Starting phenix.real_space_refine on Tue Mar 19 01:11:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7min_23857/03_2024/7min_23857_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7min_23857/03_2024/7min_23857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7min_23857/03_2024/7min_23857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7min_23857/03_2024/7min_23857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7min_23857/03_2024/7min_23857_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7min_23857/03_2024/7min_23857_updated.pdb" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 149": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 371": "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 149": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 371": "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 149": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 371": "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 149": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 371": "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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 472 Unusual residues: {' NA': 4, 'POV': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} 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: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 468 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 12.04, per 1000 atoms: 0.53 Number of scatterers: 22728 At special positions: 0 Unit cell: (134.977, 134.977, 131.494, 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: 8.02 Conformation dependent library (CDL) restraints added in 3.8 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: 120 helices and 4 sheets defined 56.9% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 132 through 147 removed outlier: 3.832A pdb=" N ARG A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.604A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.578A pdb=" N VAL A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.966A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 237 removed outlier: 3.742A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 3.523A pdb=" N ALA A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 removed outlier: 3.640A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 3.659A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 344 through 351 removed outlier: 3.503A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.667A 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 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 416 through 421 removed outlier: 4.857A pdb=" N THR A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 4.135A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 460 removed outlier: 3.906A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 507 removed outlier: 3.946A pdb=" N PHE A 489 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A 490 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 492 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 494 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS A 496 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 497 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 498 " --> pdb=" O THR A 495 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL A 499 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 501 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE A 503 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 504 " --> pdb=" O GLU A 501 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A 507 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 519 removed outlier: 3.614A pdb=" N LEU A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 541 removed outlier: 3.636A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 568 removed outlier: 3.546A pdb=" N VAL A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ARG A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLY A 568 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 585 removed outlier: 3.592A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 608 removed outlier: 3.625A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 removed outlier: 3.527A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 665 Processing helix chain 'A' and resid 669 through 684 removed outlier: 4.000A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 706 removed outlier: 3.720A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 removed outlier: 3.583A pdb=" N ARG A 714 " --> pdb=" O TRP A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 132 through 147 removed outlier: 3.832A pdb=" N ARG B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.603A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.577A pdb=" N VAL B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 218 through 224 removed outlier: 3.965A pdb=" N GLU B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 237 removed outlier: 3.742A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 3.523A pdb=" N ALA B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 283 removed outlier: 3.640A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 305 removed outlier: 3.659A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.503A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.666A 