Starting phenix.real_space_refine on Sat Feb 17 05:22:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va3_8652/02_2024/5va3_8652.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va3_8652/02_2024/5va3_8652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va3_8652/02_2024/5va3_8652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va3_8652/02_2024/5va3_8652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va3_8652/02_2024/5va3_8652.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va3_8652/02_2024/5va3_8652.pdb" } resolution = 4.0 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= 0.459 sd= 0.788 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 11476 2.51 5 N 3000 2.21 5 O 3016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 4": "NH1" <-> "NH2" Residue "A ARG 5": "NH1" <-> "NH2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 534": "NH1" <-> "NH2" Residue "A TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 860": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 4": "NH1" <-> "NH2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 488": "NH1" <-> "NH2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 860": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 488": "NH1" <-> "NH2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 672": "NH1" <-> "NH2" Residue "C TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 860": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 4": "NH1" <-> "NH2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 488": "NH1" <-> "NH2" Residue "D ARG 534": "NH1" <-> "NH2" Residue "D TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 672": "NH1" <-> "NH2" Residue "D TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 860": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 17600 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4400 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 22, 'TRANS': 536} Chain breaks: 5 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 4400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4400 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 22, 'TRANS': 536} Chain breaks: 5 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "C" Number of atoms: 4400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4400 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 22, 'TRANS': 536} Chain breaks: 5 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 4400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4400 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 22, 'TRANS': 536} Chain breaks: 5 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Time building chain proxies: 9.47, per 1000 atoms: 0.54 Number of scatterers: 17600 At special positions: 0 Unit cell: (148.761, 148.761, 120.757, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 3016 8.00 N 3000 7.00 C 11476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.97 Conformation dependent library (CDL) restraints added in 3.4 seconds 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4192 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 16 sheets defined 58.3% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 13 through 25 removed outlier: 3.688A pdb=" N THR A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.577A pdb=" N CYS A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 79 through 89 removed outlier: 3.796A pdb=" N ALA A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 432 removed outlier: 3.994A pdb=" N VAL A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Proline residue: A 426 - end of helix removed outlier: 3.725A pdb=" N LEU A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 473 removed outlier: 4.143A pdb=" N LEU A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG A 472 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 494 removed outlier: 3.943A pdb=" N ILE A 489 " --> pdb=" O HIS A 485 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 removed outlier: 3.665A pdb=" N ALA A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 505' Processing helix chain 'A' and resid 521 through 531 removed outlier: 3.782A pdb=" N LEU A 524 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 527 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.889A pdb=" N ALA A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 544 removed outlier: 3.906A pdb=" N SER A 543 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU A 544 " --> pdb=" O ARG A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 574 removed outlier: 3.863A pdb=" N VAL A 549 " --> pdb=" O TYR A 545 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 550 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 558 " --> pdb=" O MET A 554 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 572 " --> pdb=" O TRP A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 593 Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 634 through 667 removed outlier: 3.643A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN A 664 " --> pdb=" O SER A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 688 removed outlier: 3.643A pdb=" N HIS A 674 " --> pdb=" O THR A 670 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 709 removed outlier: 4.209A pdb=" N ARG A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 718 removed outlier: 4.091A pdb=" N LEU A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 Processing helix chain 'A' and resid 733 through 738 removed outlier: 3.543A pdb=" N LEU A 737 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 758 removed outlier: 3.602A pdb=" N LEU A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 843 removed outlier: 3.825A pdb=" N VAL A 841 " --> pdb=" O ASP A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 856 removed outlier: 3.572A pdb=" N ASP A 850 " --> pdb=" O PRO A 846 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 854 " --> pdb=" O ASP A 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 25 removed outlier: 3.688A pdb=" N THR B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.577A pdb=" N CYS B 49 " --> pdb=" O ASN B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 79 through 89 removed outlier: 3.796A pdb=" N ALA B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA B 85 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 432 removed outlier: 3.994A pdb=" N VAL B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP B 410 " --> pdb=" O PHE B 406 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Proline residue: B 426 - end of helix removed outlier: 3.725A pdb=" N LEU B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 473 removed outlier: 4.143A pdb=" N LEU B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 459 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG B 472 " --> pdb=" O LEU B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 494 removed outlier: 3.943A pdb=" N ILE B 489 " --> pdb=" O HIS B 485 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 494 " --> pdb=" O ALA B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 removed outlier: 3.665A pdb=" N ALA B 504 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 500 through 505' Processing helix chain 'B' and resid 521 through 531 removed outlier: 3.782A pdb=" N LEU B 524 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 527 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 538 removed outlier: 3.889A pdb=" N ALA B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.906A pdb=" N SER B 543 " --> pdb=" O ASP B 540 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU B 544 " --> pdb=" O ARG B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 574 removed outlier: 3.863A pdb=" N VAL B 549 " --> pdb=" O TYR B 545 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 550 " --> pdb=" O GLY B 546 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA B 558 " --> pdb=" O MET B 554 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 572 " --> pdb=" O TRP B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 593 Processing helix chain 'B' and resid 606 through 623 Processing helix chain 'B' and resid 634 through 667 removed outlier: 3.643A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE B 656 " --> pdb=" O TYR B 652 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 688 removed outlier: 3.643A pdb=" N HIS B 674 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 709 removed outlier: 4.209A pdb=" N ARG B 696 " --> pdb=" O PRO B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 718 removed outlier: 4.091A pdb=" N LEU B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 733 Processing helix chain 'B' and resid 733 through 738 removed outlier: 3.543A pdb=" N LEU B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 758 removed outlier: 3.602A pdb=" N LEU B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 843 removed outlier: 3.825A pdb=" N VAL B 841 " --> pdb=" O ASP B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 856 removed outlier: 3.572A pdb=" N ASP B 850 " --> pdb=" O PRO B 846 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS B 851 " --> pdb=" O GLU B 847 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 854 " --> pdb=" O ASP B 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 25 removed outlier: 3.688A pdb=" N THR C 17 " --> pdb=" O THR C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.577A pdb=" N CYS C 49 " --> pdb=" O ASN C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.796A pdb=" N ALA C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA C 85 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 86 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 432 removed outlier: 3.994A pdb=" N