56 - 1.69: 72 1.69 - 1.82: 204 Bond restraints: 23144 Sorted by residual: bond pdb=" C VAL B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.336 1.397 -0.061 1.20e-02 6.94e+03 2.60e+01 bond pdb=" C VAL C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.336 1.396 -0.060 1.20e-02 6.94e+03 2.52e+01 bond pdb=" C VAL D 154 " pdb=" N PRO D 155 " ideal model delta sigma weight residual 1.336 1.396 -0.060 1.20e-02 6.94e+03 2.51e+01 bond pdb=" C VAL A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.336 1.396 -0.060 1.20e-02 6.94e+03 2.50e+01 bond pdb=" C21 POV D 905 " pdb=" O21 POV D 905 " ideal model delta sigma weight residual 1.330 1.423 -0.093 2.00e-02 2.50e+03 2.15e+01 ... (remaining 23139 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.46: 509 106.46 - 113.54: 13217 113.54 - 120.62: 10258 120.62 - 127.71: 6796 127.71 - 134.79: 188 Bond angle restraints: 30968 Sorted by residual: angle pdb=" C ASP B 468 " pdb=" N LEU B 469 " pdb=" CA LEU B 469 " ideal model delta sigma weight residual 120.09 127.05 -6.96 1.25e+00 6.40e-01 3.10e+01 angle pdb=" C ASP A 468 " pdb=" N LEU A 469 " pdb=" CA LEU A 469 " ideal model delta sigma weight residual 120.09 127.01 -6.92 1.25e+00 6.40e-01 3.07e+01 angle pdb=" C ASP C 468 " pdb=" N LEU C 469 " pdb=" CA LEU C 469 " ideal model delta sigma weight residual 120.09 127.00 -6.91 1.25e+00 6.40e-01 3.05e+01 angle pdb=" C ASP D 468 " pdb=" N LEU D 469 " pdb=" CA LEU D 469 " ideal model delta sigma weight residual 120.09 127.00 -6.91 1.25e+00 6.40e-01 3.05e+01 angle pdb=" C GLU D 367 " pdb=" N LYS D 368 " pdb=" CA LYS D 368 " ideal model delta sigma weight residual 120.09 126.02 -5.93 1.25e+00 6.40e-01 2.25e+01 ... (remaining 30963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.61: 13298 29.61 - 59.22: 807 59.22 - 88.83: 143 88.83 - 118.45: 32 118.45 - 148.06: 20 Dihedral angle restraints: 14300 sinusoidal: 6744 harmonic: 7556 Sorted by residual: dihedral pdb=" CB CYS D 612 " pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " pdb=" CB CYS D 619 " ideal model delta sinusoidal sigma weight residual -86.00 -151.86 65.86 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual -86.00 -151.85 65.85 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual -86.00 -151.85 65.85 1 1.00e+01 1.00e-02 5.67e+01 ... (remaining 14297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2606 0.058 - 0.116: 597 0.116 - 0.173: 93 0.173 - 0.231: 21 0.231 - 0.289: 11 Chirality restraints: 3328 Sorted by residual: chirality pdb=" CG LEU D 469 " pdb=" CB LEU D 469 " pdb=" CD1 LEU D 469 " pdb=" CD2 LEU D 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CG LEU C 469 " pdb=" CB LEU C 469 " pdb=" CD1 LEU C 469 " pdb=" CD2 LEU C 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CG LEU B 469 " pdb=" CB LEU B 469 " pdb=" CD1 LEU B 469 " pdb=" CD2 LEU B 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 3325 not shown) Planarity restraints: 3712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 383 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO D 384 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 384 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 384 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 383 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 384 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 383 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 384 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 384 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 384 " 0.030 5.00e-02 4.00e+02 ... (remaining 3709 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 6737 2.84 - 3.36: 18471 3.36 - 3.87: 32746 3.87 - 4.39: 39255 4.39 - 4.90: 67924 Nonbonded interactions: 165133 Sorted by model distance: nonbonded pdb=" O LEU C 469 " pdb=" OH TYR C 540 " model vdw 2.327 2.440 nonbonded pdb=" O LEU D 469 " pdb=" OH TYR D 540 " model vdw 2.328 2.440 nonbonded pdb=" O LEU B 469 " pdb=" OH TYR B 540 " model vdw 2.328 2.440 nonbonded pdb=" O LEU A 469 " pdb=" OH TYR A 540 " model vdw 2.328 2.440 nonbonded pdb=" OD1 