Starting phenix.real_space_refine on Sun Feb 18 21:09:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mio_23858/02_2024/7mio_23858_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mio_23858/02_2024/7mio_23858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mio_23858/02_2024/7mio_23858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mio_23858/02_2024/7mio_23858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mio_23858/02_2024/7mio_23858_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mio_23858/02_2024/7mio_23858_updated.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.083 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 28 5.49 5 S 132 5.16 5 Na 1 4.78 5 C 15124 2.51 5 N 3588 2.21 5 O 4072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 729": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 729": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C ARG 375": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 690": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 729": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D ARG 375": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 729": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22945 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5372 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 18, 'TRANS': 640} Chain breaks: 1 Chain: "B" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5372 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 18, 'TRANS': 640} Chain breaks: 1 Chain: "C" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5372 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 18, 'TRANS': 640} Chain breaks: 1 Chain: "D" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5372 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 18, 'TRANS': 640} Chain breaks: 1 Chain: "A" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 365 Unusual residues: {' NA': 1, 'POV': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 364 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 364 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 364 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 11.10, per 1000 atoms: 0.48 Number of scatterers: 22945 At special positions: 0 Unit cell: (141.944, 141.944, 128.01, 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 132 16.00 P 28 15.00 Na 1 11.00 O 4072 8.00 N 3588 7.00 C 15124 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: 8.74 Conformation dependent library (CDL) restraints added in 4.2 seconds 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 8 sheets defined 53.9% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.76 Creating SS restraints... Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.706A pdb=" N LEU A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LYS A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.681A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.717A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.765A pdb=" N VAL A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 228 through 237 removed outlier: 3.778A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 299 through 305 removed outlier: 3.606A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.623A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 351 removed outlier: 3.534A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.542A pdb=" N SER A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) 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 409 removed outlier: 3.733A pdb=" N ILE A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.708A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 460 removed outlier: 3.600A pdb=" N PHE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 506 removed outlier: 3.591A pdb=" N VAL A 490 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 491 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE A 492 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 494 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS A 496 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER A 498 " --> pdb=" O THR A 495 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 499 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 501 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 503 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 541 removed outlier: 3.716A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 530 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 567 removed outlier: 4.028A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ARG A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 578 through 585 removed outlier: 3.714A pdb=" N VAL A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 606 removed outlier: 4.445A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 removed outlier: 3.689A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 665 removed outlier: 3.535A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.653A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 703 removed outlier: 3.732A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 697 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 712 No H-bonds generated for 'chain 'A' and resid 709 through 712' Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.670A pdb=" N THR A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 749 " --> pdb=" O HIS A 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 129 removed outlier: 3.706A pdb=" N LEU B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 removed outlier: 3.680A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 145 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 160 removed outlier: 3.717A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.765A pdb=" N VAL B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 228 through 237 removed outlier: 3.777A pdb=" N ALA B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 299 through 305 removed outlier: 