VAL C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP C 410 " --> pdb=" O PHE C 406 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Proline residue: C 426 - end of helix removed outlier: 3.725A pdb=" N LEU C 432 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 473 removed outlier: 4.143A pdb=" N LEU C 457 " --> pdb=" O ALA C 453 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 459 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 468 " --> pdb=" O ILE C 464 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C 471 " --> pdb=" O ILE C 467 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG C 472 " --> pdb=" O LEU C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 494 removed outlier: 3.943A pdb=" N ILE C 489 " --> pdb=" O HIS C 485 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL C 491 " --> pdb=" O GLY C 487 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C 494 " --> pdb=" O ALA C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 505 removed outlier: 3.665A pdb=" N ALA C 504 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 505 " --> pdb=" O ASP C 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 500 through 505' Processing helix chain 'C' and resid 521 through 531 removed outlier: 3.782A pdb=" N LEU C 524 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 527 " --> pdb=" O LEU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 538 removed outlier: 3.889A pdb=" N ALA C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 544 removed outlier: 3.906A pdb=" N SER C 543 " --> pdb=" O ASP C 540 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU C 544 " --> pdb=" O ARG C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 574 removed outlier: 3.863A pdb=" N VAL C 549 " --> pdb=" O TYR C 545 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 550 " --> pdb=" O GLY C 546 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA C 558 " --> pdb=" O MET C 554 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C 572 " --> pdb=" O TRP C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 593 Processing helix chain 'C' and resid 606 through 623 Processing helix chain 'C' and resid 634 through 667 removed outlier: 3.643A pdb=" N ALA C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE C 656 " --> pdb=" O TYR C 652 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN C 664 " --> pdb=" O SER C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 688 removed outlier: 3.643A pdb=" N HIS C 674 " --> pdb=" O THR C 670 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 675 " --> pdb=" O ALA C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 709 removed outlier: 4.209A pdb=" N ARG C 696 " --> pdb=" O PRO C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 718 removed outlier: 4.091A pdb=" N LEU C 717 " --> pdb=" O MET C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 733 Processing helix chain 'C' and resid 733 through 738 removed outlier: 3.543A pdb=" N LEU C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 758 removed outlier: 3.602A pdb=" N LEU C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 843 removed outlier: 3.825A pdb=" N VAL C 841 " --> pdb=" O ASP C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 856 removed outlier: 3.572A pdb=" N ASP C 850 " --> pdb=" O PRO C 846 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS C 851 " --> pdb=" O GLU C 847 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 854 " --> pdb=" O ASP C 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 25 removed outlier: 3.688A pdb=" N THR D 17 " --> pdb=" O THR D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 53 removed outlier: 3.577A pdb=" N CYS D 49 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 79 through 89 removed outlier: 3.796A pdb=" N ALA D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA D 85 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 432 removed outlier: 3.994A pdb=" N VAL D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP D 410 " --> pdb=" O PHE D 406 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Proline residue: D 426 - end of helix removed outlier: 3.725A pdb=" N LEU D 432 " --> pdb=" O SER D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 473 removed outlier: 4.143A pdb=" N LEU D 457 " --> pdb=" O ALA D 453 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 459 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 464 " --> pdb=" O ASP D 460 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 468 " --> pdb=" O ILE D 464 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG D 472 " --> pdb=" O LEU D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 494 removed outlier: 3.943A pdb=" N ILE D 489 " --> pdb=" O HIS D 485 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA D 490 " --> pdb=" O PRO D 486 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL D 491 " --> pdb=" O GLY D 487 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS D 492 " --> pdb=" O ARG D 488 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D 494 " --> pdb=" O ALA D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 505 removed outlier: 3.665A pdb=" N ALA D 504 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA D 505 " --> pdb=" O ASP D 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 500 through 505' Processing helix chain 'D' and resid 521 through 531 removed outlier: 3.782A pdb=" N LEU D 524 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA D 527 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 538 removed outlier: 3.889A pdb=" N ALA D 536 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 544 removed outlier: 3.906A pdb=" N SER D 543 " --> pdb=" O ASP D 540 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU D 544 " --> pdb=" O ARG D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 574 removed outlier: 3.863A pdb=" N VAL D 549 " --> pdb=" O TYR D 545 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU D 550 " --> pdb=" O GLY D 546 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA D 558 " --> pdb=" O MET D 554 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY D 572 " --> pdb=" O TRP D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 593 Processing helix chain 'D' and resid 606 through 623 Processing helix chain 'D' and resid 634 through 667 removed outlier: 3.643A pdb=" N ALA D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE D 656 " --> pdb=" O TYR D 652 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN D 664 " --> pdb=" O SER D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 688 removed outlier: 3.643A pdb=" N HIS D 674 " --> pdb=" O THR D 670 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 709 removed outlier: 4.209A pdb=" N ARG D 696 " --> pdb=" O PRO D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 718 removed outlier: 4.091A pdb=" N LEU D 717 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 733 Processing helix chain 'D' and resid 733 through 738 removed outlier: 3.543A pdb=" N LEU D 737 " --> pdb=" O ASN D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 758 removed outlier: 3.602A pdb=" N LEU D 751 " --> pdb=" O THR D 747 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS D 757 " --> pdb=" O ALA D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 843 removed outlier: 3.825A pdb=" N VAL D 841 " --> pdb=" O ASP D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 856 removed outlier: 3.572A pdb=" N ASP D 850 " --> pdb=" O PRO D 846 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS D 851 " --> pdb=" O GLU D 847 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER D 854 " --> pdb=" O ASP D 850 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.726A pdb=" N ILE A 31 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N CYS A 44 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE A 29 " --> pdb=" O CYS A 44 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET A 124 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 92 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 98 through 99 removed outlier: 4.167A pdb=" N PHE A 98 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE A 106 " --> pdb=" O PHE A 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain 'A' and resid 762 through 763 removed outlier: 6.854A pdb=" N ASP A 829 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 805 " --> pdb=" O TYR A 780 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 795 through 799 Processing sheet with id= 5, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.726A pdb=" N ILE B 31 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N CYS B 44 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE B 29 " --> pdb=" O CYS B 44 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET B 124 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 92 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 98 through 99 removed outlier: 4.167A pdb=" N PHE B 98 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE B 106 " --> pdb=" O PHE B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= 6 Processing sheet with id= 7, first strand: chain 'B' and resid 762 through 763 removed outlier: 6.854A pdb=" N ASP B 829 " --> pdb=" O SER B 783 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 805 " --> pdb=" O TYR B 780 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 795 through 799 Processing sheet with id= 9, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.726A pdb=" N ILE C 31 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N CYS C 44 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE C 29 " --> pdb=" O CYS C 44 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET C 124 