ASN C 298 " pdb=" ND1 HIS C 301 " model vdw 2.354 2.520 ... (remaining 165128 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 757 or resid 901 through 909)) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 118 through 757 or resid 901 through 909)) } 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.690 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 56.540 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.093 23144 Z= 0.591 Angle : 1.366 12.463 30968 Z= 0.572 Chirality : 0.054 0.289 3328 Planarity : 0.006 0.054 3712 Dihedral : 19.541 148.058 9384 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.29 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.95 (0.10), residues: 2552 helix: -4.76 (0.04), residues: 1456 sheet: 0.62 (0.60), residues: 76 loop : -2.75 (0.15), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 433 HIS 0.005 0.001 HIS A 301 PHE 0.020 0.002 PHE A 436 TYR 0.014 0.002 TYR D 451 ARG 0.009 0.001 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 2.505 Fit side-chains REVERT: A 121 LYS cc_start: 0.8366 (mttm) cc_final: 0.7949 (mtmt) REVERT: A 129 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8072 (mm-30) REVERT: A 323 MET cc_start: 0.8469 (ttm) cc_final: 0.8120 (ttp) REVERT: A 509 ARG cc_start: 0.6111 (ptp-170) cc_final: 0.5896 (mtm110) REVERT: A 561 ASN cc_start: 0.9119 (m-40) cc_final: 0.8832 (m-40) REVERT: A 743 LYS cc_start: 0.8867 (ptpt) cc_final: 0.8564 (ptmm) REVERT: B 121 LYS cc_start: 0.8366 (mttm) cc_final: 0.7948 (mtmt) REVERT: B 129 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8073 (mm-30) REVERT: B 141 ASP cc_start: 0.7769 (m-30) cc_final: 0.7511 (m-30) REVERT: B 323 MET cc_start: 0.8447 (ttm) cc_final: 0.8099 (ttp) REVERT: B 509 ARG cc_start: 0.6097 (ptp-170) cc_final: 0.5890 (mtm110) REVERT: B 561 ASN cc_start: 0.9075 (m-40) cc_final: 0.8789 (m-40) REVERT: B 743 LYS cc_start: 0.8864 (ptpt) cc_final: 0.8554 (ptmm) REVERT: C 121 LYS cc_start: 0.8396 (mttm) cc_final: 0.7972 (mtmt) REVERT: C 129 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8079 (mm-30) REVERT: C 141 ASP cc_start: 0.7769 (m-30) cc_final: 0.7512 (m-30) REVERT: C 323 MET cc_start: 0.8463 (ttm) cc_final: 0.8112 (ttp) REVERT: C 561 ASN cc_start: 0.9101 (m-40) cc_final: 0.8808 (m-40) REVERT: C 743 LYS cc_start: 0.8858 (ptpt) cc_final: 0.8555 (ptmm) REVERT: D 121 LYS cc_start: 0.8404 (mttm) cc_final: 0.7980 (mtmt) REVERT: D 129 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8079 (mm-30) REVERT: D 141 ASP cc_start: 0.7780 (m-30) cc_final: 0.7422 (m-30) REVERT: D 323 MET cc_start: 0.8499 (ttm) cc_final: 0.8156 (ttp) REVERT: D 509 ARG cc_start: 0.6144 (ptp-170) cc_final: 0.5933 (mtm110) REVERT: D 561 ASN cc_start: 0.9136 (m-40) cc_final: 0.8804 (m-40) REVERT: D 743 LYS cc_start: 0.8863 (ptpt) cc_final: 0.8565 (ptmm) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.3895 time to fit residues: 232.5863 Evaluate side-chains 255 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 232 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 394 ASN A 452 ASN A 477 HIS A 735 ASN B 220 ASN B 394 ASN B 452 ASN B 477 HIS B 735 ASN C 220 ASN C 394 ASN C 452 ASN C 477 HIS C 735 ASN D 220 ASN D 394 ASN D 452 ASN D 477 HIS D 735 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23144 Z= 0.160 Angle : 0.532 7.990 30968 Z= 0.273 Chirality : 0.039 0.133 3328 Planarity : 0.005 0.060 3712 Dihedral : 21.240 120.149 4336 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.71 % Allowed : 7.31 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.13), residues: 2552 helix: -2.72 (0.10), residues: 1448 sheet: 0.96 (0.63), residues: 76 loop : -2.44 (0.16), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 710 HIS 0.003 0.001 HIS A 301 PHE 0.023 0.001 PHE C 193 TYR 0.013 0.001 TYR A 575 ARG 0.004 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 305 time to evaluate : 2.746 Fit side-chains REVERT: A 121 LYS cc_start: 0.8180 (mttm) cc_final: 0.7758 (mtpp) REVERT: A 323 MET cc_start: 0.7979 (ttm) cc_final: 0.7615 (ttp) REVERT: A 447 PHE cc_start: 0.8509 (m-10) cc_final: 0.8219 (m-80) REVERT: A 488 MET cc_start: 0.7190 (tpp) cc_final: 0.6807 (mtp) REVERT: A 509 ARG cc_start: 0.5833 (ptp-170) cc_final: 0.5522 (mtm110) REVERT: A 546 GLU cc_start: 0.8020 (tp30) cc_final: 0.7396 (mm-30) REVERT: A 707 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7683 (pp) REVERT: A 743 LYS cc_start: 0.8860 (ptpt) cc_final: 0.8542 (ptmm) REVERT: B 121 LYS cc_start: 0.8177 (mttm) cc_final: 0.7755 (mtpp) REVERT: B 323 MET cc_start: 0.7942 (ttm) cc_final: 0.7671 (ttp) REVERT: B 447 PHE cc_start: 0.8493 (m-10) cc_final: 0.8190 (m-80) REVERT: B 488 MET cc_start: 0.7221 (tpp) cc_final: 0.6851 (mtp) REVERT: B 509 ARG cc_start: 0.5826 (ptp-170) cc_final: 0.5515 (mtm110) REVERT: B 546 GLU cc_start: 0.7994 (tp30) cc_final: 0.7364 (mm-30) REVERT: B 707 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7653 (pp) REVERT: B 743 LYS cc_start: 0.8858 (ptpt) cc_final: 0.8535 (ptmm) REVERT: C 121 LYS cc_start: 0.8196 (mttm) cc_final: 0.7772 (mtpp) REVERT: C 323 MET cc_start: 0.7974 (ttm) cc_final: 0.7607 (ttp) REVERT: C 447 PHE cc_start: 0.8510 (m-10) cc_final: 0.8214 (m-80) REVERT: C 488 MET cc_start: 0.7222 (tpp) cc_final: 0.6853 (mtp) REVERT: C 707 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7673 (pp) REVERT: C 743 LYS cc_start: 0.8854 (ptpt) cc_final: 0.8534 (ptmm) REVERT: D 121 LYS cc_start: 0.8140 (mttm) cc_final: 0.7718 (mtpp) REVERT: D 323 MET cc_start: 0.8068 (ttm) cc_final: 0.7705 (ttp) REVERT: D 447 PHE cc_start: 0.8497 (m-10) cc_final: 0.8208 (m-80) REVERT: D 488 MET cc_start: 0.7286 (tpp) cc_final: 0.7051 (mmt) REVERT: D 509 ARG cc_start: 0.5847 (ptp-170) cc_final: 0.5546 (mtm110) REVERT: D 546 GLU cc_start: 0.8066 (tp30) cc_final: 0.7486 (mm-30) REVERT: D 743 LYS cc_start: 0.8859 (ptpt) cc_final: 0.8543 (ptmm) outliers start: 39 outliers final: 15 residues processed: 328 average time/residue: 0.3914 time to fit residues: 190.8576 Evaluate side-chains 270 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 252 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 648 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 232 optimal weight: 5.9990 chunk 251 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 230 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 244 HIS B 227 GLN B 244 HIS C 227 GLN C 244 HIS D 227 GLN D 244 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23144 Z= 0.149 Angle : 0.490 8.194 30968 Z= 0.245 Chirality : 0.039 0.134 3328 Planarity : 0.004 0.054 3712 Dihedral : 19.090 105.712 4336 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.88 % Allowed : 8.58 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.15), residues: 2552 helix: -1.26 (0.13), residues: 1456 sheet: 1.11 (0.65), residues: 76 loop : -2.32 (0.16), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 710 HIS 0.004 0.001 HIS B 301 PHE 0.016 0.001 PHE C 193 TYR 0.012 0.001 TYR D 540 ARG 0.010 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 285 time to evaluate : 2.513 Fit side-chains REVERT: A 121 LYS cc_start: 0.8141 (mttm) cc_final: 0.7741 (mtpp) REVERT: A 253 LYS cc_start: 0.7580 (ttpt) cc_final: 0.7312 (ttpp) REVERT: A 323 MET cc_start: 0.8085 (ttm) cc_final: 0.7805 (ttp) REVERT: A 364 GLU cc_start: 0.7916 (pt0) cc_final: 0.7582 (pm20) REVERT: A 447 PHE cc_start: 0.8490 (m-10) cc_final: 0.8254 (m-80) REVERT: A 488 MET cc_start: 0.7207 (tpp) cc_final: 0.6867 (mtp) REVERT: A 509 ARG cc_start: 0.5926 (ptp-170) cc_final: 0.5458 (mtm110) REVERT: A 546 GLU cc_start: 0.8122 (tp30) cc_final: 0.7339 (mm-30) REVERT: A 743 LYS cc_start: 0.8858 (ptpt) cc_final: 0.8431 (ptmm) REVERT: B 121 LYS cc_start: 0.8143 (mttm) cc_final: 0.7743 (mtpp) REVERT: B 253 LYS cc_start: 0.7579 (ttpt) cc_final: 0.7310 (ttpp) REVERT: B 323 MET cc_start: 0.8061 (ttm) cc_final: 0.7781 (ttp) REVERT: B 364 GLU cc_start: 0.7836 (pt0) cc_final: 0.7469 (pm20) REVERT: B 447 PHE cc_start: 0.8474 (m-10) cc_final: 0.8234 (m-80) REVERT: B 488 MET cc_start: 0.7199 (tpp) cc_final: 0.6859 (mtp) REVERT: B 509 ARG cc_start: 0.5933 (ptp-170) cc_final: 0.5460 (mtm110) REVERT: B 546 