3.607A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.622A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.534A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 362 removed outlier: 3.542A pdb=" N SER B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) 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 409 removed outlier: 3.733A pdb=" N ILE B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 423 through 435 removed outlier: 3.709A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 460 removed outlier: 3.600A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 506 removed outlier: 3.592A pdb=" N VAL B 490 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 491 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE B 492 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 494 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS B 496 " --> pdb=" O TRP B 493 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER B 498 " --> pdb=" O THR B 495 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 499 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU B 501 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 503 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 505 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 541 removed outlier: 3.716A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 530 " --> pdb=" O PHE B 526 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 567 removed outlier: 4.028A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ARG B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 574 No H-bonds generated for 'chain 'B' and resid 572 through 574' Processing helix chain 'B' and resid 578 through 585 removed outlier: 3.714A pdb=" N VAL B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 606 removed outlier: 4.445A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 601 " --> pdb=" O PHE B 597 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 removed outlier: 3.690A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 665 removed outlier: 3.535A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 686 removed outlier: 3.653A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 703 removed outlier: 3.732A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 712 No H-bonds generated for 'chain 'B' and resid 709 through 712' Processing helix chain 'B' and resid 739 through 749 removed outlier: 3.670A pdb=" N THR B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU B 749 " --> pdb=" O HIS B 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 129 removed outlier: 3.706A pdb=" N LEU C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LYS C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG C 122 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 147 removed outlier: 3.681A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.717A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.765A pdb=" N VAL C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 228 through 237 removed outlier: 3.777A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 Processing helix chain 'C' and resid 275 through 282 Processing helix chain 'C' and resid 299 through 305 removed outlier: 3.606A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.623A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 351 removed outlier: 3.534A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 362 removed outlier: 3.542A pdb=" N SER C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) 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 409 removed outlier: 3.733A pdb=" N ILE C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 420 Processing helix chain 'C' and resid 423 through 435 removed outlier: 3.708A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 460 removed outlier: 3.600A pdb=" N PHE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 506 removed outlier: 3.592A pdb=" N VAL C 490 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 491 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE C 492 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 494 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS C 496 " --> pdb=" O TRP C 493 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER C 498 " --> pdb=" O THR C 495 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 499 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU C 501 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 503 " --> pdb=" O LYS C 500 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 541 removed outlier: 3.716A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 567 removed outlier: 4.028A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ARG C 567 " --> pdb=" O LEU C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 574 No H-bonds generated for 'chain 'C' and resid 572 through 574' Processing helix chain 'C' and resid 578 through 585 removed outlier: 3.714A pdb=" N VAL C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE C 583 " --> pdb=" O ILE C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 606 removed outlier: 4.445A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE C 601 " --> pdb=" O PHE C 597 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 removed outlier: 3.689A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 665 removed outlier: 3.535A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 686 removed outlier: 3.654A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 703 removed outlier: 3.733A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 697 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 712 No H-bonds generated for 'chain 'C' and resid 709 through 712' Processing helix chain 'C' and resid 739 through 749 removed outlier: 3.670A pdb=" N THR C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU C 749 " --> pdb=" O HIS C 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 129 removed outlier: 3.706A pdb=" N LEU D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG D 122 " --> pdb=" O ARG D 118 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 147 removed outlier: 