Starting phenix.real_space_refine on Wed Mar 4 13:51:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wyx_66379/03_2026/9wyx_66379_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wyx_66379/03_2026/9wyx_66379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wyx_66379/03_2026/9wyx_66379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wyx_66379/03_2026/9wyx_66379.map" model { file = "/net/cci-nas-00/data/ceres_data/9wyx_66379/03_2026/9wyx_66379_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wyx_66379/03_2026/9wyx_66379_neut.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 102 5.16 5 C 8646 2.51 5 N 2370 2.21 5 O 2574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13692 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2282 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Chain: "B" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2282 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Chain: "C" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2282 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Chain: "D" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2282 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Chain: "E" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2282 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Chain: "F" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2282 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Time building chain proxies: 3.18, per 1000 atoms: 0.23 Number of scatterers: 13692 At special positions: 0 Unit cell: (128.76, 119.14, 87.32, 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 102 16.00 O 2574 8.00 N 2370 7.00 C 8646 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 - 3.00 Amino acid : True - 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: 1.14 Conformation dependent library (CDL) restraints added in 723.0 milliseconds 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3252 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 6 sheets defined 84.7% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 441 through 451 Processing helix chain 'A' and resid 456 through 468 removed outlier: 3.669A pdb=" N HIS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TRP A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 497 Processing helix chain 'A' and resid 507 through 510 removed outlier: 3.713A pdb=" N PHE A 510 " --> pdb=" O ALA A 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 507 through 510' Processing helix chain 'A' and resid 512 through 531 removed outlier: 3.664A pdb=" N ASN A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 538 through 564 removed outlier: 3.623A pdb=" N ILE A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 595 removed outlier: 4.015A pdb=" N GLY A 582 " --> pdb=" O ASN A 578 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU A 583 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 625 removed outlier: 4.473A pdb=" N LYS A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 657 through 667 removed outlier: 3.804A pdb=" N ALA A 662 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Proline residue: A 663 - end of helix removed outlier: 3.520A pdb=" N ARG A 667 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 670 No H-bonds generated for 'chain 'A' and resid 668 through 670' Processing helix chain 'A' and resid 675 through 690 Processing helix chain 'A' and resid 690 through 715 removed outlier: 3.861A pdb=" N ILE A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET A 707 " --> pdb=" O HIS A 703 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'B' and resid 441 through 451 Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.590A pdb=" N HIS B 465 " --> pdb=" O ASP B 461 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TRP B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 497 Processing helix chain 'B' and resid 507 through 512 Processing helix chain 'B' and resid 512 through 532 removed outlier: 3.736A pdb=" N ASN B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER B 519 " --> pdb=" O GLN B 515 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 532 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 564 removed outlier: 3.583A pdb=" N ILE B 542 " --> pdb=" O ILE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 595 removed outlier: 4.155A pdb=" N GLY B 582 " --> pdb=" O ASN B 578 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU B 583 " --> pdb=" O LYS B 579 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 625 Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 644 through 652 Processing helix chain 'B' and resid 656 through 667 removed outlier: 3.919A pdb=" N ILE B 660 " --> pdb=" O HIS B 656 " (cutoff:3.500A) Proline residue: B 663 - end of helix Processing helix chain 'B' and resid 668 through 670 No H-bonds generated for 'chain 'B' and resid 668 through 670' Processing helix chain 'B' and resid 675 through 690 Processing helix chain 'B' and resid 690 through 715 removed outlier: 3.894A pdb=" N ARG B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 709 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 729 removed outlier: 3.776A pdb=" N ARG B 724 " --> pdb=" O ASN B 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 451 Processing helix chain 'C' and resid 456 through 468 removed outlier: 3.669A pdb=" N HIS C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TRP C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 467 " --> pdb=" O LEU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 497 Processing helix chain 'C' and resid 506 through 512 removed outlier: 4.259A pdb=" N PHE C 510 " --> pdb=" O VAL C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 532 removed outlier: 3.536A pdb=" N ASN C 518 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER C 519 " --> pdb=" O GLN C 515 