GLU cc_start: 0.8123 (tp30) cc_final: 0.7347 (mm-30) REVERT: B 743 LYS cc_start: 0.8851 (ptpt) cc_final: 0.8425 (ptmm) REVERT: C 121 LYS cc_start: 0.8174 (mttm) cc_final: 0.7766 (mtpp) REVERT: C 323 MET cc_start: 0.8080 (ttm) cc_final: 0.7802 (ttp) REVERT: C 364 GLU cc_start: 0.7910 (pt0) cc_final: 0.7580 (pm20) REVERT: C 447 PHE cc_start: 0.8483 (m-10) cc_final: 0.8243 (m-80) REVERT: C 488 MET cc_start: 0.7203 (tpp) cc_final: 0.6863 (mtp) REVERT: C 546 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7126 (mm-30) REVERT: C 743 LYS cc_start: 0.8856 (ptpt) cc_final: 0.8424 (ptmm) REVERT: D 121 LYS cc_start: 0.8184 (mttm) cc_final: 0.7771 (mtpp) REVERT: D 253 LYS cc_start: 0.7584 (ttpt) cc_final: 0.7314 (ttpp) REVERT: D 255 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8447 (mt0) REVERT: D 323 MET cc_start: 0.8130 (ttm) cc_final: 0.7848 (ttp) REVERT: D 364 GLU cc_start: 0.7901 (pt0) cc_final: 0.7589 (pm20) REVERT: D 447 PHE cc_start: 0.8498 (m-10) cc_final: 0.8275 (m-80) REVERT: D 488 MET cc_start: 0.7273 (tpp) cc_final: 0.6896 (mtp) REVERT: D 509 ARG cc_start: 0.5942 (ptp-170) cc_final: 0.5474 (mtm110) REVERT: D 546 GLU cc_start: 0.8143 (tp30) cc_final: 0.7377 (mm-30) REVERT: D 743 LYS cc_start: 0.8863 (ptpt) cc_final: 0.8438 (ptmm) outliers start: 43 outliers final: 17 residues processed: 310 average time/residue: 0.3838 time to fit residues: 177.3519 Evaluate side-chains 274 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 255 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 25 optimal weight: 0.0170 chunk 111 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 overall best weight: 1.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN B 452 ASN C 452 ASN D 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23144 Z= 0.223 Angle : 0.525 8.574 30968 Z= 0.262 Chirality : 0.041 0.148 3328 Planarity : 0.004 0.054 3712 Dihedral : 18.588 107.251 4336 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.44 % Allowed : 9.54 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.16), residues: 2552 helix: -0.60 (0.13), residues: 1488 sheet: 1.17 (0.66), residues: 76 loop : -2.18 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 710 HIS 0.005 0.001 HIS B 471 PHE 0.008 0.001 PHE C 316 TYR 0.017 0.001 TYR C 540 ARG 0.010 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 257 time to evaluate : 2.616 Fit side-chains REVERT: A 323 MET cc_start: 0.8121 (ttm) cc_final: 0.7840 (ttp) REVERT: A 364 GLU cc_start: 0.7940 (pt0) cc_final: 0.7621 (pm20) REVERT: A 447 PHE cc_start: 0.8453 (m-10) cc_final: 0.8152 (m-80) REVERT: A 488 MET cc_start: 0.7264 (tpp) cc_final: 0.6872 (mtp) REVERT: A 743 LYS cc_start: 0.8845 (ptpt) cc_final: 0.8262 (ptmm) REVERT: B 323 MET cc_start: 0.8094 (ttm) cc_final: 0.7815 (ttp) REVERT: B 364 GLU cc_start: 0.7925 (pt0) cc_final: 0.7556 (pm20) REVERT: B 447 PHE cc_start: 0.8436 (m-10) cc_final: 0.8143 (m-80) REVERT: B 488 MET cc_start: 0.7251 (tpp) cc_final: 0.6869 (mtp) REVERT: B 743 LYS cc_start: 0.8813 (ptpt) cc_final: 0.8219 (ptmm) REVERT: C 323 MET cc_start: 0.8119 (ttm) cc_final: 0.7837 (ttp) REVERT: C 364 GLU cc_start: 0.7936 (pt0) cc_final: 0.7621 (pm20) REVERT: C 447 PHE cc_start: 0.8451 (m-10) cc_final: 0.8147 (m-80) REVERT: C 488 MET cc_start: 0.7256 (tpp) cc_final: 0.6865 (mtp) REVERT: C 546 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7735 (mm-30) REVERT: C 743 LYS cc_start: 0.8845 (ptpt) cc_final: 0.8259 (ptmm) REVERT: D 255 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8410 (mt0) REVERT: D 323 MET cc_start: 0.8170 (ttm) cc_final: 0.7885 (ttp) REVERT: D 364 GLU cc_start: 0.7928 (pt0) cc_final: 0.7631 (pm20) REVERT: D 447 PHE cc_start: 0.8427 (m-10) cc_final: 0.8127 (m-80) REVERT: D 488 MET cc_start: 0.7329 (tpp) cc_final: 0.7079 (mmt) REVERT: D 743 LYS cc_start: 0.8854 (ptpt) cc_final: 0.8275 (ptmm) outliers start: 33 outliers final: 19 residues processed: 280 average time/residue: 0.3882 time to fit residues: 163.7139 Evaluate side-chains 254 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 233 