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG C 92 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 98 through 99 removed outlier: 4.167A pdb=" N PHE C 98 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE C 106 " --> pdb=" O PHE C 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'C' and resid 762 through 763 removed outlier: 6.854A pdb=" N ASP C 829 " --> pdb=" O SER C 783 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 805 " --> pdb=" O TYR C 780 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 795 through 799 Processing sheet with id= 13, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.726A pdb=" N ILE D 31 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N CYS D 44 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE D 29 " --> pdb=" O CYS D 44 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET D 124 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG D 92 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 98 through 99 removed outlier: 4.167A pdb=" N PHE D 98 " --> pdb=" O PHE D 106 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE D 106 " --> pdb=" O PHE D 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= 14 Processing sheet with id= 15, first strand: chain 'D' and resid 762 through 763 removed outlier: 6.854A pdb=" N ASP D 829 " --> pdb=" O SER D 783 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 805 " --> pdb=" O TYR D 780 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 795 through 799 856 hydrogen bonds defined for protein. 2388 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 7.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5500 1.34 - 1.46: 2368 1.46 - 1.58: 10008 1.58 - 1.70: 0 1.70 - 1.81: 152 Bond restraints: 18028 Sorted by residual: bond pdb=" N GLY D 800 " pdb=" CA GLY D 800 " ideal model delta sigma weight residual 1.447 1.469 -0.022 7.50e-03 1.78e+04 8.54e+00 bond pdb=" N GLY A 800 " pdb=" CA GLY A 800 " ideal model delta sigma weight residual 1.447 1.469 -0.022 7.50e-03 1.78e+04 8.54e+00 bond pdb=" N GLY B 800 " pdb=" CA GLY B 800 " ideal model delta sigma weight residual 1.447 1.469 -0.022 7.50e-03 1.78e+04 8.54e+00 bond pdb=" N GLY C 800 " pdb=" CA GLY C 800 " ideal model delta sigma weight residual 1.447 1.469 -0.022 7.50e-03 1.78e+04 8.54e+00 bond pdb=" CA PRO D 764 " pdb=" C PRO D 764 " ideal model delta sigma weight residual 1.517 1.544 -0.027 9.30e-03 1.16e+04 8.14e+00 ... (remaining 18023 not shown) Histogram of bond angle deviations from ideal: 100.77 - 107.42: 628 107.42 - 114.07: 9728 114.07 - 120.72: 7556 120.72 - 127.37: 6384 127.37 - 134.02: 176 Bond angle restraints: 24472 Sorted by residual: angle pdb=" N PHE A 29 " pdb=" CA PHE A 29 " pdb=" C PHE A 29 " ideal model delta sigma weight residual 108.60 115.36 -6.76 1.46e+00 4.69e-01 2.15e+01 angle pdb=" N PHE D 29 " pdb=" CA PHE D 29 " pdb=" C PHE D 29 " ideal model delta sigma weight residual 108.60 115.36 -6.76 1.46e+00 4.69e-01 2.15e+01 angle pdb=" N PHE B 29 " pdb=" CA PHE B 29 " pdb=" C PHE B 29 " ideal model delta sigma weight residual 108.60 115.36 -6.76 1.46e+00 4.69e-01 2.15e+01 angle pdb=" N PHE C 29 " pdb=" CA PHE C 29 " pdb=" C PHE C 29 " ideal model delta sigma weight residual 108.60 115.36 -6.76 1.46e+00 4.69e-01 2.15e+01 angle pdb=" N GLY D 800 " pdb=" CA GLY D 800 " pdb=" C GLY D 800 " ideal model delta sigma weight residual 110.21 114.06 -3.85 9.10e-01 1.21e+00 1.79e+01 ... (remaining 24467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.33: 9128 12.33 - 24.66: 1076 24.66 - 36.99: 236 36.99 - 49.32: 84 49.32 - 61.65: 36 Dihedral angle restraints: 10560 sinusoidal: 4064 harmonic: 6496 Sorted by residual: dihedral pdb=" CA HIS A 485 " pdb=" C HIS A 485 " pdb=" N PRO A 486 " pdb=" CA PRO A 486 " ideal model delta harmonic sigma weight residual -180.00 -155.72 -24.28 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA HIS C 485 " pdb=" C HIS C 485 " pdb=" N PRO C 486 " pdb=" CA PRO C 486 " ideal model delta harmonic sigma weight residual -180.00 -155.72 -24.28 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA HIS B 485 " pdb=" C HIS B 485 " pdb=" N PRO B 486 " pdb=" CA PRO B 486 " ideal model delta harmonic sigma weight residual -180.00 -155.72 -24.28 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 10557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1660 0.045 - 0.090: 724 0.090 - 0.135: 256 0.135 - 0.179: 108 0.179 - 0.224: 44 Chirality restraints: 2792 Sorted by residual: chirality pdb=" CA ILE A 804 " pdb=" N ILE A 804 " pdb=" C ILE A 804 " pdb=" CB ILE A 804 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE D 804 " pdb=" N ILE D 804 " pdb=" C ILE D 804 " pdb=" CB ILE D 804 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE C 804 " pdb=" N ILE C 804 " pdb=" C ILE C 804 " pdb=" CB ILE C 804 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 2789 not shown) Planarity restraints: 3068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 425 " 0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO D 426 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 426 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 426 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 425 " 0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO A 426 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 426 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 426 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 425 " -0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO B 426 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 426 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 426 " -0.043 5.00e-02 4.00e+02 ... (remaining 3065 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 32 2.36 - 3.00: 7600 3.00 - 3.63: 24436 3.63 - 4.27: 35148 4.27 - 4.90: 61236 Nonbonded interactions: 128452 Sorted by model distance: nonbonded pdb=" NH1 ARG B 752 " pdb=" CD2 HIS C 771 " model vdw 1.727 3.340 nonbonded pdb=" NH1 ARG A 752 " pdb=" CD2 HIS B 771 " model vdw 1.727 3.340 nonbonded pdb=" NH1 ARG C 752 " pdb=" CD2 HIS D 771 " model vdw 1.727 3.340 nonbonded pdb=" CD2 HIS A 771 " pdb=" NH1 ARG D 752 " model vdw 1.727 3.340 nonbonded pdb=" NH1 ARG B 56 " pdb=" OD2 ASP C 803 " model vdw 1.977 2.520 ... (remaining 128447 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' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 0.030 Extract box with map and model: 7.010 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 47.730 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 : 0.008 0.046 18028 Z= 0.535 Angle : 1.066 6.765 24472 Z= 0.730 Chirality : 0.064 0.224 2792 Planarity : 0.005 0.077 3068 Dihedral : 12.271 61.651 6368 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 1.10 % Allowed : 4.75 % Favored : 94.15 % Rotamer: Outliers : 1.30 % Allowed : 3.46 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.14), residues: 2188 helix: -2.33 (0.11), residues: 1092 sheet: -3.72 (0.35), residues: 112 loop : -2.44 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 412 HIS 0.003 0.001 HIS A 402 PHE 0.013 0.002 PHE A 494 TYR 0.017 0.002 TYR B 427 ARG 0.003 0.000 ARG C 541 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 770 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.9615 (mt0) cc_final: 0.9373 (mm110) REVERT: A 75 GLN cc_start: 0.6506 (mp10) cc_final: 0.6017 (mp10) REVERT: A 92 ARG cc_start: 0.5517 (OUTLIER) cc_final: 0.5238 (mtp-110) REVERT: A 95 GLU cc_start: 0.8933 (tt0) cc_final: 0.8163 (pp20) REVERT: A 411 ASP cc_start: 0.9641 (m-30) cc_final: 0.9414 (m-30) REVERT: A 424 PHE cc_start: 0.9435 (m-80) cc_final: 0.9141 (m-80) REVERT: A 459 VAL cc_start: 0.9565 (t) cc_final: 0.9152 (p) REVERT: A 462 MET cc_start: 0.9592 (mmm) cc_final: 0.9311 (tpt) REVERT: A 463 PHE cc_start: 0.9733 (m-80) cc_final: 0.9148 (m-80) REVERT: A 501 ASP cc_start: 0.9233 (m-30) cc_final: 0.9032 (p0) REVERT: A 574 MET cc_start: 0.7798 (mtt) cc_final: 0.7598 (mmt) REVERT: A 588 ASN cc_start: 0.9175 (t0) cc_final: 0.8725 (t0) REVERT: A 638 LYS cc_start: 0.9817 (mttt) cc_final: 0.9481 (mmtt) REVERT: A 641 SER cc_start: 0.9740 (t) cc_final: 0.9327 (p) REVERT: A 645 MET cc_start: 0.9697 (mtp) cc_final: 0.9277 (mtp) REVERT: A 656 PHE cc_start: 0.9635 (m-80) cc_final: 0.9349 (m-10) REVERT: A 676 GLN cc_start: 0.9666 (mt0) cc_final: 0.9417 (pt0) REVERT: A 681 ARG cc_start: 0.9699 (mtt180) cc_final: 0.9228 (tpp-160) REVERT: A 691 ASN cc_start: 0.9755 (m-40) cc_final: 0.9489 (t0) REVERT: A 697 LEU cc_start: 0.9955 (mt) cc_final: 0.9709 (pp) REVERT: A 698 GLU cc_start: 0.9708 (mt-10) cc_final: 0.9431 (pt0) REVERT: A 705 TRP cc_start: 0.9424 (t60) cc_final: 0.9195 (t60) REVERT: A 723 CYS cc_start: 0.9609 (m) cc_final: 0.9303 (p) REVERT: A 757 LYS cc_start: 0.9312 (mttt) cc_final: 0.9068 (mtpt) REVERT: A 768 THR cc_start: 0.9321 (p) cc_final: 0.9084 (t) REVERT: A 781 PHE cc_start: 0.9902 (m-80) cc_final: 0.9651 (m-80) REVERT: A 782 ILE cc_start: 0.9849 (mt) cc_final: 0.9566 (tp) REVERT: A 801 LYS cc_start: 0.9122 (mttt) cc_final: 0.8910 (mptt) REVERT: A 817 LYS cc_start: 0.9583 (mttt) cc_final: 0.9366 (mmmt) REVERT: A 827 TYR cc_start: 0.8780 (m-80) cc_final: 0.8560 (m-80) REVERT: A 832 LYS cc_start: 0.9624 (tttt) cc_final: 0.9289 (mtpp) REVERT: A 861 ASN cc_start: 0.9364 (t0) cc_final: 0.9032 (t0) REVERT: B 61 GLN cc_start: 0.9647 (mt0) cc_final: 0.9383 (mm110) REVERT: B 92 ARG cc_start: 0.5735 (OUTLIER) cc_final: 0.5523 (mtp-110) REVERT: B 95 GLU cc_start: 0.8895 (tt0) cc_final: 0.8244 (pp20) REVERT: B 424 PHE cc_start: 0.9385 (m-80) cc_final: 0.9090 (m-80) REVERT: B 459 VAL cc_start: 0.9592 (t) cc_final: 0.9201 (p) REVERT: B 462 MET cc_start: 0.9592 (mmm) cc_final: 0.9318 (tpt) REVERT: B 463 PHE cc_start: 0.9740 (m-80) cc_final: 0.9169 (m-80) REVERT: B 501 ASP cc_start: 0.9199 (m-30) cc_final: 0.8983 (p0) REVERT: B 588 ASN cc_start: 0.9197 (t0) cc_final: 0.8763 (t0) REVERT: B 629 ASN cc_start: 0.7614 (m110) cc_final: 0.6976 (m110) REVERT: B 638 LYS cc_start: 0.9804 (mttt) cc_final: 0.9501 (mmtt) REVERT: B 641 SER cc_start: 0.9744 (t) cc_final: 0.9346 (p) REVERT: B 645 MET cc_start: 0.9696 (mtp) cc_final: 0.9311 (mtp) REVERT: B 656 PHE cc_start: 0.9638 (m-80) cc_final: 0.9367 (m-80) REVERT: B 676 GLN cc_start: 0.9662 (mt0) cc_final: 0.9420 (pt0) REVERT: B 681 ARG cc_start: 0.9710 (mtt180) cc_final: 0.9235 (tpp-160) REVERT: B 691 ASN cc_start: 0.9738 (m-40) cc_final: 0.9458 (t0) REVERT: B 697 LEU cc_start: 0.9950 (mt) cc_final: 0.9699 (pp) REVERT: B 698 GLU cc_start: 0.9687 (mt-10) cc_final: 0.9419 (pt0) REVERT: B 705 TRP cc_start: 0.9407 (t60) cc_final: 0.9156 (t60) REVERT: B 723 CYS cc_start: 0.9588 (m) cc_final: 0.9242 (p) REVERT: B 758 PHE cc_start: 0.9633 (m-80) cc_final: 0.9168 (m-80) REVERT: B 768 THR cc_start: 0.9329 (p) cc_final: 0.9061 (t) REVERT: B 776 LEU cc_start: 0.9620 (mt) cc_final: 0.9401 (tt) REVERT: B 781 PHE cc_start: 0.9906 (m-80) cc_final: 0.9631 (m-80) REVERT: B 782 ILE cc_start: 0.9834 (mt) cc_final: 0.9617 (tp) REVERT: B 827 TYR cc_start: 0.8698 (m-80) cc_final: 0.8477 (m-80) REVERT: B 832 LYS cc_start: 0.9637 (tttt) cc_final: 0.9412 (tttm) REVERT: B 861 ASN cc_start: 0.9373 (t0) cc_final: 0.9037 (t0) REVERT: C 8 VAL cc_start: 0.9636 (m) cc_final: 0.9369 (p) REVERT: C 61 GLN cc_start: 0.9637 (mt0) cc_final: 0.9364 (mm110) REVERT: C 95 GLU cc_start: 0.8860 (tt0) cc_final: 0.8168 (tm-30) REVERT: C 420 TYR cc_start: 0.9471 (t80) cc_final: 0.9221 (t80) REVERT: C 424 PHE cc_start: 0.9355 (m-80) cc_final: 0.9062 (m-80) REVERT: C 459 VAL cc_start: 0.9607 (t) cc_final: 0.9295 (p) REVERT: C 463 PHE cc_start: 0.9733 (m-80) cc_final: 0.8857 (m-80) REVERT: C 588 ASN cc_start: 0.9146 (t0) cc_final: 0.8672 (t0) REVERT: C 629 ASN cc_start: 0.7589 (m110) cc_final: 0.6896 (m110) REVERT: C 643 CYS cc_start: 0.9630 (t) cc_final: 0.9417 (t) REVERT: C 645 MET cc_start: 0.9734 (mtp) cc_final: 0.9253 (mtp) REVERT: C 656 PHE cc_start: 0.9620 (m-80) cc_final: 0.9387 (m-10) REVERT: C 676 GLN cc_start: 0.9660 (mt0) cc_final: 0.9430 (pt0) REVERT: C 681 ARG cc_start: 0.9701 (mtt180) cc_final: 0.9208 (tpp-160) REVERT: C 682 GLU cc_start: 0.9618 (mt-10) cc_final: 0.9410 (mt-10) REVERT: C 691 ASN cc_start: 0.9745 (m-40) cc_final: 0.9478 (t0) REVERT: C 697 LEU cc_start: 0.9953 (mt) cc_final: 0.9710 (pp) REVERT: C 698 GLU cc_start: 0.9684 (mt-10) cc_final: 0.9413 (pt0) REVERT: C 705 TRP cc_start: 0.9434 (t60) cc_final: 0.9200 (t60) REVERT: C 723 CYS cc_start: 0.9542 (m) cc_final: 0.9284 (p) REVERT: C 757 LYS cc_start: 0.9289 (mttt) cc_final: 0.9053 (mtpt) REVERT: C 768 THR cc_start: 0.9302 (p) cc_final: 0.8911 (t) REVERT: C 781 PHE cc_start: 0.9884 (m-80) cc_final: 0.9662 (m-80) REVERT: C 832 LYS cc_start: 0.9602 (tttt) cc_final: 0.9260 (mtpp) REVERT: C 861 ASN cc_start: 0.9387 (t0) cc_final: 0.9060 (t0) REVERT: D 8 VAL cc_start: 0.9613 (m) cc_final: 0.9309 (p) REVERT: D 61 GLN cc_start: 0.9607 (mt0) cc_final: 0.9356 (mm110) REVERT: D 75 GLN cc_start: 0.6441 (mp10) cc_final: 0.5952 (mp10) REVERT: D 92 ARG cc_start: 0.5493 (OUTLIER) cc_final: 0.5287 (mtp-110) REVERT: D 95 GLU cc_start: 0.8890 (tt0) cc_final: 0.8108 (pp20) REVERT: D 424 PHE cc_start: 0.9396 (m-80) cc_final: 0.9088 (m-80) REVERT: D 459 VAL cc_start: 0.9576 (t) cc_final: 0.9052 (p) REVERT: D 462 MET cc_start: 0.9564 (mmm) cc_final: 0.9222 (tpt) REVERT: D 463 PHE cc_start: 0.9728 (m-80) cc_final: 0.8956 (m-80) REVERT: D 574 MET cc_start: 0.7918 (mtt) cc_final: 0.7502 (mmt) REVERT: D 588 ASN cc_start: 0.9128 (t0) cc_final: 0.8684 (t0) REVERT: D 638 LYS cc_start: 0.9790 (mttt) cc_final: 0.9548 (mmmm) REVERT: D 651 MET cc_start: 0.9540 (tpp) cc_final: 0.9289 (tpp) REVERT: D 656 PHE cc_start: 0.9618 (m-80) cc_final: 0.9197 (m-80) REVERT: D 676 GLN cc_start: 0.9668 (mt0) cc_final: 0.9429 (pt0) REVERT: D 678 LEU cc_start: 0.9644 (mt) cc_final: 0.9440 (pp) REVERT: D 681 ARG cc_start: 0.9690 (mtt180) cc_final: 0.9222 (tpp-160) REVERT: D 691 ASN cc_start: 0.9760 (m-40) cc_final: 0.9490 (t0) REVERT: D 697 LEU cc_start: 0.9956 (mt) cc_final: 0.9706 (pp) REVERT: D 698 GLU cc_start: 0.9699 (mt-10) cc_final: 0.9393 (pt0) REVERT: D 705 TRP cc_start: 0.9450 (t60) cc_final: 0.9226 (t60) REVERT: D 723 CYS cc_start: 0.9562 (m) cc_final: 0.9288 (p) REVERT: D 741 LYS cc_start: 0.9745 (mttt) cc_final: 0.9524 (pttp) REVERT: D 757 LYS cc_start: 0.9303 (mttt) cc_final: 0.9070 (mtpt) REVERT: D 768 THR cc_start: 0.9303 (p) cc_final: 0.8961 (t) REVERT: D 782 ILE cc_start: 0.9818 (mt) cc_final: 0.9613 (tp) REVERT: D 817 LYS cc_start: 0.9611 (mttt) cc_final: 0.9403 (mmmt) REVERT: D 832 LYS cc_start: 0.9593 (tttt) cc_final: 0.9202 (mtpp) REVERT: D 861 ASN cc_start: 0.9366 (t0) cc_final: 0.9005 (t0) outliers start: 24 outliers final: 8 residues processed: 786 average time/residue: 0.3333 time to fit residues: 376.3331 Evaluate side-chains 522 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 511 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 597 TYR Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 597 TYR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 597 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 20.0000 chunk 166 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 66 optimal weight: 40.0000 chunk 104 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 chunk 199 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 739 HIS A 831 HIS B 831 HIS C 470 ASN C 739 HIS C 831 HIS C 834 HIS D 470 ASN D 739 HIS D 831 HIS D 834 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18028 Z= 0.216 Angle : 0.773 11.782 24472 Z= 0.384 Chirality : 0.046 0.155 2792 Planarity : 0.005 0.046 3068 Dihedral : 6.013 58.012 2448 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.66 % Favored : 96.16 % Rotamer: Outliers : 3.08 % Allowed : 14.83 % Favored : 82.09 % 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: -1.93 (0.17), residues: 2188 helix: -0.55 (0.15), residues: 1104 sheet: -2.74 (0.29), residues: 180 loop : -1.77 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 563 HIS 0.014 0.002 HIS D 771 PHE 0.020 0.002 PHE C 686 TYR 0.012 0.001 TYR A 545 ARG 0.011 0.001 ARG D 752 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 558 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 PHE cc_start: 0.9438 (m-80) cc_final: 0.9165 (m-80) REVERT: A 459 VAL cc_start: 0.9817 (t) cc_final: 0.9397 (t) REVERT: A 462 MET cc_start: 0.9698 (mmm) cc_final: 0.9492 (tpt) REVERT: A 463 PHE cc_start: 0.9640 (m-80) cc_final: 0.9307 (m-80) REVERT: A 574 MET cc_start: 0.7890 (mtt) cc_final: 0.7642 (mmt) REVERT: A 638 LYS cc_start: 0.9838 (mttt) cc_final: 0.9527 (mmtm) REVERT: A 640 PHE cc_start: 0.9400 (t80) cc_final: 0.9070 (t80) REVERT: A 641 SER cc_start: 0.9760 (t) cc_final: 0.9392 (p) REVERT: A 645 MET cc_start: 0.9589 (mtp) cc_final: 0.9119 (ttm) REVERT: A 656 PHE cc_start: 0.9716 (m-80) cc_final: 0.9420 (m-10) REVERT: A 681 ARG cc_start: 0.9658 (mtt180) cc_final: 0.9419 (tpp-160) REVERT: A 691 ASN cc_start: 0.9773 (m-40) cc_final: 0.9546 (t0) REVERT: A 698 GLU cc_start: 0.9701 (mt-10) cc_final: 0.9372 (pt0) REVERT: A 705 TRP cc_start: 0.9387 (t60) cc_final: 0.9114 (t60) REVERT: A 748 LYS cc_start: 0.9884 (mttt) cc_final: 0.9669 (tptp) REVERT: A 757 LYS cc_start: 0.9411 (mttt) cc_final: 0.9096 (mtmt) REVERT: A 758 PHE cc_start: 0.9393 (m-80) cc_final: 0.9002 (m-80) REVERT: A 781 PHE cc_start: 0.9905 (m-80) cc_final: 0.9602 (m-80) REVERT: A 801 LYS cc_start: 0.9108 (mttt) cc_final: 0.8899 (mptt) REVERT: B 424 PHE cc_start: 0.9398 (m-80) cc_final: 0.9123 (m-80) REVERT: B 459 VAL cc_start: 0.9843 (t) cc_final: 0.9477 (t) REVERT: B 463 PHE cc_start: 0.9619 (m-80) cc_final: 0.8653 (m-80) REVERT: B 501 ASP cc_start: 0.8745 (m-30) cc_final: 0.8278 (p0) REVERT: B 629 ASN cc_start: 0.7545 (m110) cc_final: 0.6945 (m110) REVERT: B 638 LYS cc_start: 0.9839 (mttt) cc_final: 0.9327 (mmtm) REVERT: B 640 PHE cc_start: 0.9403 (t80) cc_final: 0.9077 (t80) REVERT: B 641 SER cc_start: 0.9753 (t) cc_final: 0.9362 (p) REVERT: B 642 ILE cc_start: 0.9407 (mm) cc_final: 0.8859 (mm) REVERT: B 645 MET cc_start: 0.9574 (mtp) cc_final: 0.9325 (mtp) REVERT: B 681 ARG cc_start: 0.9660 (mtt180) cc_final: 0.9404 (tpp-160) REVERT: B 691 ASN cc_start: 0.9762 (m-40) cc_final: 0.9514 (t0) REVERT: B 698 GLU cc_start: 0.9678 (mt-10) cc_final: 0.9426 (pt0) REVERT: B 705 TRP cc_start: 0.9367 (t60) cc_final: 0.9104 (t60) REVERT: B 758 PHE cc_start: 0.9304 (m-80) cc_final: 0.8962 (m-80) REVERT: B 781 PHE cc_start: 0.9906 (m-80) cc_final: 0.9625 (m-80) REVERT: C 424 PHE cc_start: 0.9359 (m-80) cc_final: 0.9085 (m-80) REVERT: C 459 VAL cc_start: 0.9841 (t) cc_final: 0.9553 (p) REVERT: C 463 PHE cc_start: 0.9347 (m-80) cc_final: 0.8968 (m-80) REVERT: C 629 ASN cc_start: 0.7469 (m110) cc_final: 0.6743 (m110) REVERT: C 638 LYS cc_start: 0.9728 (mmtt) cc_final: 0.9474 (mmtp) REVERT: C 640 PHE cc_start: 0.9328 (t80) cc_final: 0.8989 (t80) REVERT: C 691 ASN cc_start: 0.9772 (m-40) cc_final: 0.9543 (t0) REVERT: C 698 GLU cc_start: 0.9677 (mt-10) cc_final: 0.9360 (pt0) REVERT: C 705 TRP cc_start: 0.9384 (t60) cc_final: 0.9122 (t60) REVERT: C 757 LYS cc_start: 0.9391 (mttt) cc_final: 0.9129 (mtmt) REVERT: C 781 PHE cc_start: 0.9858 (m-80) cc_final: 0.9632 (m-80) REVERT: C 830 LEU cc_start: 0.9851 (pt) cc_final: 0.9450 (tt) REVERT: D 424 PHE cc_start: 0.9397 (m-80) cc_final: 0.9123 (m-80) REVERT: D 459 VAL cc_start: 0.9793 (t) cc_final: 0.9350 (t) REVERT: D 462 MET cc_start: 0.9652 (mmm) cc_final: 0.9274 (tpt) REVERT: D 463 PHE cc_start: 0.9362 (m-80) cc_final: 0.9037 (m-80) REVERT: D 617 PHE cc_start: 0.9730 (t80) cc_final: 0.9494 (t80) REVERT: D 638 LYS cc_start: 0.9883 (mttt) cc_final: 0.9524 (mmtm) REVERT: D 640 PHE cc_start: 0.9422 (t80) cc_final: 0.8997 (t80) REVERT: D 641 SER cc_start: 0.9842 (t) cc_final: 0.9559 (p) REVERT: D 656 PHE cc_start: 0.9687 (m-80) cc_final: 0.9184 (m-10) REVERT: D 681 ARG cc_start: 0.9618 (mtt180) cc_final: 0.9400 (tpp-160) REVERT: D 691 ASN cc_start: 0.9790 (m-40) cc_final: 0.9590 (t0) REVERT: D 698 GLU cc_start: 0.9675 (mt-10) cc_final: 0.9411 (pt0) REVERT: D 705 TRP cc_start: 0.9406 (t60) cc_final: 0.9162 (t60) REVERT: D 757 LYS cc_start: 0.9409 (mttt) cc_final: 0.8995 (mtmt) REVERT: D 775 LEU cc_start: 0.9434 (tp) cc_final: 0.9218 (tp) REVERT: D 827 TYR cc_start: 0.8752 (m-80) cc_final: 0.8356 (m-80) outliers start: 57 outliers final: 36 residues processed: 597 average time/residue: 0.3221 time to fit residues: 277.3216 Evaluate side-chains 500 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 464 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 760 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 660 SER Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 30.0000 chunk 62 optimal weight: 0.9980 chunk 166 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 55 optimal weight: 70.0000 chunk 200 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 178 optimal weight: 20.0000 chunk 198 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 160 optimal weight: 40.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN B 470 ASN ** B 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18028 Z= 0.198 Angle : 0.729 12.049 24472 Z= 0.354 Chirality : 0.046 0.264 2792 Planarity : 0.004 0.064 3068 Dihedral : 5.205 31.251 2428 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.70 % Favored : 96.12 % Rotamer: Outliers : 3.30 % Allowed : 17.97 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.18), residues: 2188 helix: -0.22 (0.15), residues: 1124 sheet: -2.29 (0.32), residues: 180 loop : -1.40 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 705 HIS 0.019 0.002 HIS D 70 PHE 0.023 0.002 PHE B 557 TYR 0.012 0.001 TYR A 427 ARG 0.008 0.001 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 494 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 PHE cc_start: 0.9449 (m-80) cc_final: 0.9160 (m-80) REVERT: A 459 VAL cc_start: 0.9783 (t) cc_final: 0.9448 (t) REVERT: A 463 PHE cc_start: 0.9646 (m-80) cc_final: 0.9187 (m-80) REVERT: A 638 LYS cc_start: 0.9879 (mttt) cc_final: 0.9530 (mmtm) REVERT: A 640 PHE cc_start: 0.9446 (t80) cc_final: 0.9038 (t80) REVERT: A 641 SER cc_start: 0.9816 (t) cc_final: 0.9426 (p) REVERT: A 645 MET cc_start: 0.9547 (mtp) cc_final: 0.9259 (ttm) REVERT: A 656 PHE cc_start: 0.9685 (m-80) cc_final: 0.9360 (m-10) REVERT: A 748 LYS cc_start: 0.9880 (mttt) cc_final: 0.9626 (tptp) REVERT: A 757 LYS cc_start: 0.9321 (mttt) cc_final: 0.8948 (mtmt) REVERT: A 758 PHE cc_start: 0.9259 (m-80) cc_final: 0.8854 (m-80) REVERT: A 833 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9155 (mm) REVERT: B 7 HIS cc_start: 0.7254 (t70) cc_final: 0.6686 (t70) REVERT: B 424 PHE cc_start: 0.9415 (m-80) cc_final: 0.9109 (m-80) REVERT: B 459 VAL cc_start: 0.9787 (t) cc_final: 0.9489 (t) REVERT: B 463 PHE cc_start: 0.9153 (m-80) cc_final: 0.8614 (m-80) REVERT: B 629 ASN cc_start: 0.6848 (m110) cc_final: 0.6540 (m110) REVERT: B 638 LYS cc_start: 0.9833 (mttt) cc_final: 0.9529 (mmtm) REVERT: B 640 PHE cc_start: 0.9412 (t80) cc_final: 0.9187 (t80) REVERT: B 641 SER cc_start: 0.9743 (t) cc_final: 0.9417 (p) REVERT: B 656 PHE cc_start: 0.9610 (m-10) cc_final: 0.9396 (m-10) REVERT: B 681 ARG cc_start: 0.9658 (mtt180) cc_final: 0.9417 (tpp-160) REVERT: B 691 ASN cc_start: 0.9787 (m-40) cc_final: 0.9580 (t0) REVERT: B 698 GLU cc_start: 0.9670 (mt-10) cc_final: 0.9442 (pt0) REVERT: B 758 PHE cc_start: 0.9233 (m-80) cc_final: 0.8833 (m-80) REVERT: C 424 PHE cc_start: 0.9374 (m-80) cc_final: 0.9065 (m-80) REVERT: C 629 ASN cc_start: 0.6491 (m110) cc_final: 0.5939 (m110) REVERT: C 645 MET cc_start: 0.9670 (mtp) cc_final: 0.9263 (ttm) REVERT: C 656 PHE cc_start: 0.9577 (m-10) cc_final: 0.9375 (m-10) REVERT: C 681 ARG cc_start: 0.9588 (mmm160) cc_final: 0.9203 (tpp-160) REVERT: C 699 GLU cc_start: 0.9708 (mt-10) cc_final: 0.9470 (pp20) REVERT: C 757 LYS cc_start: 0.9257 (mttt) cc_final: 0.8856 (mtmt) REVERT: C 758 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8922 (m-80) REVERT: C 833 ILE cc_start: 0.9502 (OUTLIER) cc_final: 0.9287 (mm) REVERT: D 7 HIS cc_start: 0.7332 (t70) cc_final: 0.7020 (t70) REVERT: D 424 PHE cc_start: 0.9408 (m-80) cc_final: 0.9106 (m-80) REVERT: D 617 PHE cc_start: 0.9757 (t80) cc_final: 0.9495 (t80) REVERT: D 638 LYS cc_start: 0.9879 (mttt) cc_final: 0.9506 (mmtm) REVERT: D 640 PHE cc_start: 0.9476 (t80) cc_final: 0.9106 (t80) REVERT: D 641 SER cc_start: 0.9870 (t) cc_final: 0.9593 (p) REVERT: D 656 PHE cc_start: 0.9573 (m-80) cc_final: 0.9290 (m-10) REVERT: D 744 ARG cc_start: 0.9680 (ptp-170) cc_final: 0.9362 (mmp80) REVERT: D 758 PHE cc_start: 0.9191 (m-80) cc_final: 0.8949 (m-80) REVERT: D 830 LEU cc_start: 0.9865 (pt) cc_final: 0.9481 (tt) REVERT: D 832 LYS cc_start: 0.9556 (OUTLIER) cc_final: 0.9346 (mtpp) REVERT: D 833 ILE cc_start: 0.9630 (OUTLIER) cc_final: 0.9383 (mm) outliers start: 61 outliers final: 44 residues processed: 529 average time/residue: 0.2944 time to fit residues: 232.3743 Evaluate side-chains 488 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 439 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 829 ASP Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 619 PHE Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 833 ILE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 833 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 0.0770 chunk 150 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 95 optimal weight: 20.0000 chunk 134 optimal weight: 50.0000 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 50.0000 chunk 104 optimal weight: 30.0000 chunk 190 optimal weight: 6.9990 chunk 57 optimal weight: 50.0000 overall best weight: 11.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 834 HIS ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18028 Z= 0.261 Angle : 0.730 11.890 24472 Z= 0.367 Chirality : 0.045 0.172 2792 Planarity : 0.004 0.046 3068 Dihedral : 5.102 21.008 2424 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.11 % Favored : 95.70 % Rotamer: Outliers : 4.38 % Allowed : 20.18 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.18), residues: 2188 helix: 0.15 (0.16), residues: 1072 sheet: -2.52 (0.26), residues: 276 loop : -1.02 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 705 HIS 0.018 0.002 HIS B 70 PHE 0.024 0.002 PHE D 557 TYR 0.016 0.002 TYR B 427 ARG 0.007 0.001 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 468 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 PHE cc_start: 0.9503 (m-80) cc_final: 0.9217 (m-80) REVERT: A 463 PHE cc_start: 0.9674 (m-80) cc_final: 0.9151 (m-80) REVERT: A 638 LYS cc_start: 0.9880 (mttt) cc_final: 0.9630 (mttp) REVERT: A 641 SER cc_start: 0.9839 (t) cc_final: 0.9545 (p) REVERT: A 645 MET cc_start: 0.9553 (mtp) cc_final: 0.9114 (ttm) REVERT: A 656 PHE cc_start: 0.9611 (m-80) cc_final: 0.9324 (m-10) REVERT: A 681 ARG cc_start: 0.9659 (mmm160) cc_final: 0.9270 (tpp-160) REVERT: A 705 TRP cc_start: 0.9393 (t60) cc_final: 0.9187 (t60) REVERT: A 757 LYS cc_start: 0.9376 (mttt) cc_final: 0.8878 (mtmt) REVERT: A 758 PHE cc_start: 0.9092 (m-80) cc_final: 0.8771 (m-80) REVERT: B 7 HIS cc_start: 0.7503 (t70) cc_final: 0.7126 (t70) REVERT: B 424 PHE cc_start: 0.9466 (m-80) cc_final: 0.9179 (m-80) REVERT: B 462 MET cc_start: 0.9603 (tpt) cc_final: 0.9311 (tpt) REVERT: B 619 PHE cc_start: 0.9823 (OUTLIER) cc_final: 0.9217 (t80) REVERT: B 640 PHE cc_start: 0.9487 (t80) cc_final: 0.9062 (t80) REVERT: B 641 SER cc_start: 0.9819 (t) cc_final: 0.9514 (p) REVERT: B 758 PHE cc_start: 0.9031 (m-80) cc_final: 0.8599 (m-80) REVERT: B 832 LYS cc_start: 0.9645 (tttt) cc_final: 0.9421 (mtpp) REVERT: C 127 LEU cc_start: 0.9477 (tp) cc_final: 0.9264 (tp) REVERT: C 424 PHE cc_start: 0.9416 (m-80) cc_final: 0.9116 (m-80) REVERT: C 640 PHE cc_start: 0.9450 (t80) cc_final: 0.9071 (t80) REVERT: C 645 MET cc_start: 0.9645 (mtp) cc_final: 0.9349 (ttm) REVERT: C 705 TRP cc_start: 0.9404 (t60) cc_final: 0.9200 (t60) REVERT: C 758 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8625 (m-80) REVERT: C 830 LEU cc_start: 0.9848 (pt) cc_final: 0.9395 (tt) REVERT: D 7 HIS cc_start: 0.7472 (t70) cc_final: 0.7254 (t70) REVERT: D 424 PHE cc_start: 0.9442 (m-80) cc_final: 0.9151 (m-80) REVERT: D 463 PHE cc_start: 0.9608 (m-80) cc_final: 0.9062 (m-80) REVERT: D 638 LYS cc_start: 0.9884 (mttt) cc_final: 0.9540 (mmtm) REVERT: D 641 SER cc_start: 0.9875 (t) cc_final: 0.9629 (p) REVERT: D 744 ARG cc_start: 0.9710 (ptp-170) cc_final: 0.9373 (mmp80) REVERT: D 782 ILE cc_start: 0.9781 (mp) cc_final: 0.9551 (tp) REVERT: D 830 LEU cc_start: 0.9839 (pt) cc_final: 0.9538 (tt) REVERT: D 832 LYS cc_start: 0.9589 (OUTLIER) cc_final: 0.9333 (tttm) REVERT: D 833 ILE cc_start: 0.9667 (OUTLIER) cc_final: 0.9281 (mm) outliers start: 81 outliers final: 63 residues processed: 513 average time/residue: 0.2905 time to fit residues: 222.6634 Evaluate side-chains 502 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 435 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 829 ASP Chi-restraints excluded: chain B residue 836 ASP Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 838 LEU Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 660 SER Chi-restraints excluded: chain D residue 714 ASN Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 844 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 158 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 181 optimal weight: 30.0000 chunk 146 optimal weight: 9.9990 chunk 0 optimal weight: 70.0000 chunk 108 optimal weight: 40.0000 chunk 190 optimal weight: 30.0000 chunk 53 optimal weight: 5.9990 overall best weight: 8.