3.680A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D 140 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 145 " --> pdb=" O ASP D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 160 removed outlier: 3.717A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 183 through 196 removed outlier: 3.765A pdb=" N VAL D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 228 through 237 removed outlier: 3.777A pdb=" N ALA D 232 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 275 through 282 Processing helix chain 'D' and resid 299 through 305 removed outlier: 3.606A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 removed outlier: 3.624A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 351 removed outlier: 3.534A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 362 removed outlier: 3.542A pdb=" N SER D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) 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 409 removed outlier: 3.734A pdb=" N ILE D 407 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 420 Processing helix chain 'D' and resid 423 through 435 removed outlier: 3.708A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 460 removed outlier: 3.600A pdb=" N PHE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 506 removed outlier: 3.591A pdb=" N VAL D 490 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D 491 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE D 492 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA D 494 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS D 496 " --> pdb=" O TRP D 493 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER D 498 " --> pdb=" O THR D 495 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D 499 " --> pdb=" O CYS D 496 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU D 501 " --> pdb=" O SER D 498 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D 503 " --> pdb=" O LYS D 500 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 505 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 541 removed outlier: 3.715A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 567 removed outlier: 4.028A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ARG D 567 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 574 No H-bonds generated for 'chain 'D' and resid 572 through 574' Processing helix chain 'D' and resid 578 through 585 removed outlier: 3.714A pdb=" N VAL D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE D 583 " --> pdb=" O ILE D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 606 removed outlier: 4.446A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE D 601 " --> pdb=" O PHE D 597 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 removed outlier: 3.690A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 665 removed outlier: 3.534A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 686 removed outlier: 3.654A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 703 removed outlier: 3.733A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 712 No H-bonds generated for 'chain 'D' and resid 709 through 712' Processing helix chain 'D' and resid 739 through 749 removed outlier: 3.670A pdb=" N THR D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU D 749 " --> pdb=" O HIS D 745 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 732 through 737 removed outlier: 3.606A pdb=" N LEU A 732 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 385 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 719 through 724 removed outlier: 3.918A pdb=" N VAL A 723 " --> pdb=" O ASP A 727 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 732 through 737 removed outlier: 3.605A pdb=" N LEU B 732 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 385 " --> pdb=" O TYR B 382 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 719 through 724 removed outlier: 3.919A pdb=" N VAL B 723 " --> pdb=" O ASP B 727 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP B 727 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 732 through 737 removed outlier: 3.606A pdb=" N LEU C 732 " --> pdb=" O TYR C 390 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL C 385 " --> pdb=" O TYR C 382 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 719 through 724 removed outlier: 3.918A pdb=" N VAL C 723 " --> pdb=" O ASP C 727 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 732 through 737 removed outlier: 3.606A pdb=" N LEU D 732 " --> pdb=" O TYR D 390 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL D 385 " --> pdb=" O TYR D 382 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 719 through 724 removed outlier: 3.918A pdb=" N VAL D 723 " --> pdb=" O ASP D 727 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1884 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: 7.33 Time building geometry restraints manager: 9.49 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: 3523 1.31 - 1.44: 6077 1.44 - 1.57: 13504 1.57 - 1.70: 56 1.70 - 1.82: 216 Bond restraints: 23376 Sorted by residual: bond pdb=" C21 POV B 903 " pdb=" O21 POV B 903 " ideal model delta sigma weight residual 1.330 1.427 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C21 POV D 905 " pdb=" O21 POV D 905 " ideal model delta sigma weight residual 1.330 1.427 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C21 POV C 903 " pdb=" O21 POV C 903 " ideal model delta sigma weight residual 1.330 1.427 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C21 POV A 907 " pdb=" O21 POV A 907 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.31e+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 2.07e+01 ... (remaining 23371 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.39: 489 106.39 - 113.57: 13343 113.57 - 120.75: 10694 120.75 - 127.94: 6612 127.94 - 135.12: 194 Bond angle restraints: 31332 Sorted by residual: angle pdb=" C THR B 411 " pdb=" N ASN B 412 " pdb=" CA ASN B 412 " ideal model delta sigma weight residual 125.66 135.12 -9.46 1.85e+00 2.92e-01 2.61e+01 angle pdb=" C THR A 411 " pdb=" N ASN