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 211 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 178 ASN C 178 ASN D 178 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 23144 Z= 0.366 Angle : 0.607 9.379 30968 Z= 0.304 Chirality : 0.044 0.180 3328 Planarity : 0.004 0.052 3712 Dihedral : 19.227 111.340 4336 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.93 % Allowed : 10.29 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.16), residues: 2552 helix: -0.44 (0.14), residues: 1480 sheet: 1.20 (0.66), residues: 76 loop : -2.16 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 521 HIS 0.005 0.001 HIS B 471 PHE 0.011 0.001 PHE A 524 TYR 0.014 0.002 TYR C 451 ARG 0.010 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 225 time to evaluate : 2.490 Fit side-chains REVERT: A 364 GLU cc_start: 0.7985 (pt0) cc_final: 0.7687 (pm20) REVERT: A 368 LYS cc_start: 0.8470 (ttpt) cc_final: 0.8069 (mmmm) REVERT: A 447 PHE cc_start: 0.8467 (m-10) cc_final: 0.8124 (m-80) REVERT: A 679 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7392 (tt0) REVERT: B 364 GLU cc_start: 0.7956 (pt0) cc_final: 0.7646 (pm20) REVERT: B 368 LYS cc_start: 0.8470 (ttpt) cc_final: 0.8067 (mmmm) REVERT: B 447 PHE cc_start: 0.8450 (m-10) cc_final: 0.8112 (m-80) REVERT: B 679 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7397 (tt0) REVERT: C 364 GLU cc_start: 0.7984 (pt0) cc_final: 0.7687 (pm20) REVERT: C 368 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8070 (mmmm) REVERT: C 447 PHE cc_start: 0.8464 (m-10) cc_final: 0.8104 (m-80) REVERT: C 546 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7778 (mm-30) REVERT: C 679 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7419 (tt0) REVERT: D 364 GLU cc_start: 0.7940 (pt0) cc_final: 0.7682 (pm20) REVERT: D 368 LYS cc_start: 0.8436 (ttpt) cc_final: 0.8028 (mmmm) REVERT: D 447 PHE cc_start: 0.8490 (m-10) cc_final: 0.8148 (m-80) REVERT: D 679 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7470 (tt0) outliers start: 44 outliers final: 29 residues processed: 248 average time/residue: 0.3810 time to fit residues: 142.7788 Evaluate side-chains 236 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 206 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 GLN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 684 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 145 optimal weight: 0.0970 chunk 61 optimal weight: 0.6980 chunk 247 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 81 optimal weight: 0.3980 chunk 130 optimal weight: 10.0000 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23144 Z= 0.119 Angle : 0.460 9.594 30968 Z= 0.231 Chirality : 0.038 0.156 3328 Planarity : 0.004 0.052 3712 Dihedral : 17.491 103.870 4336 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.44 % Allowed : 10.55 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.16), residues: 2552 helix: 0.33 (0.14), residues: 1456 sheet: 1.10 (0.66), residues: 76 loop : -1.80 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 710 HIS 0.002 0.000 HIS A 471 PHE 0.012 0.001 PHE C 316 TYR 0.015 0.001 TYR C 540 ARG 0.005 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 259 time to evaluate : 2.476 Fit side-chains REVERT: A 323 MET cc_start: 0.8300 (ttp) cc_final: 0.8089 (ttp) REVERT: A 364 GLU cc_start: 0.7964 (pt0) cc_final: 0.7657 (pm20) REVERT: A 368 LYS cc_start: 0.8393 (ttpt) cc_final: 0.8085 (mmmt) REVERT: A 447 PHE cc_start: 0.8394 (m-10) cc_final: 0.8116 (m-80) REVERT: A 475 LEU cc_start: 0.1703 (OUTLIER) cc_final: 0.1379 (tm) REVERT: A 488 MET cc_start: 0.7275 (mmt) cc_final: 0.6662 (mtp) REVERT: B 323 MET cc_start: 0.8280 (ttp) cc_final: 0.8068 (ttp) REVERT: B 364 GLU cc_start: 0.7957 (pt0) cc_final: 0.7603 (pm20) REVERT: B 368 LYS cc_start: 0.8396 (ttpt) cc_final: 0.8090 (mmmt) REVERT: B 447 PHE cc_start: 0.8377 (m-10) cc_final: 0.8108 (m-80) REVERT: B 475 LEU cc_start: 0.1658 (OUTLIER) cc_final: 0.1333 (tm) REVERT: B 488 MET cc_start: 0.7237 (mmt) cc_final: 0.6642 (mtp) REVERT: C 323 MET cc_start: 0.8299 (ttp) cc_final: 0.8085 (ttp) REVERT: C 