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 695 GLN ** B 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 GLN ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18028 Z= 0.220 Angle : 0.742 13.066 24472 Z= 0.362 Chirality : 0.046 0.191 2792 Planarity : 0.004 0.042 3068 Dihedral : 5.083 21.915 2424 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.98 % Favored : 95.84 % Rotamer: Outliers : 4.22 % Allowed : 22.94 % Favored : 72.84 % 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: -0.80 (0.18), residues: 2188 helix: 0.15 (0.16), residues: 1076 sheet: -1.82 (0.29), residues: 228 loop : -0.86 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 705 HIS 0.016 0.001 HIS B 70 PHE 0.026 0.002 PHE D 640 TYR 0.013 0.001 TYR C 427 ARG 0.011 0.001 ARG C 681 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 464 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 PHE cc_start: 0.9513 (m-80) cc_final: 0.9222 (m-80) REVERT: A 459 VAL cc_start: 0.9737 (t) cc_final: 0.9402 (p) REVERT: A 462 MET cc_start: 0.9633 (tpt) cc_final: 0.9411 (tpt) REVERT: A 463 PHE cc_start: 0.9519 (m-80) cc_final: 0.9040 (m-80) REVERT: A 640 PHE cc_start: 0.9468 (t80) cc_final: 0.9109 (t80) REVERT: A 641 SER cc_start: 0.9839 (t) cc_final: 0.9488 (p) REVERT: A 645 MET cc_start: 0.9511 (mtp) cc_final: 0.9134 (ttm) REVERT: A 656 PHE cc_start: 0.9585 (m-80) cc_final: 0.9251 (m-10) REVERT: A 681 ARG cc_start: 0.9621 (mmm160) cc_final: 0.9251 (tpp-160) REVERT: A 705 TRP cc_start: 0.9336 (t60) cc_final: 0.9121 (t60) REVERT: A 782 ILE cc_start: 0.9712 (mp) cc_final: 0.9362 (tp) REVERT: B 7 HIS cc_start: 0.7486 (t70) cc_final: 0.7068 (t70) REVERT: B 60 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8971 (pmm) REVERT: B 127 LEU cc_start: 0.9333 (tp) cc_final: 0.8949 (tp) REVERT: B 424 PHE cc_start: 0.9485 (m-80) cc_final: 0.9196 (m-80) REVERT: B 462 MET cc_start: 0.9604 (tpt) cc_final: 0.9293 (tpt) REVERT: B 619 PHE cc_start: 0.9807 (OUTLIER) cc_final: 0.9242 (t80) REVERT: B 623 THR cc_start: 0.9574 (OUTLIER) cc_final: 0.8239 (p) REVERT: B 638 LYS cc_start: 0.9869 (mttt) cc_final: 0.9560 (mmtm) REVERT: B 640 PHE cc_start: 0.9487 (t80) cc_final: 0.9038 (t80) REVERT: B 641 SER cc_start: 0.9839 (t) cc_final: 0.9521 (p) REVERT: B 758 PHE cc_start: 0.9054 (m-80) cc_final: 0.8750 (m-80) REVERT: B 782 ILE cc_start: 0.9752 (mp) cc_final: 0.9381 (tp) REVERT: C 424 PHE cc_start: 0.9449 (m-80) cc_final: 0.9142 (m-80) REVERT: C 640 PHE cc_start: 0.9469 (t80) cc_final: 0.9049 (t80) REVERT: C 645 MET cc_start: 0.9629 (mtp) cc_final: 0.9361 (ttm) REVERT: C 758 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: C 830 LEU cc_start: 0.9848 (pt) cc_final: 0.9403 (tt) REVERT: C 832 LYS cc_start: 0.9633 (tttt) cc_final: 0.9358 (tttm) REVERT: D 127 LEU cc_start: 0.9383 (tp) cc_final: 0.9077 (tp) REVERT: D 424 PHE cc_start: 0.9475 (m-80) cc_final: 0.9171 (m-80) REVERT: D 623 THR cc_start: 0.9509 (OUTLIER) cc_final: 0.8324 (p) REVERT: D 638 LYS cc_start: 0.9883 (mttt) cc_final: 0.9607 (mtpp) REVERT: D 640 PHE cc_start: 0.9505 (t80) cc_final: 0.9086 (t80) REVERT: D 641 SER cc_start: 0.9874 (t) cc_final: 0.9660 (p) REVERT: D 681 ARG cc_start: 0.9597 (mmm160) cc_final: 0.9225 (tpp-160) REVERT: D 782 ILE cc_start: 0.9781 (mp) cc_final: 0.9376 (tp) REVERT: D 801 LYS cc_start: 0.9299 (mttp) cc_final: 0.9091 (mmtm) outliers start: 78 outliers final: 60 residues processed: 505 average time/residue: 0.2934 time to fit residues: 220.5976 Evaluate side-chains 500 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 435 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 829 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 660 SER Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 720 PHE Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 844 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 42 optimal weight: 40.0000 chunk 124 optimal weight: 6.9990 chunk 52 optimal weight: 30.0000 chunk 212 optimal weight: 50.0000 chunk 176 optimal weight: 0.0770 chunk 98 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 111 optimal weight: 0.5980 overall best weight: 3.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18028 Z= 0.201 Angle : 0.759 12.770 24472 Z= 0.365 Chirality : 0.046 0.232 2792 Planarity : 0.004 0.039 3068 Dihedral : 4.971 21.283 2424 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.75 % Favored : 96.07 % Rotamer: Outliers : 4.38 % Allowed : 24.95 % Favored : 70.67 % 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: -0.93 (0.18), residues: 2188 helix: -0.07 (0.15), residues: 1104 sheet: -1.69 (0.31), residues: 200 loop : -0.89 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 705 HIS 0.007 0.001 HIS B 70 PHE 0.027 0.002 PHE A 551 TYR 0.026 0.001 TYR D 652 ARG 0.019 0.001 ARG B 681 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 458 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.9527 (tp) cc_final: 0.9212 (tp) REVERT: A 424 PHE cc_start: 0.9518 (m-80) cc_final: 0.9221 (m-80) REVERT: A 459 VAL cc_start: 0.9740 (t) cc_final: 0.9394 (p) REVERT: A 462 MET cc_start: 0.9644 (tpt) cc_final: 0.9428 (tpt) REVERT: A 463 PHE cc_start: 0.9514 (m-80) cc_final: 0.9024 (m-80) REVERT: A 640 PHE cc_start: 0.9443 (t80) cc_final: 0.9029 (t80) REVERT: A 641 SER cc_start: 0.9849 (t) cc_final: 0.9490 (p) REVERT: A 645 MET cc_start: 0.9507 (mtp) cc_final: 0.9224 (ttm) REVERT: A 651 MET cc_start: 0.9748 (tpp) cc_final: 0.9547 (mmm) REVERT: A 656 PHE cc_start: 0.9491 (m-80) cc_final: 0.9016 (m-80) REVERT: A 681 ARG cc_start: 0.9600 (mmm160) cc_final: 0.9220 (tpp-160) REVERT: A 695 GLN cc_start: 0.9745 (pt0) cc_final: 0.9372 (tp-100) REVERT: A 705 TRP cc_start: 0.9332 (t60) cc_final: 0.9129 (t60) REVERT: A 758 PHE cc_start: 0.9510 (m-80) cc_final: 0.9198 (m-80) REVERT: A 782 ILE cc_start: 0.9717 (mp) cc_final: 0.9336 (tp) REVERT: A 833 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8903 (mp) REVERT: B 7 HIS cc_start: 0.7380 (t70) cc_final: 0.7076 (t70) REVERT: B 127 LEU cc_start: 0.9382 (tp) cc_final: 0.8956 (tp) REVERT: B 424 PHE cc_start: 0.9501 (m-80) cc_final: 0.9203 (m-80) REVERT: B 462 MET cc_start: 0.9606 (tpt) cc_final: 0.9297 (tpt) REVERT: B 619 PHE cc_start: 0.9818 (OUTLIER) cc_final: 0.9219 (t80) REVERT: B 623 THR cc_start: 0.9608 (OUTLIER) cc_final: 0.8290 (p) REVERT: B 638 LYS cc_start: 0.9874 (mttt) cc_final: 0.9572 (mmtm) REVERT: B 640 PHE cc_start: 0.9486 (t80) cc_final: 0.9009 (t80) REVERT: B 641 SER cc_start: 0.9838 (t) cc_final: 0.9487 (p) REVERT: B 712 ASP cc_start: 0.9647 (t0) cc_final: 0.9410 (p0) REVERT: B 758 PHE cc_start: 0.9114 (m-80) cc_final: 0.8779 (m-80) REVERT: B 782 ILE cc_start: 0.9760 (mp) cc_final: 0.9369 (tp) REVERT: C 127 LEU cc_start: 0.9333 (tp) cc_final: 0.8951 (tp) REVERT: C 420 TYR cc_start: 0.9589 (t80) cc_final: 0.9312 (t80) REVERT: C 424 PHE cc_start: 0.9462 (m-80) cc_final: 0.9200 (m-80) REVERT: C 640 PHE cc_start: 0.9467 (t80) cc_final: 0.9030 (t80) REVERT: C 645 MET cc_start: 0.9607 (mtp) cc_final: 0.9389 (ttm) REVERT: C 758 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8567 (m-80) REVERT: C 830 LEU cc_start: 0.9846 (pt) cc_final: 0.9394 (tt) REVERT: C 832 LYS cc_start: 0.9630 (tttt) cc_final: 0.9368 (ttpp) REVERT: D 127 LEU cc_start: 0.9425 (tp) cc_final: 0.9136 (tp) REVERT: D 424 PHE cc_start: 0.9498 (m-80) cc_final: 0.9195 (m-80) REVERT: D 623 THR cc_start: 0.9452 (OUTLIER) cc_final: 0.8313 (p) REVERT: D 638 LYS cc_start: 0.9886 (mttt) cc_final: 0.9631 (mtpp) REVERT: D 640 PHE cc_start: 0.9495 (t80) cc_final: 0.9127 (t80) REVERT: D 641 SER cc_start: 0.9878 (t) cc_final: 0.9648 (p) REVERT: D 681 ARG cc_start: 0.9584 (mmm160) cc_final: 0.9190 (tpp-160) REVERT: D 744 ARG cc_start: 0.9722 (ptp-170) cc_final: 0.9362 (mmp80) REVERT: D 758 PHE cc_start: 0.9237 (m-80) cc_final: 0.8898 (m-80) REVERT: D 782 ILE cc_start: 0.9774 (mp) cc_final: 0.9447 (tp) REVERT: D 801 LYS cc_start: 0.9278 (mttp) cc_final: 0.9078 (mmtm) outliers start: 81 outliers final: 65 residues processed: 502 average time/residue: 0.2822 time to fit residues: 215.4441 Evaluate side-chains 511 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 441 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 720 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 829 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 741 LYS Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 660 SER Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 714 ASN Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 802 ASN Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 844 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 212 optimal weight: 40.0000 chunk 132 optimal weight: 20.0000 chunk 129 optimal weight: 0.2980 chunk 97 optimal weight: 5.