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 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.857A pdb=" N THR B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 435 removed outlier: 4.135A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 460 removed outlier: 3.906A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 507 removed outlier: 3.945A pdb=" N PHE B 489 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL B 490 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 492 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 494 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS B 496 " --> pdb=" O TRP B 493 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 497 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 498 " --> pdb=" O THR B 495 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL B 499 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 501 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 503 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 504 " --> pdb=" O GLU B 501 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 505 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU B 507 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 519 removed outlier: 3.615A pdb=" N LEU B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER B 518 " --> pdb=" O GLN B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 541 removed outlier: 3.636A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 568 removed outlier: 3.546A pdb=" N VAL B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ARG B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLY B 568 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 585 removed outlier: 3.591A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 608 removed outlier: 3.625A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 removed outlier: 3.525A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 665 Processing helix chain 'B' and resid 669 through 684 removed outlier: 4.000A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 706 removed outlier: 3.721A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 removed outlier: 3.584A pdb=" N ARG B 714 " --> pdb=" O TRP B 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.833A pdb=" N ARG C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.604A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.578A pdb=" N VAL C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 218 through 224 removed outlier: 3.966A pdb=" N GLU C 224 " --> pdb=" O ASN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 removed outlier: 3.742A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 3.523A pdb=" N ALA C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 283 removed outlier: 3.640A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 305 removed outlier: 3.659A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 344 through 351 removed outlier: 3.502A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.667A 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 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 416 through 421 removed outlier: 4.858A pdb=" N THR C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 435 removed outlier: 4.135A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 460 removed outlier: 3.906A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 507 removed outlier: 3.945A pdb=" N PHE C 489 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL C 490 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 492 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C 494 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS C 496 " --> pdb=" O TRP C 493 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 497 " --> pdb=" O ALA C 494 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 498 " --> pdb=" O THR C 495 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL C 499 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU C 501 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE C 503 " --> pdb=" O LYS C 500 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 504 " --> pdb=" O GLU C 501 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU C 507 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 519 removed outlier: 3.615A pdb=" N LEU C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER C 518 " --> pdb=" O GLN C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 541 removed outlier: 3.635A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 568 removed outlier: 3.547A pdb=" N VAL C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ARG C 567 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLY C 568 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 585 removed outlier: 3.591A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 608 removed outlier: 3.624A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 removed outlier: 3.526A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 665 Processing helix chain 'C' and resid 669 through 684 removed outlier: 3.999A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 706 removed outlier: 3.720A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 removed outlier: 3.584A pdb=" N ARG C 714 " --> pdb=" O TRP C 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 