364 GLU cc_start: 0.7965 (pt0) cc_final: 0.7657 (pm20) REVERT: C 368 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8089 (mmmt) REVERT: C 447 PHE cc_start: 0.8395 (m-10) cc_final: 0.8116 (m-80) REVERT: C 475 LEU cc_start: 0.1682 (OUTLIER) cc_final: 0.1358 (tm) REVERT: C 488 MET cc_start: 0.7249 (mmt) cc_final: 0.6644 (mtp) REVERT: C 546 GLU cc_start: 0.8162 (tp30) cc_final: 0.7829 (mm-30) REVERT: D 323 MET cc_start: 0.8342 (ttp) cc_final: 0.8133 (ttp) REVERT: D 364 GLU cc_start: 0.7954 (pt0) cc_final: 0.7669 (pm20) REVERT: D 368 LYS cc_start: 0.8392 (ttpt) cc_final: 0.8089 (mmmt) REVERT: D 447 PHE cc_start: 0.8423 (m-10) cc_final: 0.8148 (m-80) REVERT: D 475 LEU cc_start: 0.2125 (OUTLIER) cc_final: 0.1911 (tm) REVERT: D 488 MET cc_start: 0.7321 (tpp) cc_final: 0.6968 (mtp) outliers start: 33 outliers final: 12 residues processed: 281 average time/residue: 0.3681 time to fit residues: 158.5556 Evaluate side-chains 246 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 230 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 703 PHE Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 141 optimal weight: 0.2980 chunk 180 optimal weight: 0.0030 chunk 140 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23144 Z= 0.208 Angle : 0.502 9.622 30968 Z= 0.252 Chirality : 0.040 0.147 3328 Planarity : 0.004 0.050 3712 Dihedral : 17.539 106.433 4336 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.83 % Allowed : 12.43 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2552 helix: 0.45 (0.14), residues: 1488 sheet: 1.11 (0.66), residues: 76 loop : -1.94 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 710 HIS 0.003 0.001 HIS B 471 PHE 0.010 0.001 PHE A 316 TYR 0.017 0.001 TYR B 540 ARG 0.006 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 224 time to evaluate : 2.942 Fit side-chains REVERT: A 364 GLU cc_start: 0.7998 (pt0) cc_final: 0.7647 (pm20) REVERT: A 368 LYS cc_start: 0.8398 (ttpt) cc_final: 0.8004 (mmmm) REVERT: A 447 PHE cc_start: 0.8428 (m-10) cc_final: 0.8111 (m-80) REVERT: A 475 LEU cc_start: 0.1759 (OUTLIER) cc_final: 0.1073 (tp) REVERT: A 488 MET cc_start: 0.7394 (mmt) cc_final: 0.6717 (mtp) REVERT: B 364 GLU cc_start: 0.7999 (pt0) cc_final: 0.7625 (pm20) REVERT: B 368 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8001 (mmmm) REVERT: B 447 PHE cc_start: 0.8412 (m-10) cc_final: 0.8104 (m-80) REVERT: B 475 LEU cc_start: 0.1727 (OUTLIER) cc_final: 0.1038 (tp) REVERT: B 488 MET cc_start: 0.7386 (mmt) cc_final: 0.6714 (mtp) REVERT: C 364 GLU cc_start: 0.7996 (pt0) cc_final: 0.7646 (pm20) REVERT: C 368 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8134 (mmmt) REVERT: C 447 PHE cc_start: 0.8485 (m-10) cc_final: 0.8172 (m-80) REVERT: C 475 LEU cc_start: 0.1941 (OUTLIER) cc_final: 0.1261 (tp) REVERT: C 488 MET cc_start: 0.7388 (mmt) cc_final: 0.6712 (mtp) REVERT: C 546 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7789 (mm-30) REVERT: D 364 GLU cc_start: 0.7990 (pt0) cc_final: 0.7688 (pm20) REVERT: D 368 LYS cc_start: 0.8374 (ttpt) cc_final: 0.7997 (mmmm) REVERT: D 447 PHE cc_start: 0.8474 (m-10) cc_final: 0.8153 (m-80) REVERT: D 475 LEU cc_start: 0.2614 (OUTLIER) cc_final: 0.2242 (tm) REVERT: D 488 MET cc_start: 0.7362 (tpp) cc_final: 0.7106 (mmt) outliers start: 19 outliers final: 13 residues processed: 239 average time/residue: 0.3810 time to fit residues: 138.9212 Evaluate side-chains 233 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 215 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 703 PHE Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 703 PHE Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 475 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 168 optimal weight: 0.0370 chunk 121 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23144 Z= 0.133 Angle : 0.459 10.368 30968 Z= 0.230 Chirality : 0.038 0.149 3328 Planarity : 0.003 0.052 3712 Dihedral : 16.831 103.333 4336 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.05 % Allowed : 12.61 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.17), residues: 