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 528 " --> pdb=" O TYR C 524 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU C 530 " --> pdb=" O LYS C 526 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 531 " --> pdb=" O SER C 527 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER C 532 " --> pdb=" O VAL C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 564 removed outlier: 3.640A pdb=" N ILE C 542 " --> pdb=" O ILE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 595 removed outlier: 4.093A pdb=" N GLY C 582 " --> pdb=" O ASN C 578 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU C 583 " --> pdb=" O LYS C 579 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE C 584 " --> pdb=" O THR C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 625 Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 644 through 652 Processing helix chain 'C' and resid 656 through 667 removed outlier: 3.921A pdb=" N ILE C 660 " --> pdb=" O HIS C 656 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 662 " --> pdb=" O ASP C 658 " (cutoff:3.500A) Proline residue: C 663 - end of helix Processing helix chain 'C' and resid 668 through 670 No H-bonds generated for 'chain 'C' and resid 668 through 670' Processing helix chain 'C' and resid 675 through 690 Processing helix chain 'C' and resid 690 through 715 removed outlier: 3.532A pdb=" N TYR C 694 " --> pdb=" O GLY C 690 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE C 706 " --> pdb=" O LEU C 702 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG C 708 " --> pdb=" O GLU C 704 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 730 Processing helix chain 'D' and resid 438 through 451 Proline residue: D 443 - end of helix Processing helix chain 'D' and resid 456 through 468 removed outlier: 4.157A pdb=" N HIS D 465 " --> pdb=" O ASP D 461 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TRP D 466 " --> pdb=" O ALA D 462 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU D 467 " --> pdb=" O LEU D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 497 Processing helix chain 'D' and resid 507 through 510 removed outlier: 3.697A pdb=" N PHE D 510 " --> pdb=" O ALA D 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 507 through 510' Processing helix chain 'D' and resid 512 through 532 removed outlier: 3.987A pdb=" N SER D 519 " --> pdb=" O GLN D 515 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 528 " --> pdb=" O TYR D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 564 Processing helix chain 'D' and resid 568 through 595 removed outlier: 4.024A pdb=" N GLY D 582 " --> pdb=" O ASN D 578 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LEU D 583 " --> pdb=" O LYS D 579 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE D 584 " --> pdb=" O THR D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 625 removed outlier: 4.394A pdb=" N LYS D 605 " --> pdb=" O ALA D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 removed outlier: 3.577A pdb=" N ASP D 639 " --> pdb=" O CYS D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 652 Processing helix chain 'D' and resid 657 through 667 Proline residue: D 663 - end of helix removed outlier: 3.634A pdb=" N ARG D 667 " --> pdb=" O PRO D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 670 No H-bonds generated for 'chain 'D' and resid 668 through 670' Processing helix chain 'D' and resid 675 through 690 Processing helix chain 'D' and resid 690 through 715 removed outlier: 3.516A pdb=" N TYR D 694 " --> pdb=" O GLY D 690 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG D 708 " --> pdb=" O GLU D 704 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR D 709 " --> pdb=" O GLU D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 729 Processing helix chain 'E' and resid 441 through 451 Processing helix chain 'E' and resid 456 through 468 removed outlier: 3.858A pdb=" N HIS E 465 " --> pdb=" O ASP E 461 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TRP E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 467 " --> pdb=" O LEU E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 497 Processing helix chain 'E' and resid 507 through 510 removed outlier: 3.725A pdb=" N PHE E 510 " --> pdb=" O ALA E 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 507 through 510' Processing helix chain 'E' and resid 512 through 531 removed outlier: 3.584A pdb=" N SER E 519 " --> pdb=" O GLN E 515 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS E 529 " --> pdb=" O VAL E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 534 No H-bonds generated for 'chain 'E' and resid 532 through 534' Processing helix chain 'E' and resid 538 through 564 removed outlier: 3.549A pdb=" N ILE E 542 " --> pdb=" O ILE E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 595 removed outlier: 3.952A pdb=" N GLY E 582 " --> pdb=" O ASN E 578 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU E 583 " --> pdb=" O LYS E 579 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE E 584 " --> pdb=" O THR E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 625 removed outlier: 4.547A pdb=" N LYS E 605 " --> pdb=" O ALA E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 641 removed outlier: 3.761A pdb=" N ASP E 639 " --> pdb=" O CYS E 635 " (cutoff:3.500A) Processing helix chain 'E' and resid 644 through 652 Processing helix chain 'E' and resid 657 through 667 removed outlier: 3.676A pdb=" N ALA E 662 " --> pdb=" O ASP E 658 " (cutoff:3.500A) Proline residue: E 663 - end of helix removed outlier: 3.661A pdb=" N ARG E 667 " --> pdb=" O PRO E 663 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 670 No H-bonds generated for 'chain 'E' and resid 668 through 670' Processing helix chain 'E' and resid 675 through 690 Processing helix chain 'E' and resid 690 through 715 removed outlier: 3.615A pdb=" N TYR E 694 " --> pdb=" O