132 through 147 removed outlier: 3.832A pdb=" N ARG D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 161 removed outlier: 3.604A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.578A pdb=" N VAL D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 218 through 224 removed outlier: 3.965A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 237 removed outlier: 3.742A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.523A pdb=" N ALA D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 283 removed outlier: 3.640A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 305 removed outlier: 3.658A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 344 through 351 removed outlier: 3.503A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.666A 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 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.500A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 4.858A pdb=" N THR D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 435 removed outlier: 4.135A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 460 removed outlier: 3.906A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 507 removed outlier: 3.945A pdb=" N PHE D 489 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL D 490 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE D 492 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA D 494 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS D 496 " --> pdb=" O TRP D 493 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 497 " --> pdb=" O ALA D 494 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 498 " --> pdb=" O THR D 495 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL D 499 " --> pdb=" O CYS D 496 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU D 501 " --> pdb=" O SER D 498 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE D 503 " --> pdb=" O LYS D 500 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D 504 " --> pdb=" O GLU D 501 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE D 505 " --> pdb=" O GLY D 502 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU D 507 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 519 removed outlier: 3.615A pdb=" N LEU D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER D 518 " --> pdb=" O GLN D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 541 removed outlier: 3.637A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 568 removed outlier: 3.546A pdb=" N VAL D 552 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ARG D 567 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLY D 568 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 585 removed outlier: 3.591A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 608 removed outlier: 3.625A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 removed outlier: 3.525A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 665 Processing helix chain 'D' and resid 669 through 684 removed outlier: 3.999A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 706 removed outlier: 3.721A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 714 removed outlier: 3.584A pdb=" N ARG D 714 " --> pdb=" O TRP D 710 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 732 through 737 removed outlier: 3.579A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 732 through 737 removed outlier: 3.579A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 732 through 737 removed outlier: 3.579A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 732 through 737 removed outlier: 3.579A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) 739 hydrogen bonds defined for protein. 2097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.74 Time building geometry restraints manager: 8.78 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 - 1.43: 6004 1.43 - 1.56: 13412 1.56 - 1.69: 92 1.69 - 1.81: 204 Bond restraints: 23144 Sorted by residual: bond pdb=" C21 POV B 906 " pdb=" O21 POV B 906 " ideal model delta sigma weight residual 1.330 1.422 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C21 POV D 908 " pdb=" O21 POV D 908 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C21 POV C 906 " pdb=" O21 POV C 906 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C21 POV B 902 " pdb=" O21 POV B 902 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C21 POV A 903 " pdb=" O21 POV A 903 " ideal model delta sigma weight residual 1.330 1.421 -0.091 2.00e-02 2.50e+03 2.06e+01 ... (remaining 23139 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.38: 507 106.38 - 113.31: 13037 113.31 - 120.24: 8367 120.24 - 127.17: 8841 127.17 - 134.10: 216 Bond angle restraints: 30968 Sorted by residual: angle pdb=" C LEU C 473 " pdb=" N ALA C 474 " pdb=" CA ALA C 474 " ideal model delta sigma weight residual 121.54 131.07 -9.53 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C GLN D 313 " pdb=" N ASN D 314 " pdb=" CA ASN D 314 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.48e+01 angle pdb=" C GLN B 313 " pdb=" N ASN B 314 " pdb=" CA ASN B 314 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 angle pdb=" C LEU D 473 " pdb=" N ALA D 474 " pdb=" CA ALA D 474 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 angle pdb=" C GLN A 313 " pdb=" N ASN A 314 " pdb=" CA ASN A 314 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 ... (remaining 30963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.35: 13517 34.35 - 68.71: 638 68.71 - 103.06: 88 103.06 - 137.41: 41 137.41 - 171.77: 16 Dihedral angle restraints: 14300 sinusoidal: 6744 harmonic: 7556 Sorted by residual: 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 -153.10 67.10 1 1.00e+01 1.00e-02 5.86e+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 -153.10 67.10 1 1.00e+01 1.00e-02 5.86e+01 dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual -86.00 -153.08 67.08 1 1.00e+01 1.00e-02 5.86e+01 ... (remaining 14297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2620 0.058 - 0.117: 578 0.117 - 0.175: 90 0.175 - 0.233: 28 0.233 - 0.291: 12 Chirality restraints: 3328 Sorted by residual: 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 2.12e+00 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 2.08e+00 chirality pdb=" CG LEU A 469 " pdb=" CB LEU A 469 " pdb=" CD1 LEU A 469 " pdb=" CD2 LEU A 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 3325 not shown) Planarity restraints: 3712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 509 " 0.049 5.00e-02 4.00e+02 7.47e-02 8.93e+00 pdb=" N PRO C 510 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 510 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 510 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 509 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO B 510 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 510 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 510 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 509 " 0.049 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO A 510 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " 0.041 5.00e-02 4.00e+02 ... (remaining 3709 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6482 2.82 - 3.34: 18829 3.34 - 3.86: 33390 3.86 - 4.38: 41334 4.38 - 4.90: 71565 Nonbonded interactions: 171600 Sorted by model distance: nonbonded pdb="NA NA A 910 " pdb="NA NA A 911 " model vdw 2.303 1.900 nonbonded pdb=" OG SER C 444 " pdb=" O14 POV C 905 " model vdw 2.330 2.440 nonbonded pdb=" OG SER B 444 " pdb=" O14 POV B 905 " model vdw 2.331 2.440 nonbonded pdb=" OG SER D 444 " pdb=" O14 POV D 907 " model vdw 2.332 2.440 nonbonded pdb=" OG SER A 444 " pdb=" O14 POV A 902 " model vdw 2.335 2.440 ... (remaining 171595 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 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: 0.010 Extract box with map and model: 4.930 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 56.860 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.120 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.092 23144 Z= 0.673 Angle : 1.464 13.634 30968 Z= 0.661 Chirality : 0.053 0.291 3328 Planarity : 0.007 0.075 3712 Dihedral : 20.415 171.766 9384 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.58 % Favored : 95.26 % Rotamer: Outliers : 0.18 % Allowed : 5.60 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.07 (0.10), residues: 2552 helix: -4.60 (0.04), residues: 1564 sheet: -0.94 (0.54), residues: 76 loop : -2.78 (0.16), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 692 HIS 0.010 0.001 HIS A 301 PHE 0.034 0.003 PHE D 526 TYR 0.015 0.003 TYR D 451 ARG 0.010 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 360 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 356 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ASN cc_start: 0.8200 (p0) cc_final: 0.7695 (p0) REVERT: A 185 GLU cc_start: 0.7336 (mp0) cc_final: 0.7066 (mp0) REVERT: A 257 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8027 (mm-30) REVERT: A 434 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8346 (mmtt) REVERT: A 440 MET cc_start: 0.9020 (mtp) cc_final: 0.8677 (mtp) REVERT: A 645 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7707 (tp40) REVERT: B 182 ASN cc_start: 0.8209 (p0) cc_final: 0.7716 (p0) REVERT: B 185 GLU cc_start: 0.7213 (mp0) cc_final: 0.7005 (mp0) REVERT: B 440 MET cc_start: 0.9007 (mtp) cc_final: 0.8715 (mtp) REVERT: B 645 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7625 (tp40) REVERT: C 182 ASN cc_start: 0.8173 (p0) cc_final: 0.7648 (p0) REVERT: C 185 GLU cc_start: 0.7328 (mp0) cc_final: 0.7094 (mp0) REVERT: C 257 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7999 (mm-30) REVERT: C 434 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8383 (mmtt) REVERT: C 440 MET cc_start: 0.9041 (mtp) cc_final: 0.8732 (mtp) REVERT: C 645 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7707 (tp40) REVERT: D 182 ASN cc_start: 0.8213 (p0) cc_final: 0.7713 (p0) REVERT: D 440 MET cc_start: 0.9008 (mtp) cc_final: 0.8723 (mtp) REVERT: D 645 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7656 (tp40) outliers start: 4 outliers final: 0 residues processed: 360 average time/residue: 0.4019 time to fit residues: 210.6280 Evaluate side-chains 243 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.508 ------------------------------------------------------------------------------- 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: 6.