2552 helix: 0.95 (0.14), residues: 1460 sheet: 1.06 (0.66), residues: 76 loop : -1.69 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 710 HIS 0.002 0.000 HIS D 301 PHE 0.012 0.001 PHE C 316 TYR 0.015 0.001 TYR B 540 ARG 0.003 0.000 ARG C 712 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 240 time to evaluate : 2.747 Fit side-chains REVERT: A 364 GLU cc_start: 0.7978 (pt0) cc_final: 0.7631 (pm20) REVERT: A 368 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8075 (mmmt) REVERT: A 447 PHE cc_start: 0.8275 (m-10) cc_final: 0.7949 (m-80) REVERT: A 475 LEU cc_start: 0.1742 (OUTLIER) cc_final: 0.1026 (tp) REVERT: A 488 MET cc_start: 0.7326 (mmt) cc_final: 0.6732 (mtp) REVERT: B 364 GLU cc_start: 0.7983 (pt0) cc_final: 0.7623 (pm20) REVERT: B 368 LYS cc_start: 0.8370 (ttpt) cc_final: 0.8069 (mmmt) REVERT: B 447 PHE cc_start: 0.8260 (m-10) cc_final: 0.7937 (m-80) REVERT: B 475 LEU cc_start: 0.1738 (OUTLIER) cc_final: 0.1020 (tp) REVERT: B 488 MET cc_start: 0.7358 (mmt) cc_final: 0.6735 (mtp) REVERT: C 364 GLU cc_start: 0.7976 (pt0) cc_final: 0.7631 (pm20) REVERT: C 368 LYS cc_start: 0.8373 (ttpt) cc_final: 0.8076 (mmmt) REVERT: C 447 PHE cc_start: 0.8272 (m-10) cc_final: 0.7946 (m-80) REVERT: C 475 LEU cc_start: 0.1762 (OUTLIER) cc_final: 0.1070 (tp) REVERT: C 488 MET cc_start: 0.7321 (mmt) cc_final: 0.6726 (mtp) REVERT: C 509 ARG cc_start: 0.6025 (mtm110) cc_final: 0.5729 (mtm-85) REVERT: C 546 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7809 (mm-30) REVERT: D 364 GLU cc_start: 0.7966 (pt0) cc_final: 0.7644 (pm20) REVERT: D 368 LYS cc_start: 0.8361 (ttpt) cc_final: 0.8084 (mmmt) REVERT: D 447 PHE cc_start: 0.8305 (m-10) cc_final: 0.7977 (m-80) REVERT: D 475 LEU cc_start: 0.2644 (OUTLIER) cc_final: 0.2259 (tm) REVERT: D 488 MET cc_start: 0.7276 (tpp) cc_final: 0.7001 (mtp) outliers start: 24 outliers final: 9 residues processed: 252 average time/residue: 0.3666 time to fit residues: 142.1893 Evaluate side-chains 238 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 224 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 229 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 180 optimal weight: 0.0020 chunk 70 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23144 Z= 0.138 Angle : 0.465 9.992 30968 Z= 0.234 Chirality : 0.039 0.141 3328 Planarity : 0.003 0.052 3712 Dihedral : 16.470 101.728 4336 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.92 % Allowed : 12.57 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.17), residues: 2552 helix: 1.00 (0.14), residues: 1508 sheet: 1.07 (0.66), residues: 76 loop : -1.79 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 710 HIS 0.002 0.001 HIS A 301 PHE 0.011 0.001 PHE A 316 TYR 0.014 0.001 TYR B 540 ARG 0.003 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 247 time to evaluate : 2.589 Fit side-chains REVERT: A 364 GLU cc_start: 0.7986 (pt0) cc_final: 0.7627 (pm20) REVERT: A 368 LYS cc_start: 0.8297 (ttpt) cc_final: 0.7995 (mmmt) REVERT: A 447 PHE cc_start: 0.8256 (m-10) cc_final: 0.7940 (m-80) REVERT: A 475 LEU cc_start: 0.1815 (OUTLIER) cc_final: 0.1084 (tp) REVERT: A 488 MET cc_start: 0.7227 (mmt) cc_final: 0.6640 (mtp) REVERT: B 364 GLU cc_start: 0.7990 (pt0) cc_final: 0.7619 (pm20) REVERT: B 368 LYS cc_start: 0.8294 (ttpt) cc_final: 0.7991 (mmmt) REVERT: B 447 PHE cc_start: 0.8239 (m-10) cc_final: 0.7928 (m-80) REVERT: B 475 LEU cc_start: 0.1807 (OUTLIER) cc_final: 0.1077 (tp) REVERT: B 488 MET cc_start: 0.7216 (mmt) cc_final: 0.6638 (mtp) REVERT: C 364 GLU cc_start: 0.7985 (pt0) cc_final: 0.7626 (pm20) REVERT: C 368 LYS cc_start: 0.8294 (ttpt) cc_final: 0.7995 (mmmt) REVERT: C 447 PHE cc_start: 0.8252 (m-10) cc_final: 0.7938 (m-80) REVERT: C 475 LEU cc_start: 0.1788 (OUTLIER) cc_final: 0.1063 (tp) REVERT: C 488 MET cc_start: 0.7218 (mmt) cc_final: 0.6632 (mtp) REVERT: C 509 ARG cc_start: 0.6096 (mtm110) cc_final: 0.5809 (mtm-85) REVERT: C 546 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7746 (mm-30) REVERT: D 364 GLU cc_start: 0.7977 (pt0) cc_final: 0.7644 (pm20) REVERT: D 368 