A 412 " pdb=" CA ASN A 412 " ideal model delta sigma weight residual 125.66 135.08 -9.42 1.85e+00 2.92e-01 2.59e+01 angle pdb=" C THR D 411 " pdb=" N ASN D 412 " pdb=" CA ASN D 412 " ideal model delta sigma weight residual 125.66 135.06 -9.40 1.85e+00 2.92e-01 2.58e+01 angle pdb=" C THR C 411 " pdb=" N ASN C 412 " pdb=" CA ASN C 412 " ideal model delta sigma weight residual 125.66 135.05 -9.39 1.85e+00 2.92e-01 2.58e+01 angle pdb=" C12 POV D 904 " pdb=" N POV D 904 " pdb=" C14 POV D 904 " ideal model delta sigma weight residual 107.13 120.14 -13.01 3.00e+00 1.11e-01 1.88e+01 ... (remaining 31327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.42: 13668 31.42 - 62.84: 631 62.84 - 94.26: 57 94.26 - 125.67: 20 125.67 - 157.09: 20 Dihedral angle restraints: 14396 sinusoidal: 6608 harmonic: 7788 Sorted by residual: dihedral pdb=" CA THR A 411 " pdb=" C THR A 411 " pdb=" N ASN A 412 " pdb=" CA ASN A 412 " ideal model delta harmonic sigma weight residual -180.00 -154.14 -25.86 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA THR B 411 " pdb=" C THR B 411 " pdb=" N ASN B 412 " pdb=" CA ASN B 412 " ideal model delta harmonic sigma weight residual -180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA THR C 411 " pdb=" C THR C 411 " pdb=" N ASN C 412 " pdb=" CA ASN C 412 " ideal model delta harmonic sigma weight residual -180.00 -154.20 -25.80 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 14393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2389 0.053 - 0.105: 873 0.105 - 0.158: 110 0.158 - 0.211: 32 0.211 - 0.264: 8 Chirality restraints: 3412 Sorted by residual: chirality pdb=" CB VAL C 154 " pdb=" CA VAL C 154 " pdb=" CG1 VAL C 154 " pdb=" CG2 VAL C 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB VAL A 154 " pdb=" CA VAL A 154 " pdb=" CG1 VAL A 154 " pdb=" CG2 VAL A 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB VAL D 154 " pdb=" CA VAL D 154 " pdb=" CG1 VAL D 154 " pdb=" CG2 VAL D 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 3409 not shown) Planarity restraints: 3788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 343 " -0.039 5.00e-02 4.00e+02 5.86e-02 5.50e+00 pdb=" N PRO D 344 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 344 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 344 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 343 " 0.039 5.00e-02 4.00e+02 5.86e-02 5.50e+00 pdb=" N PRO B 344 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 344 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 344 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 343 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO A 344 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " 0.033 5.00e-02 4.00e+02 ... (remaining 3785 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 7441 2.87 - 3.38: 19776 3.38 - 3.89: 32939 3.89 - 4.39: 39899 4.39 - 4.90: 68413 Nonbonded interactions: 168468 Sorted by model distance: nonbonded pdb=" OG SER B 444 " pdb=" O14 POV B 904 " model vdw 2.363 2.440 nonbonded pdb=" OG SER C 444 " pdb=" O14 POV C 904 " model vdw 2.365 2.440 nonbonded pdb=" OG SER D 444 " pdb=" O14 POV D 906 " model vdw 2.368 2.440 nonbonded pdb=" OG SER A 444 " pdb=" O14 POV A 901 " model vdw 2.372 2.440 nonbonded pdb=" OD1 ASN A 298 " pdb=" ND1 HIS A 301 " model vdw 2.374 2.520 ... (remaining 168463 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 58 through 752 or resid 901 through 907)) 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: 1.180 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: 5.070 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 59.790 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.140 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 0.097 23376 Z= 0.634 Angle : 1.323 13.009 31332 Z= 0.579 Chirality : 0.054 0.264 3412 Planarity : 0.006 0.059 3788 Dihedral : 18.150 157.093 9320 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.34 % Allowed : 5.08 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.90 (0.11), residues: 2620 helix: -4.50 (0.05), residues: 1580 sheet: 0.67 (0.64), residues: 56 loop : -2.79 (0.16), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 481 HIS 0.011 0.003 HIS B 301 PHE 0.025 0.003 PHE C 703 TYR 0.019 0.003 TYR C 451 ARG 0.005 0.001 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 489 time to evaluate : 3.701 Fit side-chains REVERT: A 254 TYR cc_start: 0.8370 (m-10) cc_final: 0.8008 (m-80) REVERT: A 282 MET cc_start: 0.8122 (mtm) cc_final: 0.7796 (mtp) REVERT: A 330 ASN cc_start: 0.8536 (m-40) cc_final: 0.8206 (m110) REVERT: A 371 ARG cc_start: 0.8150 (tpt170) cc_final: 0.7827 (tpt170) REVERT: A 487 ARG cc_start: 0.7906 (mtt180) cc_final: 0.7467 (ttm170) REVERT: A 518 SER cc_start: 0.8948 (t) cc_final: 0.8672 (p) REVERT: A 525 VAL cc_start: 0.9204 (t) cc_final: 0.8948 (m) REVERT: A 690 ARG cc_start: 0.8256 (mtt-85) cc_final: 0.7254 (mtm110) REVERT: B 253 LYS cc_start: 0.8504 (mmtm) cc_final: 0.8292 (ttmm) REVERT: B 254 TYR cc_start: 0.8334 (m-10) cc_final: 0.7939 (m-80) REVERT: B 282 MET cc_start: 0.8157 (mtm) cc_final: 0.7794 (mtp) REVERT: B 330 ASN cc_start: 0.8521 (m-40) cc_final: 0.8306 (m-40) REVERT: B 371 ARG cc_start: 0.8192 (tpt170) cc_final: 0.7861 (tpt170) REVERT: B 419 MET cc_start: 0.9375 (mtm) cc_final: 0.9132 (mtp) REVERT: B 487 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7473 (ttm170) REVERT: B 525 VAL cc_start: 0.9206 (t) cc_final: 0.8939 (m) REVERT: B 690 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7293 (mtm110) REVERT: C 253 LYS cc_start: 0.8533 (mmtm) cc_final: 0.8329 (ttmm) REVERT: C 254 TYR cc_start: 0.8351 (m-10) cc_final: 0.7952 (m-80) REVERT: C 282 MET cc_start: 0.8119 (mtm) cc_final: 0.7761 (mtp) REVERT: C 435 LYS cc_start: 0.8732 (mtpt) cc_final: 0.8392 (mtpp) REVERT: C 487 ARG cc_start: 0.7940 (mtt180) cc_final: 0.7492 (ttm170) REVERT: C 525 VAL cc_start: 0.9186 (t) cc_final: 0.8951 (m) REVERT: C 690 ARG cc_start: 0.8240 (mtt-85) cc_final: 0.7354 (mtm110) REVERT: D 254 TYR cc_start: 0.8332 (m-10) cc_final: 0.7956 (m-80) REVERT: D 282 MET cc_start: 0.8136 (mtm) cc_final: 0.7799 (mtp) REVERT: D 330 ASN cc_start: 0.8516 (m-40) cc_final: 0.8226 (m-40) REVERT: D 371 ARG cc_start: 0.8172 (tpt170) cc_final: 0.7839 (tpt170) REVERT: D 419 MET cc_start: 0.9374 (mtm) cc_final: 0.9137 (mtp) REVERT: D 435 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8359 (mtpp) REVERT: D 487 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7472 (ttm170) REVERT: D 525 VAL cc_start: 0.9201 (t) cc_final: 0.8951 (m) REVERT: D 690 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.7255 (mtm110) outliers start: 8 outliers final: 4 residues processed: 497 average time/residue: 0.3463 time to fit residues: 266.7589 Evaluate side-chains 340 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 336 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain D residue 737 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 1.9990 chunk 197 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 chunk 132 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 178 ASN A 197 ASN A 205 ASN A 394 ASN B 178 ASN B 197 ASN B 205 ASN B 394 ASN B 647 ASN C 74 GLN C 197 ASN C 205 ASN C 394 ASN C 647 ASN D 197 ASN D 205 ASN D 394 ASN D 647 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23376 Z= 0.123 Angle : 0.499 7.347 31332 Z= 0.258 Chirality : 0.037 0.155 3412 Planarity : 0.004 0.037 3788 Dihedral : 19.338 153.794 4072 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.69 % Allowed : 9.69 % Favored : 88.62 % 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: -3.72 (0.14), residues: 2620 helix: -2.60 (0.10), residues: 1528 sheet: -0.38 (0.54), residues: 88 loop : -2.17 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 559 HIS 0.002 0.000 HIS B 301 PHE 0.018 0.001 PHE C 449 TYR 0.010 0.001 TYR A 208 ARG 0.002 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 410 time to evaluate : 2.696 Fit side-chains REVERT: A 162 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7260 (mt) REVERT: A 202 ARG cc_start: 0.8200 (mtp85) cc_final: 0.7748 (mtp85) REVERT: A 254 TYR cc_start: 0.8238 (m-10) cc_final: 0.7957 (m-80) REVERT: A 323 MET cc_start: 0.8961 (ttp) cc_final: 0.8715 (ttm) REVERT: A 330 ASN cc_start: 0.8503 (m-40) cc_final: 0.8232 (m-40) REVERT: A 332 GLU cc_start: 0.7666 (mp0) cc_final: 0.7378 (mp0) REVERT: A 334 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8683 (mt-10) REVERT: A 690 ARG cc_start: 0.8078 (mtt-85) cc_final: 0.7108 (mtm110) REVERT: B 202 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7777 (mtp85) REVERT: B 254 TYR cc_start: 0.8215 (m-10) cc_final: 0.7905 (m-80) REVERT: B 690 ARG cc_start: 0.8092 (mtt-85) cc_final: 0.7115 (mtm110) REVERT: C 140 GLN cc_start: 0.7393 (pt0) cc_final: 0.7120 (mm-40) REVERT: C 162 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7171 (mt) REVERT: C 202 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7788 (mtp85) REVERT: C 254 TYR cc_start: 0.8245 (m-10) cc_final: 0.7924 (m-80) REVERT: C 334 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8606 (mt-10) REVERT: C 487 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7656 (ttm170) REVERT: C 518 SER cc_start: 0.8845 (t) cc_final: 0.8459 (p) REVERT: C 690 ARG cc_start: 0.8155 (mtt-85) cc_final: 0.7162 (mtm110) REVERT: D 202 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7784 (mtp85) REVERT: D 254 TYR cc_start: 0.8215 (m-10) cc_final: 0.7867 (m-80) REVERT: D 518 SER cc_start: 0.8865 (t) cc_final: 0.8483 (p) REVERT: D 690 ARG cc_start: 0.8086 (mtt-85) cc_final: 0.7093 (mtm110) outliers start: 40 outliers final: 27 residues processed: 441 average time/residue: 0.3750 time to fit residues: 248.9713 Evaluate side-chains 379 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 348 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 713 SER Chi-restraints excluded: chain D residue 737 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 10.0000 chunk 73 optimal weight: 0.0980 chunk 196 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 236 optimal weight: 0.0040 chunk 255 optimal weight: 0.8980 chunk 210 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 256 HIS ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 256 HIS ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 ASN C 180 ASN C 256 HIS ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN D 180 ASN D 256 HIS ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23376 Z= 0.267 Angle : 0.558 8.010 31332 Z= 0.285 Chirality : 0.040 0.162 3412 Planarity : 0.003 0.032 3788 Dihedral : 17.952 88.310 4072 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.27 % Allowed : 9.77 % Favored : 85.96 % 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: -2.43 (0.15), residues: 2620 helix: -1.35 (0.13), residues: 1528 sheet: -0.06 (0.54), residues: 88 loop : -2.01 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 521 HIS 0.009 0.001 HIS D 301 PHE 0.016 0.002 PHE C 449 TYR 0.018 0.002 TYR A 451 ARG 0.004 0.000 ARG A 696 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 348 time to evaluate : 2.485 Fit side-chains REVERT: A 140 GLN cc_start: 0.7477 (pt0) cc_final: 0.7225 (mm-40) REVERT: A 246 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7365 (pmmt) REVERT: A 330 ASN cc_start: 0.8486 (m-40) cc_final: 0.8096 (t0) REVERT: A 332 GLU cc_start: 0.7943 (mp0) cc_final: 0.7723 (mp0) REVERT: A 334 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8577 (mm-30) REVERT: A 690 ARG cc_start: 0.8333 (mtt-85) cc_final: 0.7332 (mtm110) REVERT: B 137 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7926 (mm-30) REVERT: B 185 GLU cc_start: 0.7455 (mp0) cc_final: 0.7213 (mp0) REVERT: B 246 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7410 (pmmt) REVERT: B 690 ARG cc_start: 0.8411 (mtt-85) cc_final: 0.7320 (mtm110) REVERT: C 137 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7979 (mm-30) REVERT: C 140 GLN cc_start: 0.7475 (pt0) cc_final: 0.7243 (mm-40) REVERT: C 185 GLU cc_start: 0.7455 (mp0) cc_final: 0.7228 (mp0) REVERT: C 246 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7388 (pmmt) REVERT: C 330 ASN cc_start: 0.8409 (m-40) cc_final: 0.8114 (t0) REVERT: C 332 GLU cc_start: 0.7942 (mp0) cc_final: 0.7729 (mp0) REVERT: C 334 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8649 (mm-30) REVERT: C 422 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8132 (mt) REVERT: C 487 ARG cc_start: 0.7906 (mtt180) cc_final: 0.7640 (ttm170) REVERT: C 545 LYS cc_start: 0.7270 (pptt) cc_final: 0.6923 (pptt) REVERT: C 690 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.7350 (mtm110) REVERT: D 137 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7938 (mm-30) REVERT: D 185 GLU cc_start: 0.7463 (mp0) cc_final: 0.7262 (mp0) REVERT: D 246 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7414 (pmmt) REVERT: D 690 ARG cc_start: 0.8395 (mtt-85) cc_final: 0.7274 (mtm110) outliers start: 101 outliers final: 71 residues processed: 416 average time/residue: 0.3523 time to fit residues: 225.9880 Evaluate side-chains 411 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 333 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 713 SER Chi-restraints excluded: chain D residue 737 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 20.0000 chunk 177 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 237 optimal weight: 7.9990 chunk 251 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.8467 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 23376 Z= 0.333 Angle : 0.588 7.515 31332 Z= 0.299 Chirality : 0.042 0.178 3412 Planarity : 0.003 0.033 3788 Dihedral : 17.684 92.777 4072 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.53 % Allowed : 11.55 % Favored : 83.93 % 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: -2.06 (0.16), residues: 2620 helix: -0.94 (0.13), residues: 1544 sheet: 0.02 (0.54), residues: 88 loop : -2.04 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 521 HIS 0.011 0.001 HIS A 301 PHE 0.013 0.002 PHE B 316 TYR 0.020 0.002 TYR B 208 ARG 0.005 0.001 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 364 time to evaluate : 2.671 Fit side-chains REVERT: A 246 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7387 (pmmt) REVERT: A 330 ASN cc_start: 0.8396 (m-40) cc_final: 0.7937 (t0) REVERT: A 332 GLU cc_start: 0.8113 (mp0) cc_final: 0.7589 (mp0) REVERT: A 334 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8693 (mm-30) REVERT: A 668 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8869 (tt) REVERT: A 690 ARG cc_start: 0.8342 (mtt-85) cc_final: 0.7223 (mtm110) REVERT: B 136 ARG cc_start: 0.8025 (mtt180) cc_final: 0.7719 (mmm-85) REVERT: B 185 GLU cc_start: 0.7517 (mp0) cc_final: 0.7228 (mp0) REVERT: B 246 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7387 (pmmt) REVERT: B 668 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8880 (tt) REVERT: B 690 ARG cc_start: 0.8421 (mtt-85) cc_final: 0.7310 (mtm110) REVERT: C 140 GLN cc_start: 0.7462 (pt0) cc_final: 0.7241 (mm-40) REVERT: C 185 GLU cc_start: 0.7509 (mp0) cc_final: 0.7216 (mp0) REVERT: C 246 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7394 (pmmt) REVERT: C 330 ASN cc_start: 0.8368 (m-40) cc_final: 0.8022 (t0) REVERT: C 332 GLU cc_start: 0.8115 (mp0) cc_final: 0.7638 (mp0) REVERT: C 334 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8695 (mm-30) REVERT: C 487 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7606 (ttm170) REVERT: C 545 LYS cc_start: 0.7447 (pptt) cc_final: 0.7183 (pptt) REVERT: C 668 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8876 (tt) REVERT: C 690 ARG cc_start: 0.8446 (mtt-85) cc_final: 0.7303 (mtm110) REVERT: D 136 ARG cc_start: 0.8048 (mtt180) cc_final: 0.7730 (mmm-85) REVERT: D 185 GLU cc_start: 0.7527 (mp0) cc_final: 0.7228 (mp0) REVERT: D 246 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7390 (pmmt) REVERT: D 668 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8886 (tt) REVERT: D 690 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.7175 (mtm110) outliers start: 107 outliers final: 77 residues processed: 449 average time/residue: 0.3610 time to fit residues: 250.3224 Evaluate side-chains 438 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 351 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 713 SER Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 187 optimal weight: 0.6980 chunk 103 optimal weight: 30.0000 chunk 214 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 225 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 overall best weight: 5.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 ASN B 561 ASN C 561 ASN D 561 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 23376 Z= 0.509 Angle : 0.706 10.216 31332 Z= 0.356 Chirality : 0.047 0.201 3412 Planarity : 0.004 0.036 3788 Dihedral : 17.888 103.259 4072 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 5.16 % Allowed : 13.07 % Favored : 81.77 % 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: -2.16 (0.15), residues: 2620 helix: -0.98 (0.13), residues: 1540 sheet: 0.01 (0.53), residues: 88 loop : -2.17 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 521 HIS 0.013 0.002 HIS C 301 PHE 0.021 0.002 PHE A 193 TYR 0.024 0.003 TYR A 208 ARG 0.005 0.001 ARG B 696 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 351 time to evaluate : 2.779 Fit side-chains REVERT: A 161 LYS cc_start: 0.8127 (mmpt) cc_final: 0.7896 (mmmt) REVERT: A 246 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7386 (pmmt) REVERT: A 334 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8601 (mm-30) REVERT: A 668 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8865 (tt) REVERT: B 136 ARG cc_start: 0.8105 (mtt180) cc_final: 0.7734 (mmm-85) REVERT: B 161 LYS cc_start: 0.7999 (mmpt) cc_final: 0.7771 (mmmt) REVERT: B 246 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7387 (pmmt) REVERT: B 668 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8861 (tt) REVERT: C 140 GLN cc_start: 0.7486 (pt0) cc_final: 0.7221 (mm-40) REVERT: C 246 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7388 (pmmt) REVERT: C 334 