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 220 ASN A 477 HIS A 523 HIS A 643 ASN B 178 ASN B 220 ASN B 314 ASN B 477 HIS B 523 HIS B 643 ASN C 178 ASN C 220 ASN C 314 ASN C 477 HIS C 523 HIS C 643 ASN D 178 ASN D 314 ASN D 477 HIS D 523 HIS D 643 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 23144 Z= 0.368 Angle : 0.673 8.026 30968 Z= 0.344 Chirality : 0.044 0.190 3328 Planarity : 0.006 0.058 3712 Dihedral : 23.594 166.122 4336 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.35 % Favored : 95.49 % Rotamer: Outliers : 1.36 % Allowed : 8.41 % Favored : 90.24 % 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: -3.59 (0.13), residues: 2552 helix: -2.29 (0.10), residues: 1568 sheet: -0.40 (0.53), residues: 76 loop : -2.44 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 692 HIS 0.008 0.001 HIS C 301 PHE 0.023 0.002 PHE A 316 TYR 0.018 0.002 TYR A 321 ARG 0.004 0.001 ARG D 567 *********************** 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 277 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 246 time to evaluate : 2.650 Fit side-chains REVERT: A 257 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8007 (mm-30) REVERT: A 434 LYS cc_start: 0.8402 (mtpt) cc_final: 0.8130 (mmtt) REVERT: A 645 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7765 (tp40) REVERT: B 182 ASN cc_start: 0.8224 (p0) cc_final: 0.7813 (p0) REVERT: B 320 MET cc_start: 0.9133 (mmt) cc_final: 0.8795 (mmt) REVERT: B 645 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7646 (tp40) REVERT: C 182 ASN cc_start: 0.8173 (p0) cc_final: 0.7770 (p0) REVERT: C 320 MET cc_start: 0.9187 (mmt) cc_final: 0.8775 (mmt) REVERT: C 434 LYS cc_start: 0.8395 (mtpt) cc_final: 0.8176 (mmtt) REVERT: C 645 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7711 (tp40) REVERT: D 182 ASN cc_start: 0.8152 (p0) cc_final: 0.7867 (p0) REVERT: D 320 MET cc_start: 0.9138 (mmt) cc_final: 0.8797 (mmt) REVERT: D 645 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7662 (tp40) outliers start: 31 outliers final: 11 residues processed: 267 average time/residue: 0.3509 time to fit residues: 142.9712 Evaluate side-chains 220 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 209 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 64 optimal weight: 20.0000 chunk 232 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 230 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.8636 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23144 Z= 0.191 Angle : 0.522 7.619 30968 Z= 0.266 Chirality : 0.039 0.197 3328 Planarity : 0.004 0.051 3712 Dihedral : 21.424 165.225 4336 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.49 % Allowed : 10.16 % Favored : 88.35 % 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: -2.03 (0.15), residues: 2552 helix: -0.84 (0.12), residues: 1556 sheet: -0.11 (0.53), residues: 76 loop : -2.20 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 710 HIS 0.005 0.001 HIS C 301 PHE 0.018 0.001 PHE A 193 TYR 0.018 0.001 TYR A 540 ARG 0.004 0.000 ARG B 714 *********************** 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 270 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 236 time to evaluate : 2.509 Fit side-chains REVERT: A 538 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7718 (t80) REVERT: A 645 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7722 (tp40) REVERT: B 320 MET cc_start: 0.9117 (mmt) cc_final: 0.8704 (mmt) REVERT: B 645 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7620 (tp40) REVERT: C 320 MET cc_start: 0.9174 (mmt) cc_final: 0.8745 (mmt) REVERT: C 611 LYS cc_start: 0.7314 (tptt) cc_final: 0.7112 (tptt) REVERT: C 627 ASP cc_start: 0.8154 (m-30) cc_final: 0.7799 (m-30) REVERT: C 645 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7723 (tp40) REVERT: D 320 MET cc_start: 0.9116 (mmt) cc_final: 0.8732 (mmt) REVERT: D 538 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7714 (t80) REVERT: D 627 ASP cc_start: 0.8081 (m-30) cc_final: 0.7782 (m-30) REVERT: D 645 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7643 (tp40) outliers start: 34 outliers final: 10 residues processed: 262 average time/residue: 0.3376 time to fit residues: 137.8069 Evaluate side-chains 229 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 217 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 0.2980 chunk 175 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 647 ASN B 647 ASN C 647 ASN D 647 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23144 Z= 0.170 Angle : 0.510 8.771 30968 Z= 0.254 Chirality : 0.038 0.178 3328 Planarity : 0.003 0.043 3712 Dihedral : 20.559 164.860 4336 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.84 % Allowed : 10.64 % Favored : 87.52 % 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: -1.24 (0.16), residues: 2552 helix: -0.07 (0.13), residues: 1532 sheet: 0.04 (0.53), residues: 76 loop : -2.09 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 710 HIS 0.005 0.001 HIS A 301 PHE 0.016 0.001 PHE A 506 TYR 0.020 0.001 TYR A 540 ARG 0.003 0.000 ARG A 714 *********************** 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 263 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 221 time to evaluate : 2.552 Fit side-chains REVERT: A 538 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7743 (t80) REVERT: A 645 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7724 (tp40) REVERT: B 538 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7774 (t80) REVERT: B 645 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7616 (tp40) REVERT: C 538 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7763 (t80) REVERT: C 627 ASP cc_start: 0.8085 (m-30) cc_final: 0.7740 (m-30) REVERT: C 645 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7686 (tp40) REVERT: D 538 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7733 (t80) REVERT: D 627 ASP cc_start: 0.8044 (m-30) cc_final: 0.7755 (m-30) REVERT: D 645 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7632 (tp40) outliers start: 42 outliers final: 12 residues processed: 255 average time/residue: 0.3468 time to fit residues: 137.4292 Evaluate side-chains 226 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 210 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain B residue 538 PHE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 211 optimal weight: 0.0980 chunk 171 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23144 Z= 0.169 Angle : 0.502 8.445 30968 Z= 0.252 Chirality : 0.038 0.261 3328 Planarity : 0.003 0.048 3712 Dihedral : 19.776 164.900 4336 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.31 % Allowed : 10.73 % Favored : 87.96 % 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: -0.70 (0.16), residues: 2552 helix: 0.42 (0.13), residues: 1532 sheet: 0.48 (0.55), residues: 76 loop : -2.01 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 710 HIS 0.005 0.001 HIS A 301 PHE 0.016 0.001 PHE A 506 TYR 0.021 0.001 TYR D 540 ARG 0.003 0.000 ARG B 714 *********************** 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 258 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 228 time to evaluate : 2.449 Fit side-chains REVERT: A 645 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7694 (tp40) REVERT: B 542 PHE cc_start: 0.7279 (m-10) cc_final: 0.7012 (m-80) REVERT: B 645 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7610 (tp40) REVERT: C 627 ASP cc_start: 0.8089 (m-30) cc_final: 0.7745 (m-30) REVERT: C 645 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7688 (tp40) REVERT: D 627 ASP cc_start: 0.8044 (m-30) cc_final: 0.7759 (m-30) REVERT: D 645 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7635 (tp40) outliers start: 30 outliers final: 17 residues processed: 242 average time/residue: 0.3670 time to fit residues: 137.1254 Evaluate side-chains 229 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 212 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 145 optimal weight: 0.0970 chunk 61 optimal weight: 10.0000 chunk 247 optimal weight: 0.7980 chunk 205 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 overall best weight: 2.3382 ------------------------------------------------------------------------------- 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: 0.8655 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23144 Z= 0.217 Angle : 0.534 8.513 30968 Z= 0.264 Chirality : 0.040 0.142 3328 Planarity : 0.003 0.044 3712 Dihedral : 19.514 165.676 4336 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.44 % Allowed : 11.16 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2552 helix: 0.64 (0.13), residues: 1532 sheet: 0.43 (0.56), residues: 76 loop : -1.98 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 710 HIS 0.006 0.001 HIS C 301 PHE 0.018 0.001 PHE A 506 TYR 0.023 0.002 TYR A 540 ARG 0.004 0.000 ARG A 714 *********************** 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 250 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 217 time to evaluate : 2.667 Fit side-chains REVERT: A 645 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7696 (tp40) REVERT: A 711 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7661 (mt) REVERT: B 645 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7601 (tp40) REVERT: B 711 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7839 (mt) REVERT: C 627 ASP cc_start: 0.8144 (m-30) cc_final: 0.7777 (m-30) REVERT: C 645 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7688 (tp40) REVERT: D 627 ASP cc_start: 0.8095 (m-30) cc_final: 0.7794 (m-30) REVERT: D 645 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7613 (tp40) REVERT: D 711 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7839 (mt) outliers start: 33 outliers final: 18 residues processed: 238 average time/residue: 0.3383 time to fit residues: 127.5813 Evaluate side-chains 228 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 207 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 340 ASP Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 743 LYS 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: 2.9990 chunk 141 optimal weight: 10.0000 chunk 180 optimal weight: 0.0040 chunk 140 optimal weight: 0.1980 chunk 208 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 246 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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: 0.8563 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23144 Z= 0.108 Angle : 0.458 7.841 30968 Z= 0.225 Chirality : 0.036 0.131 3328 Planarity : 0.003 0.042 3712 Dihedral : 18.306 166.057 4336 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.31 % Allowed : 11.34 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2552 helix: 1.09 (0.14), residues: 1552 sheet: 0.59 (0.57), residues: 76 loop : -2.06 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 710 HIS 0.001 0.000 HIS B 301 PHE 0.017 0.001 PHE D 506 TYR 0.024 0.001 TYR D 540 ARG 0.004 0.000 ARG B 714 *********************** 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 285 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 255 time to evaluate : 2.678 Fit side-chains REVERT: A 538 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7692 (t80) REVERT: A 541 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7209 (mt) REVERT: A 627 ASP cc_start: 0.8000 (m-30) cc_final: 0.7605 (m-30) REVERT: A 645 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7679 (tp40) REVERT: A 711 LEU cc_start: 0.7844 (mm) cc_final: 0.7614 (mt) REVERT: B 538 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7621 (t80) REVERT: B 542 PHE cc_start: 0.7160 (m-10) cc_final: 0.6859 (m-80) REVERT: B 627 ASP cc_start: 0.7934 (m-30) cc_final: 0.7643 (m-30) REVERT: B 645 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7599 (tp40) REVERT: B 711 LEU cc_start: 0.8022 (mm) cc_final: 0.7772 (mt) REVERT: C 538 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7622 (t80) REVERT: C 541 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7078 (mt) REVERT: C 542 PHE cc_start: 0.7183 (m-10) cc_final: 0.6854 (m-80) REVERT: C 627 ASP cc_start: 0.8048 (m-30) cc_final: 0.7649 (m-30) REVERT: C 645 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7659 (tp40) REVERT: D 488 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8091 (mtp) REVERT: D 538 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7671 (t80) REVERT: D 627 ASP cc_start: 0.7972 (m-30) cc_final: 0.7640 (m-30) REVERT: D 645 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7619 (tp40) outliers start: 30 outliers final: 16 residues processed: 274 average time/residue: 0.3384 time to fit residues: 144.7812 Evaluate side-chains 248 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 225 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 538 PHE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 340 ASP Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 147 optimal weight: 0.0970 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.8597 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23144 Z= 0.141 Angle : 0.490 8.762 30968 Z= 0.243 Chirality : 0.038 0.147 3328 Planarity : 0.003 0.041 3712 Dihedral : 18.078 170.482 4336 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.05 % Allowed : 12.04 % Favored : 86.91 % 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: 0.19 (0.16), residues: 2552 helix: 1.29 (0.14), residues: 1552 sheet: 0.78 (0.57), residues: 76 loop : -2.01 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 710 HIS 0.004 0.001 HIS A 301 PHE 0.023 0.001 PHE B 193 TYR 0.030 0.001 TYR A 540 ARG 0.004 0.000 ARG A 714 *********************** 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 243 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 219 time to evaluate : 2.688 Fit side-chains REVERT: A 542 PHE cc_start: 0.7278 (m-10) cc_final: 0.6953 (m-80) REVERT: A 645 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7702 (tp40) REVERT: A 711 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7633 (mt) REVERT: B 542 PHE cc_start: 0.7236 (m-10) cc_final: 0.6933 (m-80) REVERT: B 645 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7632 (tp40) REVERT: B 711 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7846 (mt) REVERT: C 542 PHE cc_start: 0.7211 (m-10) cc_final: 0.6891 (m-80) REVERT: C 627 ASP cc_start: 0.8056 (m-30) cc_final: 0.7716 (m-30) REVERT: C 645 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7704 (tp40) REVERT: D 488 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8085 (mtp) REVERT: D 627 ASP cc_start: 0.8011 (m-30) cc_final: 0.7727 (m-30) REVERT: D 645 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7647 (tp40) REVERT: D 711 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7814 (mt) outliers start: 24 outliers final: 15 residues processed: 235 average time/residue: 0.3197 time to fit residues: 120.5706 Evaluate side-chains 235 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 216 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 340 ASP Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 150 optimal weight: 0.0970 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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: 0.8585 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23144 Z= 0.128 Angle : 0.472 8.106 30968 Z= 0.234 Chirality : 0.037 0.157 3328 Planarity : 0.003 0.040 3712 Dihedral : 17.666 171.361 4336 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.01 % Allowed : 11.82 % Favored : 87.17 % 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: 0.39 (0.17), residues: 2552 helix: 1.45 (0.14), residues: 1552 sheet: 0.89 (0.57), residues: 76 loop : -1.95 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 710 HIS 0.003 0.000 HIS B 301 PHE 0.021 0.001 PHE B 193 TYR 0.024 0.001 TYR D 540 ARG 0.004 0.000 ARG C 714 *********************** 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 250 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 227 time to evaluate : 2.632 Fit side-chains REVERT: A 542 PHE cc_start: 0.7251 (m-10) cc_final: 0.6918 (m-80) REVERT: A 562 MET cc_start: 