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7988 (mmmt) REVERT: D 447 PHE cc_start: 0.8286 (m-10) cc_final: 0.7967 (m-80) REVERT: D 475 LEU cc_start: 0.2817 (OUTLIER) cc_final: 0.2323 (tm) REVERT: D 488 MET cc_start: 0.7293 (tpp) cc_final: 0.6868 (mtp) outliers start: 21 outliers final: 11 residues processed: 256 average time/residue: 0.3931 time to fit residues: 150.7306 Evaluate side-chains 246 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 230 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 156 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23144 Z= 0.188 Angle : 0.502 10.792 30968 Z= 0.251 Chirality : 0.040 0.140 3328 Planarity : 0.004 0.051 3712 Dihedral : 16.561 102.155 4336 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.88 % Allowed : 12.70 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2552 helix: 0.99 (0.14), residues: 1512 sheet: 1.03 (0.66), residues: 76 loop : -1.77 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 710 HIS 0.003 0.001 HIS D 301 PHE 0.011 0.001 PHE C 316 TYR 0.018 0.001 TYR C 540 ARG 0.010 0.000 ARG B 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 231 time to evaluate : 2.579 Fit side-chains REVERT: A 364 GLU cc_start: 0.7977 (pt0) cc_final: 0.7641 (pm20) REVERT: A 368 LYS cc_start: 0.8337 (ttpt) cc_final: 0.8063 (mmmt) REVERT: A 447 PHE cc_start: 0.8278 (m-10) cc_final: 0.7944 (m-80) REVERT: A 475 LEU cc_start: 0.1949 (OUTLIER) cc_final: 0.1229 (tp) REVERT: A 488 MET cc_start: 0.7245 (mmt) cc_final: 0.6639 (mtp) REVERT: B 364 GLU cc_start: 0.7982 (pt0) cc_final: 0.7633 (pm20) REVERT: B 368 LYS cc_start: 0.8334 (ttpt) cc_final: 0.8057 (mmmt) REVERT: B 447 PHE cc_start: 0.8264 (m-10) cc_final: 0.7934 (m-80) REVERT: B 475 LEU cc_start: 0.1897 (OUTLIER) cc_final: 0.1180 (tp) REVERT: B 488 MET cc_start: 0.7236 (mmt) cc_final: 0.6635 (mtp) REVERT: C 364 GLU cc_start: 0.7973 (pt0) cc_final: 0.7633 (pm20) REVERT: C 368 LYS cc_start: 0.8336 (ttpt) cc_final: 0.8063 (mmmt) REVERT: C 447 PHE cc_start: 0.8275 (m-10) cc_final: 0.7940 (m-80) REVERT: C 475 LEU cc_start: 0.1924 (OUTLIER) cc_final: 0.1208 (tp) REVERT: C 488 MET cc_start: 0.7237 (mmt) cc_final: 0.6629 (mtp) REVERT: C 509 ARG cc_start: 0.6062 (mtm110) cc_final: 0.5788 (mtm-85) REVERT: C 546 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: D 141 ASP cc_start: 0.7679 (m-30) cc_final: 0.7468 (m-30) REVERT: D 364 GLU cc_start: 0.7965 (pt0) cc_final: 0.7653 (pm20) REVERT: D 368 LYS cc_start: 0.8326 (ttpt) cc_final: 0.8069 (mmmt) REVERT: D 447 PHE cc_start: 0.8310 (m-10) cc_final: 0.7972 (m-80) REVERT: D 488 MET cc_start: 0.7250 (tpp) cc_final: 0.6940 (mtp) outliers start: 20 outliers final: 13 residues processed: 242 average time/residue: 0.3856 time to fit residues: 140.2183 Evaluate side-chains 248 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 231 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 337 ARG Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 545 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 4.9990 chunk 62 optimal weight: 0.0050 chunk 187 optimal weight: 0.8980 chunk 29 optimal weight: 0.0670 chunk 56 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 overall best weight: 0.5332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.096192 restraints weight = 29784.243| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.52 r_work: 0.2818 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23144 Z= 0.122 Angle : 0.463 10.604 30968 Z= 0.232 Chirality : 0.038 0.140 3328 Planarity : 0.004 0.055 3712 Dihedral : 15.887 98.354 4336 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.79 % Allowed : 12.96 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2552 helix: 1.40 (0.14), residues: 1464 sheet: 0.99 (0.66), residues: 76 loop : -1.52 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 710 HIS 0.002 0.000 HIS C 301 PHE 0.011 0.001 PHE C 316 TYR 0.018 0.001 TYR A 540 ARG 0.010 0.000 ARG A 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4416.73 seconds wall clock time: 80 minutes 59.89 seconds (4859.89 seconds total)