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** B 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 ASN ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.6424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18028 Z= 0.190 Angle : 0.763 14.609 24472 Z= 0.366 Chirality : 0.046 0.210 2792 Planarity : 0.004 0.034 3068 Dihedral : 4.801 20.118 2424 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.52 % Favored : 96.30 % Rotamer: Outliers : 4.11 % Allowed : 27.33 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 2188 helix: -0.09 (0.15), residues: 1136 sheet: -1.41 (0.33), residues: 252 loop : -0.68 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 705 HIS 0.004 0.001 HIS A 762 PHE 0.020 0.002 PHE D 656 TYR 0.025 0.001 TYR D 707 ARG 0.005 0.000 ARG B 681 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 455 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 VAL cc_start: 0.8804 (t) cc_final: 0.8473 (p) REVERT: A 127 LEU cc_start: 0.9490 (tp) cc_final: 0.9193 (tp) REVERT: A 424 PHE cc_start: 0.9529 (m-80) cc_final: 0.9226 (m-80) REVERT: A 459 VAL cc_start: 0.9752 (t) cc_final: 0.9410 (p) REVERT: A 462 MET cc_start: 0.9646 (tpt) cc_final: 0.9436 (tpt) REVERT: A 463 PHE cc_start: 0.9521 (m-80) cc_final: 0.9035 (m-80) REVERT: A 640 PHE cc_start: 0.9472 (t80) cc_final: 0.9102 (t80) REVERT: A 641 SER cc_start: 0.9850 (t) cc_final: 0.9495 (p) REVERT: A 645 MET cc_start: 0.9423 (mtp) cc_final: 0.9215 (ttm) REVERT: A 651 MET cc_start: 0.9753 (tpp) cc_final: 0.9544 (mmm) REVERT: A 656 PHE cc_start: 0.9446 (m-80) cc_final: 0.9031 (m-80) REVERT: A 681 ARG cc_start: 0.9581 (mmm160) cc_final: 0.9187 (tpp-160) REVERT: A 758 PHE cc_start: 0.9478 (m-80) cc_final: 0.8705 (m-80) REVERT: A 782 ILE cc_start: 0.9637 (mp) cc_final: 0.9310 (tp) REVERT: B 7 HIS cc_start: 0.7396 (t70) cc_final: 0.7016 (t70) REVERT: B 424 PHE cc_start: 0.9515 (m-80) cc_final: 0.9213 (m-80) REVERT: B 462 MET cc_start: 0.9606 (tpt) cc_final: 0.9381 (tpt) REVERT: B 619 PHE cc_start: 0.9818 (OUTLIER) cc_final: 0.9239 (t80) REVERT: B 623 THR cc_start: 0.9594 (OUTLIER) cc_final: 0.8076 (p) REVERT: B 638 LYS cc_start: 0.9875 (mttt) cc_final: 0.9583 (mmtm) REVERT: B 640 PHE cc_start: 0.9476 (t80) cc_final: 0.9119 (t80) REVERT: B 641 SER cc_start: 0.9836 (t) cc_final: 0.9513 (p) REVERT: B 699 GLU cc_start: 0.9794 (mt-10) cc_final: 0.9392 (mt-10) REVERT: B 712 ASP cc_start: 0.9654 (t0) cc_final: 0.9421 (p0) REVERT: B 758 PHE cc_start: 0.9166 (m-80) cc_final: 0.8793 (m-80) REVERT: B 776 LEU cc_start: 0.8966 (tt) cc_final: 0.8744 (tt) REVERT: B 782 ILE cc_start: 0.9701 (mp) cc_final: 0.9354 (tp) REVERT: C 127 LEU cc_start: 0.9353 (tp) cc_final: 0.9097 (tp) REVERT: C 420 TYR cc_start: 0.9586 (t80) cc_final: 0.9307 (t80) REVERT: C 424 PHE cc_start: 0.9483 (m-80) cc_final: 0.9216 (m-80) REVERT: C 640 PHE cc_start: 0.9483 (t80) cc_final: 0.9019 (t80) REVERT: C 645 MET cc_start: 0.9591 (mtp) cc_final: 0.9385 (ttm) REVERT: C 758 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8654 (m-80) REVERT: C 776 LEU cc_start: 0.9109 (tt) cc_final: 0.8838 (tt) REVERT: C 830 LEU cc_start: 0.9847 (pt) cc_final: 0.9309 (tt) REVERT: D 127 LEU cc_start: 0.9444 (tp) cc_final: 0.8963 (tp) REVERT: D 424 PHE cc_start: 0.9506 (m-80) cc_final: 0.9201 (m-80) REVERT: D 462 MET cc_start: 0.9446 (tpt) cc_final: 0.9114 (tpt) REVERT: D 623 THR cc_start: 0.9433 (OUTLIER) cc_final: 0.8260 (p) REVERT: D 638 LYS cc_start: 0.9899 (mttt) cc_final: 0.9617 (mmtm) REVERT: D 640 PHE cc_start: 0.9483 (t80) cc_final: 0.9143 (t80) REVERT: D 641 SER cc_start: 0.9880 (t) cc_final: 0.9635 (p) REVERT: D 681 ARG cc_start: 0.9566 (mmm160) cc_final: 0.9174 (tpp-160) REVERT: D 758 PHE cc_start: 0.9200 (m-80) cc_final: 0.8902 (m-80) REVERT: D 782 ILE cc_start: 0.9790 (mp) cc_final: 0.9467 (tp) REVERT: D 801 LYS cc_start: 0.9244 (mttp) cc_final: 0.9040 (mmtm) outliers start: 76 outliers final: 67 residues processed: 494 average time/residue: 0.3005 time to fit residues: 225.3807 Evaluate side-chains 509 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 438 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 660 SER Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 829 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 720 PHE Chi-restraints excluded: chain C residue 741 LYS Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 660 SER Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 714 ASN Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 802 ASN Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 844 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 50.0000 chunk 84 optimal weight: 0.1980 chunk 126 optimal weight: 40.0000 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 30.0000 chunk 134 optimal weight: 30.0000 chunk 144 optimal weight: 50.0000 chunk 104 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 192 optimal weight: 30.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 834 HIS ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18028 Z= 0.191 Angle : 0.772 13.511 24472 Z= 0.368 Chirality : 0.046 0.309 2792 Planarity : 0.003 0.034 3068 Dihedral : 4.719 21.334 2424 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.11 % Favored : 96.71 % Rotamer: Outliers : 3.90 % Allowed : 28.52 % Favored : 67.59 % 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: -0.75 (0.18), residues: 2188 helix: -0.03 (0.15), residues: 1136 sheet: -1.37 (0.33), residues: 248 loop : -0.65 (0.24), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 563 HIS 0.006 0.001 HIS C 70 PHE 0.028 0.002 PHE A 551 TYR 0.019 0.001 TYR D 707 ARG 0.004 0.000 ARG B 681 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 453 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.9506 (tp) cc_final: 0.9180 (tp) REVERT: A 424 PHE cc_start: 0.9542 (m-80) cc_final: 0.9244 (m-80) REVERT: A 459 VAL cc_start: 0.9766 (t) cc_final: 0.9434 (p) REVERT: A 462 MET cc_start: 0.9651 (tpt) cc_final: 0.9444 (tpt) REVERT: A 463 PHE cc_start: 0.9537 (m-80) cc_final: 0.9056 (m-80) REVERT: A 640 PHE cc_start: 0.9472 (t80) cc_final: 0.9130 (t80) REVERT: A 641 SER cc_start: 0.9848 (t) cc_final: 0.9511 (p) REVERT: A 645 MET cc_start: 0.9419 (mtp) cc_final: 0.9186 (ttm) REVERT: A 651 MET cc_start: 0.9763 (tpp) cc_final: 0.9549 (mmm) REVERT: A 656 PHE cc_start: 0.9449 (m-80) cc_final: 0.9019 (m-80) REVERT: A 681 ARG cc_start: 0.9578 (mmm160) cc_final: 0.9183 (tpp-160) REVERT: A 758 PHE cc_start: 0.9262 (m-80) cc_final: 0.8669 (m-80) REVERT: A 782 ILE cc_start: 0.9644 (mp) cc_final: 0.9418 (tp) REVERT: A 830 LEU cc_start: 0.9771 (pp) cc_final: 0.9371 (tt) REVERT: A 833 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8554 (mp) REVERT: A 844 MET cc_start: 0.9530 (mtm) cc_final: 0.9290 (ptp) REVERT: B 7 HIS cc_start: 0.7425 (t70) cc_final: 0.7121 (t70) REVERT: B 127 LEU cc_start: 0.9259 (tp) cc_final: 0.8895 (tp) REVERT: B 424 PHE cc_start: 0.9510 (m-80) cc_final: 0.9217 (m-80) REVERT: B 462 MET cc_start: 0.9616 (tpt) cc_final: 0.9314 (tpt) REVERT: B 619 PHE cc_start: 0.9818 (OUTLIER) cc_final: 0.9223 (t80) REVERT: B 623 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.7991 (p) REVERT: B 638 LYS cc_start: 0.9870 (mttt) cc_final: 0.9599 (mmtm) REVERT: B 640 PHE cc_start: 0.9474 (t80) cc_final: 0.9114 (t80) REVERT: B 641 SER cc_start: 0.9843 (t) cc_final: 0.9531 (p) REVERT: B 712 ASP cc_start: 0.9654 (t0) cc_final: 0.9429 (p0) REVERT: B 758 PHE cc_start: 0.9198 (m-80) cc_final: 0.8798 (m-80) REVERT: B 782 ILE cc_start: 0.9698 (mp) cc_final: 0.9341 (tp) REVERT: C 127 LEU cc_start: 0.9373 (tp) cc_final: 0.9113 (tp) REVERT: C 420 TYR cc_start: 0.9597 (t80) cc_final: 0.9305 (t80) REVERT: C 424 PHE cc_start: 0.9495 (m-80) cc_final: 0.9228 (m-80) REVERT: C 640 PHE cc_start: 0.9477 (t80) cc_final: 0.9038 (t80) REVERT: C 656 PHE cc_start: 0.9414 (m-10) cc_final: 0.9107 (m-80) REVERT: C 681 ARG cc_start: 0.9615 (mmm160) cc_final: 0.9272 (tpm170) REVERT: C 758 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8724 (m-80) REVERT: C 830 LEU cc_start: 0.9817 (pt) cc_final: 0.9436 (tt) REVERT: D 424 PHE cc_start: 0.9524 (m-80) cc_final: 0.9220 (m-80) REVERT: D 462 MET cc_start: 0.9486 (tpt) cc_final: 0.9159 (tpt) REVERT: D 623 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.8184 (p) REVERT: D 638 LYS cc_start: 0.9897 (mttt) cc_final: 0.9640 (mmtm) REVERT: D 640 PHE cc_start: 0.9486 (t80) cc_final: 0.9158 (t80) REVERT: D 641 SER cc_start: 0.9878 (t) cc_final: 0.9638 (p) REVERT: D 656 PHE cc_start: 0.9070 (m-80) cc_final: 0.8809 (m-80) REVERT: D 681 ARG cc_start: 0.9551 (mmm160) cc_final: 0.9193 (tpp-160) REVERT: D 758 PHE cc_start: 0.9240 (m-80) cc_final: 0.8889 (m-80) REVERT: D 782 ILE cc_start: 0.9797 (mp) cc_final: 0.9518 (tp) outliers start: 72 outliers final: 59 residues processed: 486 average time/residue: 0.2659 time to fit residues: 198.2246 Evaluate side-chains 491 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 427 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 660 SER Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 829 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 720 PHE Chi-restraints excluded: chain C residue 741 LYS Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 714 ASN Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 844 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 7.9990 chunk 185 optimal weight: 40.0000 chunk 197 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 155 optimal weight: 30.0000 chunk 60 optimal weight: 50.0000 chunk 178 optimal weight: 40.0000 chunk 186 optimal weight: 6.9990 chunk 196 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 HIS ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.6828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18028 Z= 0.232 Angle : 0.813 13.475 24472 Z= 0.389 Chirality : 0.046 0.321 2792 Planarity : 0.004 0.069 3068 Dihedral : 4.779 20.785 2424 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.30 % Favored : 95.52 % Rotamer: Outliers : 3.95 % Allowed : 29.76 % Favored : 66.29 % 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: -0.74 (0.18), residues: 2188 helix: 0.00 (0.15), residues: 1144 sheet: -1.29 (0.33), residues: 248 loop : -0.72 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 563 HIS 0.021 0.001 HIS A 70 PHE 0.028 0.002 PHE D 551 TYR 0.025 0.002 TYR C 812 ARG 0.022 0.001 ARG C 