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8598 (mm-30) REVERT: C 487 ARG cc_start: 0.7974 (mtt180) cc_final: 0.7690 (ttm170) REVERT: C 668 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8878 (tt) REVERT: C 690 ARG cc_start: 0.8481 (mtt-85) cc_final: 0.7336 (mtm110) REVERT: D 136 ARG cc_start: 0.8136 (mtt180) cc_final: 0.7783 (mmm-85) REVERT: D 161 LYS cc_start: 0.8003 (mmpt) cc_final: 0.7776 (mmmt) REVERT: D 246 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7386 (pmmt) REVERT: D 668 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8874 (tt) outliers start: 122 outliers final: 93 residues processed: 450 average time/residue: 0.3450 time to fit residues: 240.9694 Evaluate side-chains 447 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 344 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 246 LYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 454 THR Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 713 SER Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 6.9990 chunk 226 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 251 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN C 205 ASN C 330 ASN D 205 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23376 Z= 0.136 Angle : 0.466 8.921 31332 Z= 0.239 Chirality : 0.037 0.136 3412 Planarity : 0.003 0.031 3788 Dihedral : 15.901 90.376 4072 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.71 % Allowed : 15.27 % Favored : 82.02 % 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: -1.30 (0.16), residues: 2620 helix: -0.25 (0.14), residues: 1480 sheet: 0.95 (0.64), residues: 64 loop : -1.78 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 380 HIS 0.003 0.001 HIS C 301 PHE 0.021 0.001 PHE D 193 TYR 0.013 0.001 TYR D 208 ARG 0.007 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 387 time to evaluate : 2.437 Fit side-chains REVERT: A 136 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7784 (mmm-85) REVERT: A 334 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8494 (mm-30) REVERT: A 419 MET cc_start: 0.9181 (mtm) cc_final: 0.8947 (mtp) REVERT: B 136 ARG cc_start: 0.8193 (mtt180) cc_final: 0.7841 (mmm-85) REVERT: C 136 ARG cc_start: 0.8050 (mtt180) cc_final: 0.7792 (mmm-85) REVERT: C 334 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8498 (mm-30) REVERT: C 487 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7574 (ttm170) REVERT: C 690 ARG cc_start: 0.8355 (mtt-85) cc_final: 0.7166 (mtm110) REVERT: D 136 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7837 (mmm-85) outliers start: 64 outliers final: 27 residues processed: 442 average time/residue: 0.3369 time to fit residues: 232.3555 Evaluate side-chains 383 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 354 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 713 SER Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 143 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN B 216 GLN C 216 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23376 Z= 0.284 Angle : 0.555 8.214 31332 Z= 0.282 Chirality : 0.041 0.156 3412 Planarity : 0.003 0.032 3788 Dihedral : 16.090 93.442 4072 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.05 % Allowed : 15.61 % Favored : 81.35 % 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: -1.40 (0.16), residues: 2620 helix: -0.24 (0.14), residues: 1504 sheet: 0.08 (0.55), residues: 88 loop : -2.01 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 380 HIS 0.009 0.001 HIS B 301 PHE 0.012 0.001 PHE A 316 TYR 0.019 0.002 TYR C 208 ARG 0.006 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 349 time to evaluate : 2.546 Fit side-chains REVERT: A 334 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8522 (mm-30) REVERT: B 136 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7811 (mmm-85) REVERT: B 334 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8515 (mm-30) REVERT: C 136 ARG cc_start: 0.8156 (mtt180) cc_final: 0.7822 (mmm-85) REVERT: C 334 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8502 (mm-30) REVERT: C 487 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7621 (ttm170) REVERT: D 136 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7807 (mmm-85) REVERT: D 334 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8518 (mm-30) outliers start: 72 outliers final: 58 residues processed: 410 average time/residue: 0.3485 time to fit residues: 223.2467 Evaluate side-chains 407 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 345 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 713 SER Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 159 optimal weight: 0.4980 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 196 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 585 HIS B 585 HIS C 205 ASN C 585 HIS D 216 GLN D 585 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23376 Z= 0.117 Angle : 0.450 8.353 31332 Z= 0.230 Chirality : 0.036 0.144 3412 Planarity : 0.003 0.030 3788 Dihedral : 14.848 88.647 4072 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.99 % Allowed : 16.62 % Favored : 81.39 % 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: -0.83 (0.16), residues: 2620 helix: 0.17 (0.14), residues: 1492 sheet: 1.11 (0.65), residues: 64 loop : -1.66 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 380 HIS 0.004 0.001 HIS C 301 PHE 0.010 0.001 PHE C 449 TYR 0.012 0.001 TYR D 208 ARG 0.006 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 361 time to evaluate : 2.266 Fit side-chains REVERT: A 136 ARG cc_start: 0.8213 (mtt180) cc_final: 0.7850 (mmm-85) REVERT: A 334 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8502 (mm-30) REVERT: A 419 MET cc_start: 0.9169 (mtm) cc_final: 0.8920 (mtp) REVERT: A 702 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7667 (mm-30) REVERT: B 136 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7880 (mmm-85) REVERT: B 702 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7646 (mm-30) REVERT: C 136 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7866 (mmm-85) REVERT: C 334 