0.9312 (mmm) cc_final: 0.9068 (mmt) REVERT: A 645 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7710 (tp40) REVERT: A 711 LEU cc_start: 0.7883 (mm) cc_final: 0.7661 (mt) REVERT: B 542 PHE cc_start: 0.7193 (m-10) cc_final: 0.6896 (m-80) REVERT: B 562 MET cc_start: 0.9212 (mmm) cc_final: 0.8960 (mmt) REVERT: B 645 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7618 (tp40) REVERT: B 711 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7853 (mt) REVERT: C 542 PHE cc_start: 0.7190 (m-10) cc_final: 0.6857 (m-80) REVERT: C 562 MET cc_start: 0.9291 (mmm) cc_final: 0.9051 (mmt) REVERT: C 627 ASP cc_start: 0.8040 (m-30) cc_final: 0.7689 (m-30) REVERT: C 645 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7690 (tp40) REVERT: D 488 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.8043 (mtp) REVERT: D 538 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7677 (t80) REVERT: D 562 MET cc_start: 0.9214 (mmm) cc_final: 0.8964 (mmt) REVERT: D 627 ASP cc_start: 0.7990 (m-30) cc_final: 0.7696 (m-30) REVERT: D 645 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7638 (tp40) REVERT: D 711 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7834 (mt) outliers start: 23 outliers final: 17 residues processed: 244 average time/residue: 0.3337 time to fit residues: 129.3654 Evaluate side-chains 240 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 219 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 340 ASP Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 255 optimal weight: 0.8980 chunk 234 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 124 optimal weight: 0.1980 chunk 161 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.8588 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23144 Z= 0.132 Angle : 0.481 10.003 30968 Z= 0.237 Chirality : 0.038 0.237 3328 Planarity : 0.003 0.040 3712 Dihedral : 17.314 169.974 4336 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.92 % Allowed : 12.61 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2552 helix: 1.49 (0.13), residues: 1576 sheet: 0.99 (0.58), residues: 76 loop : -1.89 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 710 HIS 0.003 0.001 HIS B 301 PHE 0.025 0.001 PHE D 193 TYR 0.027 0.001 TYR D 540 ARG 0.004 0.000 ARG A 714 ********************** 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: 21 poor density : 230 time to evaluate : 2.459 Fit side-chains REVERT: A 542 PHE cc_start: 0.7225 (m-10) cc_final: 0.6898 (m-80) REVERT: A 562 MET cc_start: 0.9313 (mmm) cc_final: 0.9083 (mmt) REVERT: A 645 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7712 (tp40) REVERT: A 711 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7657 (mt) REVERT: B 159 MET cc_start: 0.8352 (tpp) cc_final: 0.8105 (tpp) REVERT: B 542 PHE cc_start: 0.7167 (m-10) cc_final: 0.6869 (m-80) REVERT: B 562 MET cc_start: 0.9220 (mmm) cc_final: 0.8969 (mmt) REVERT: B 645 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7618 (tp40) REVERT: B 711 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7857 (mt) REVERT: C 159 MET cc_start: 0.8193 (tpp) cc_final: 0.7982 (tpp) REVERT: C 542 PHE cc_start: 0.7153 (m-10) cc_final: 0.6829 (m-80) REVERT: C 562 MET cc_start: 0.9295 (mmm) cc_final: 0.9060 (mmt) REVERT: C 627 ASP cc_start: 0.8044 (m-30) cc_final: 0.7684 (m-30) REVERT: C 645 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7684 (tp40) REVERT: D 488 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8089 (mtp) REVERT: D 542 PHE cc_start: 0.7293 (m-10) cc_final: 0.7031 (m-80) REVERT: D 562 MET cc_start: 0.9225 (mmm) cc_final: 0.8982 (mmt) REVERT: D 627 ASP cc_start: 0.7998 (m-30) cc_final: 0.7696 (m-30) REVERT: D 645 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7631 (tp40) REVERT: D 711 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7883 (mt) outliers start: 21 outliers final: 16 residues processed: 244 average time/residue: 0.3252 time to fit residues: 126.4351 Evaluate side-chains 241 residues out of total 2284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 221 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 340 ASP Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 29 optimal weight: 0.0970 chunk 56 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 85 optimal weight: 0.0980 chunk 208 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 178 optimal weight: 0.0020 overall best weight: 0.3788 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.134864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.091750 restraints weight = 32077.439| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.42 r_work: 0.2872 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23144 Z= 0.112 Angle : 0.465 9.465 30968 Z= 0.228 Chirality : 0.037 0.221 3328 Planarity : 0.003 0.038 3712 Dihedral : 16.585 169.531 4336 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.88 % Allowed : 12.57 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2552 helix: 1.67 (0.14), residues: 1576 sheet: 1.21 (0.59), residues: 76 loop : -1.87 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 710 HIS 0.002 0.000 HIS B 301 PHE 0.021 0.001 PHE B 193 TYR 0.024 0.001 TYR A 540 ARG 0.006 0.000 ARG B 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4328.58 seconds wall clock time: 79 minutes 0.64 seconds (4740.64 seconds total)