814 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 435 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.9492 (tp) cc_final: 0.9277 (tp) REVERT: A 410 TRP cc_start: 0.9068 (t60) cc_final: 0.8775 (t60) REVERT: A 459 VAL cc_start: 0.9773 (t) cc_final: 0.9452 (p) REVERT: A 463 PHE cc_start: 0.9557 (m-80) cc_final: 0.9082 (m-80) REVERT: A 640 PHE cc_start: 0.9482 (t80) cc_final: 0.9157 (t80) REVERT: A 641 SER cc_start: 0.9852 (t) cc_final: 0.9515 (p) REVERT: A 645 MET cc_start: 0.9420 (mtp) cc_final: 0.9142 (ttm) REVERT: A 652 TYR cc_start: 0.9176 (t80) cc_final: 0.8949 (t80) REVERT: A 656 PHE cc_start: 0.9497 (m-80) cc_final: 0.9097 (m-80) REVERT: A 681 ARG cc_start: 0.9576 (mmm160) cc_final: 0.9177 (tpp-160) REVERT: A 758 PHE cc_start: 0.9339 (m-80) cc_final: 0.9053 (m-80) REVERT: A 782 ILE cc_start: 0.9622 (mp) cc_final: 0.9398 (tp) REVERT: A 788 GLU cc_start: 0.9417 (pm20) cc_final: 0.9199 (pm20) REVERT: A 830 LEU cc_start: 0.9766 (pp) cc_final: 0.9360 (tt) REVERT: A 833 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8752 (mp) REVERT: B 127 LEU cc_start: 0.9258 (tp) cc_final: 0.8998 (tp) REVERT: B 462 MET cc_start: 0.9612 (tpt) cc_final: 0.9307 (tpt) REVERT: B 619 PHE cc_start: 0.9826 (OUTLIER) cc_final: 0.9225 (t80) REVERT: B 623 THR cc_start: 0.9460 (OUTLIER) cc_final: 0.7994 (p) REVERT: B 638 LYS cc_start: 0.9873 (mttt) cc_final: 0.9622 (mmtm) REVERT: B 640 PHE cc_start: 0.9484 (t80) cc_final: 0.8983 (t80) REVERT: B 641 SER cc_start: 0.9853 (t) cc_final: 0.9510 (p) REVERT: B 712 ASP cc_start: 0.9633 (t0) cc_final: 0.9370 (p0) REVERT: B 758 PHE cc_start: 0.9218 (m-80) cc_final: 0.8834 (m-80) REVERT: B 782 ILE cc_start: 0.9684 (mp) cc_final: 0.9416 (tp) REVERT: B 830 LEU cc_start: 0.9854 (pt) cc_final: 0.9487 (tt) REVERT: C 127 LEU cc_start: 0.9378 (tp) cc_final: 0.9118 (tp) REVERT: C 420 TYR cc_start: 0.9611 (t80) cc_final: 0.9324 (t80) REVERT: C 424 PHE cc_start: 0.9510 (m-80) cc_final: 0.9245 (m-80) REVERT: C 640 PHE cc_start: 0.9522 (t80) cc_final: 0.9171 (t80) REVERT: C 645 MET cc_start: 0.9268 (ttm) cc_final: 0.8518 (ttt) REVERT: C 656 PHE cc_start: 0.9428 (m-10) cc_final: 0.9111 (m-80) REVERT: C 758 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8792 (m-80) REVERT: C 830 LEU cc_start: 0.9829 (pt) cc_final: 0.9409 (tt) REVERT: D 127 LEU cc_start: 0.9372 (tp) cc_final: 0.9150 (tp) REVERT: D 410 TRP cc_start: 0.9219 (t60) cc_final: 0.8987 (t60) REVERT: D 462 MET cc_start: 0.9529 (tpt) cc_final: 0.9252 (tpt) REVERT: D 619 PHE cc_start: 0.9719 (OUTLIER) cc_final: 0.9228 (t80) REVERT: D 638 LYS cc_start: 0.9889 (mttt) cc_final: 0.9646 (mmtm) REVERT: D 640 PHE cc_start: 0.9501 (t80) cc_final: 0.9193 (t80) REVERT: D 641 SER cc_start: 0.9873 (t) cc_final: 0.9648 (p) REVERT: D 782 ILE cc_start: 0.9736 (mp) cc_final: 0.9492 (tp) outliers start: 73 outliers final: 67 residues processed: 473 average time/residue: 0.2872 time to fit residues: 208.1921 Evaluate side-chains 502 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 430 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 597 TYR Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 829 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 720 PHE Chi-restraints excluded: chain C residue 741 LYS Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 714 ASN Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 844 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 99 optimal weight: 30.0000 chunk 145 optimal weight: 20.0000 chunk 219 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 134 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 GLN D 687 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.6972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18028 Z= 0.226 Angle : 0.844 14.421 24472 Z= 0.403 Chirality : 0.046 0.333 2792 Planarity : 0.004 0.040 3068 Dihedral : 4.804 20.251 2424 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.79 % Favored : 96.02 % Rotamer: Outliers : 3.84 % Allowed : 30.63 % Favored : 65.53 % 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: -0.78 (0.18), residues: 2188 helix: -0.04 (0.15), residues: 1132 sheet: -1.19 (0.33), residues: 248 loop : -0.77 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 410 HIS 0.017 0.001 HIS D 70 PHE 0.029 0.002 PHE A 551 TYR 0.018 0.001 TYR D 707 ARG 0.009 0.000 ARG D 681 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 437 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.9497 (tp) cc_final: 0.9279 (tp) REVERT: A 410 TRP cc_start: 0.8974 (t60) cc_final: 0.8767 (t60) REVERT: A 459 VAL cc_start: 0.9756 (t) cc_final: 0.9526 (p) REVERT: A 463 PHE cc_start: 0.9594 (m-80) cc_final: 0.9154 (m-80) REVERT: A 640 PHE cc_start: 0.9482 (t80) cc_final: 0.9160 (t80) REVERT: A 641 SER cc_start: 0.9853 (t) cc_final: 0.9469 (p) REVERT: A 645 MET cc_start: 0.9408 (mtp) cc_final: 0.9023 (ttm) REVERT: A 656 PHE cc_start: 0.9474 (m-80) cc_final: 0.9091 (m-80) REVERT: A 681 ARG cc_start: 0.9574 (mmm160) cc_final: 0.9167 (tpp-160) REVERT: A 758 PHE cc_start: 0.9364 (m-80) cc_final: 0.9054 (m-80) REVERT: A 782 ILE cc_start: 0.9626 (mp) cc_final: 0.9403 (tp) REVERT: A 788 GLU cc_start: 0.9416 (pm20) cc_final: 0.9201 (pm20) REVERT: A 830 LEU cc_start: 0.9757 (pp) cc_final: 0.9349 (tt) REVERT: A 844 MET cc_start: 0.9520 (mtm) cc_final: 0.9315 (ptp) REVERT: B 127 LEU cc_start: 0.9260 (tp) cc_final: 0.8990 (tp) REVERT: B 462 MET cc_start: 0.9612 (tpt) cc_final: 0.9308 (tpt) REVERT: B 619 PHE cc_start: 0.9823 (OUTLIER) cc_final: 0.9181 (t80) REVERT: B 623 THR cc_start: 0.9451 (OUTLIER) cc_final: 0.7909 (p) REVERT: B 638 LYS cc_start: 0.9872 (mttt) cc_final: 0.9634 (mmtm) REVERT: B 640 PHE cc_start: 0.9486 (t80) cc_final: 0.9174 (t80) REVERT: B 641 SER cc_start: 0.9856 (t) cc_final: 0.9549 (p) REVERT: B 758 PHE cc_start: 0.9217 (m-80) cc_final: 0.8847 (m-80) REVERT: B 782 ILE cc_start: 0.9685 (mp) cc_final: 0.9411 (tp) REVERT: B 830 LEU cc_start: 0.9854 (pt) cc_final: 0.9485 (tt) REVERT: C 127 LEU cc_start: 0.9384 (tp) cc_final: 0.9094 (tp) REVERT: C 410 TRP cc_start: 0.9168 (t60) cc_final: 0.8903 (t60) REVERT: C 420 TYR cc_start: 0.9612 (t80) cc_final: 0.9328 (t80) REVERT: C 424 PHE cc_start: 0.9521 (m-80) cc_final: 0.9258 (m-80) REVERT: C 640 PHE cc_start: 0.9522 (t80) cc_final: 0.9152 (t80) REVERT: C 645 MET cc_start: 0.9249 (ttm) cc_final: 0.8543 (ttt) REVERT: C 656 PHE cc_start: 0.9417 (m-10) cc_final: 0.9093 (m-80) REVERT: C 681 ARG cc_start: 0.9622 (mmm160) cc_final: 0.9271 (tpm170) REVERT: C 758 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8843 (m-80) REVERT: C 830 LEU cc_start: 0.9828 (pt) cc_final: 0.9350 (tt) REVERT: D 462 MET cc_start: 0.9527 (tpt) cc_final: 0.9227 (tpt) REVERT: D 619 PHE cc_start: 0.9722 (OUTLIER) cc_final: 0.9263 (t80) REVERT: D 638 LYS cc_start: 0.9891 (mttt) cc_final: 0.9652 (mmtm) REVERT: D 640 PHE cc_start: 0.9499 (t80) cc_final: 0.9194 (t80) REVERT: D 641 SER cc_start: 0.9871 (t) cc_final: 0.9642 (p) REVERT: D 758 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.8946 (m-80) REVERT: D 782 ILE cc_start: 0.9754 (mp) cc_final: 0.9419 (tp) REVERT: D 801 LYS cc_start: 0.9371 (mttp) cc_final: 0.9163 (mmtm) outliers start: 71 outliers final: 65 residues processed: 475 average time/residue: 0.2611 time to fit residues: 190.4293 Evaluate side-chains 493 residues out of total 1908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 423 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 597 TYR Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 682 GLU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 597 TYR Chi-restraints excluded: chain B residue 619 PHE Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 829 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 693 LEU Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 720 PHE Chi-restraints excluded: chain C residue 741 LYS Chi-restraints excluded: chain C residue 758 PHE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 788 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain C residue 844 MET Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 619 PHE Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 693 LEU Chi-restraints excluded: chain D residue 714 ASN Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 758 PHE Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 822 VAL Chi-restraints excluded: chain D residue 844 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 73 optimal weight: 40.0000 chunk 179 optimal weight: 40.0000 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 687 HIS ** C 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.072561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.054030 restraints weight = 80283.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.056077 restraints weight = 50715.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.057580 restraints weight = 36726.830| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.7118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18028 Z= 0.216 Angle : 0.863 13.908 24472 Z= 0.407 Chirality : 0.046 0.325 2792 Planarity : 0.004 0.034 3068 Dihedral : 4.771 23.435 2424 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.34 % Favored : 95.48 % Rotamer: Outliers : 3.84 % Allowed : 31.17 % Favored : 64.99 % 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: -0.72 (0.18), residues: 2188 helix: 0.04 (0.16), residues: 1104 sheet: -1.04 (0.33), residues: 248 loop : -0.80 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 563 HIS 0.016 0.001 HIS D 70 PHE 0.029 0.002 PHE A 551 TYR 0.014 0.001 TYR D 652 ARG 0.006 0.000 ARG C 814 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6084.62 seconds wall clock time: 109 minutes 53.35 seconds (6593.35 seconds total)