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8460 (mm-30) REVERT: C 487 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7655 (ttm170) REVERT: C 702 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7653 (mm-30) REVERT: D 136 ARG cc_start: 0.8199 (mtt180) cc_final: 0.7874 (mmm-85) REVERT: D 702 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7678 (mm-30) outliers start: 47 outliers final: 37 residues processed: 405 average time/residue: 0.3393 time to fit residues: 212.2273 Evaluate side-chains 392 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 353 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 0.0770 chunk 240 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 233 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 220 optimal weight: 0.2980 chunk 232 optimal weight: 0.0030 overall best weight: 1.0752 ------------------------------------------------------------------------------- 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: 0.8389 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23376 Z= 0.142 Angle : 0.468 9.677 31332 Z= 0.237 Chirality : 0.037 0.147 3412 Planarity : 0.003 0.029 3788 Dihedral : 14.427 85.988 4072 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.24 % Allowed : 17.13 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2620 helix: 0.33 (0.14), residues: 1488 sheet: 1.36 (0.66), residues: 64 loop : -1.62 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 380 HIS 0.004 0.001 HIS A 301 PHE 0.013 0.001 PHE A 449 TYR 0.013 0.001 TYR D 208 ARG 0.003 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 359 time to evaluate : 2.247 Fit side-chains REVERT: A 136 ARG cc_start: 0.8195 (mtt180) cc_final: 0.7863 (mmm-85) REVERT: A 334 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8537 (mm-30) REVERT: A 702 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7677 (mm-30) REVERT: B 136 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7884 (mmm-85) REVERT: B 702 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7668 (mm-30) REVERT: C 136 ARG cc_start: 0.8198 (mtt180) cc_final: 0.7868 (mmm-85) REVERT: C 161 LYS cc_start: 0.7916 (mmpt) cc_final: 0.7693 (mmmt) REVERT: C 334 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8482 (mm-30) REVERT: C 487 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7688 (ttm170) REVERT: C 702 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7679 (mm-30) REVERT: D 136 ARG cc_start: 0.8171 (mtt180) cc_final: 0.7878 (mmm-85) REVERT: D 702 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7678 (mm-30) outliers start: 53 outliers final: 44 residues processed: 401 average time/residue: 0.3395 time to fit residues: 210.2914 Evaluate side-chains 394 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 348 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 5.9990 chunk 246 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 259 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 126 optimal weight: 0.4980 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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: 0.8466 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 23376 Z= 0.332 Angle : 0.587 8.969 31332 Z= 0.296 Chirality : 0.042 0.167 3412 Planarity : 0.003 0.032 3788 Dihedral : 15.390 91.268 4072 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.37 % Allowed : 17.17 % Favored : 80.46 % 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: -1.10 (0.16), residues: 2620 helix: -0.04 (0.14), residues: 1516 sheet: 0.54 (0.56), residues: 88 loop : -1.86 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 433 HIS 0.010 0.001 HIS B 301 PHE 0.014 0.002 PHE B 449 TYR 0.019 0.002 TYR D 208 ARG 0.004 0.000 ARG B 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 356 time to evaluate : 2.507 Fit side-chains REVERT: A 136 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7861 (mmm-85) REVERT: A 161 LYS cc_start: 0.7987 (mmpt) cc_final: 0.7762 (mmmt) REVERT: A 334 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8545 (mm-30) REVERT: B 136 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7891 (mmm-85) REVERT: C 136 ARG cc_start: 0.8209 (mtt180) cc_final: 0.7890 (mmm-85) REVERT: C 161 LYS cc_start: 0.7958 (mmpt) cc_final: 0.7724 (mmmt) REVERT: C 334 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8487 (mm-30) REVERT: C 487 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7636 (ttm170) REVERT: D 136 ARG cc_start: 0.8181 (mtt180) cc_final: 0.7876 (mmm-85) outliers start: 56 outliers final: 47 residues processed: 404 average time/residue: 0.3430 time to fit residues: 213.9472 Evaluate side-chains 401 residues out of total 2364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 352 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain D residue 584 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 749 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.6980 chunk 219 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 190 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 206 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 212 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN C 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.156982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.111354 restraints weight = 27347.018| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.29 r_work: 0.2828 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23376 Z= 0.132 Angle : 0.461 8.221 31332 Z= 0.235 Chirality : 0.037 0.147 3412 Planarity : 0.003 0.030 3788 Dihedral : 14.292 85.438 4072 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.07 % Allowed : 17.34 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2620 helix: 0.33 (0.14), residues: 1488 sheet: 1.43 (0.67), residues: 64 loop : -1.62 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 380 HIS 0.004 0.001 HIS C 301 PHE 0.023 0.001 PHE A 193 TYR 0.013 0.001 TYR C 208 ARG 0.003 0.000 ARG C 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5182.72 seconds wall clock time: 94 minutes 26.82 seconds (5666.82 seconds total)