GLY E 690 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE E 706 " --> pdb=" O LEU E 702 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET E 707 " --> pdb=" O HIS E 703 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG E 708 " --> pdb=" O GLU E 704 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR E 709 " --> pdb=" O GLU E 705 " (cutoff:3.500A) Processing helix chain 'E' and resid 720 through 729 Processing helix chain 'F' and resid 441 through 451 Processing helix chain 'F' and resid 456 through 468 removed outlier: 3.888A pdb=" N HIS F 465 " --> pdb=" O ASP F 461 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TRP F 466 " --> pdb=" O ALA F 462 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU F 467 " --> pdb=" O LEU F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 497 Processing helix chain 'F' and resid 506 through 511 removed outlier: 4.035A pdb=" N PHE F 510 " --> pdb=" O VAL F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 512 through 532 removed outlier: 3.514A pdb=" N ASN F 518 " --> pdb=" O SER F 514 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER F 519 " --> pdb=" O GLN F 515 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA F 520 " --> pdb=" O THR F 516 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL F 528 " --> pdb=" O TYR F 524 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS F 529 " --> pdb=" O VAL F 525 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU F 530 " --> pdb=" O LYS F 526 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR F 531 " --> pdb=" O SER F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 564 removed outlier: 3.533A pdb=" N ILE F 542 " --> pdb=" O ILE F 538 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS F 563 " --> pdb=" O TYR F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 568 through 595 removed outlier: 4.025A pdb=" N GLY F 582 " --> pdb=" O ASN F 578 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU F 583 " --> pdb=" O LYS F 579 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE F 584 " --> pdb=" O THR F 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 602 through 625 Processing helix chain 'F' and resid 635 through 641 removed outlier: 3.540A pdb=" N ASP F 639 " --> pdb=" O CYS F 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 644 through 652 Processing helix chain 'F' and resid 657 through 667 removed outlier: 3.604A pdb=" N ALA F 662 " --> pdb=" O ASP F 658 " (cutoff:3.500A) Proline residue: F 663 - end of helix Processing helix chain 'F' and resid 668 through 670 No H-bonds generated for 'chain 'F' and resid 668 through 670' Processing helix chain 'F' and resid 675 through 690 Processing helix chain 'F' and resid 690 through 715 removed outlier: 3.505A pdb=" N TYR F 694 " --> pdb=" O GLY F 690 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG F 708 " --> pdb=" O GLU F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 720 through 731 removed outlier: 4.265A pdb=" N GLY F 731 " --> pdb=" O LEU F 727 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 500 through 501 Processing sheet with id=AA2, first strand: chain 'B' and resid 500 through 501 Processing sheet with id=AA3, first strand: chain 'C' and resid 500 through 501 Processing sheet with id=AA4, first strand: chain 'D' and resid 500 through 501 Processing sheet with id=AA5, first strand: chain 'E' and resid 500 through 501 Processing sheet with id=AA6, first strand: chain 'F' and resid 500 through 501 973 hydrogen bonds defined for protein. 2901 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: 2.24 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4541 1.34 - 1.46: 1699 1.46 - 1.57: 7536 1.57 - 1.69: 0 1.69 - 1.81: 174 Bond restraints: 13950 Sorted by residual: bond pdb=" CA HIS C 649 " pdb=" C HIS C 649 " ideal model delta sigma weight residual 1.524 1.503 0.021 1.24e-02 6.50e+03 2.86e+00 bond pdb=" CA HIS C 653 " pdb=" C HIS C 653 " ideal model delta sigma weight residual 1.523 1.505 0.019 1.34e-02 5.57e+03 1.92e+00 bond pdb=" C ALA F 662 " pdb=" N PRO F 663 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.23e-02 6.61e+03 1.91e+00 bond pdb=" C LEU C 648 " pdb=" N HIS C 649 " ideal model delta sigma weight residual 1.334 1.317 0.017 1.27e-02 6.20e+03 1.85e+00 bond pdb=" CA GLY F 731 " pdb=" C GLY F 731 " ideal model delta sigma weight residual 1.515 1.503 0.013 9.30e-03 1.16e+04 1.83e+00 ... (remaining 13945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 18504 1.75 - 3.51: 297 3.51 - 5.26: 46 5.26 - 7.01: 10 7.01 - 8.77: 1 Bond angle restraints: 18858 Sorted by residual: angle pdb=" N GLY D 690 " pdb=" CA GLY D 690 " pdb=" C GLY D 690 " ideal model delta sigma weight residual 114.90 107.91 6.99 1.54e+00 4.22e-01 2.06e+01 angle pdb=" N GLY E 690 " pdb=" CA GLY E 690 " pdb=" C GLY E 690 " ideal model delta sigma weight residual 114.90 108.27 6.63 1.54e+00 4.22e-01 1.85e+01 angle pdb=" N SER E 449 " pdb=" CA SER E 449 " pdb=" C SER E 449 " ideal model delta sigma weight residual 111.28 107.18 4.10 1.09e+00 8.42e-01 1.42e+01 angle pdb=" N PHE D 643 " pdb=" CA PHE D 643 " pdb=" C PHE D 643 " ideal model delta sigma weight residual 109.76 115.43 -5.67 1.64e+00 3.72e-01 1.19e+01 angle pdb=" C ILE A 494 " pdb=" CA ILE A 494 " pdb=" CB ILE A 494 " ideal model delta sigma weight residual 112.22 107.86 4.36 1.38e+00 5.25e-01 9.99e+00 ... (remaining 18853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 7182 17.22 - 34.43: 999 34.43 - 51.65: 237 51.65 - 68.86: 60 68.86 - 86.08: 24 Dihedral angle restraints: 8502 sinusoidal: 3486 harmonic: 5016 Sorted by residual: dihedral pdb=" CB GLU F 530 " pdb=" CG GLU F 530 " pdb=" CD GLU F 530 " pdb=" OE1 GLU F 530 " ideal model delta sinusoidal sigma weight residual 0.00 86.08 -86.08 1 3.00e+01 1.11e-03 9.94e+00 dihedral pdb=" CB GLU B 571 " pdb=" CG GLU B 571 " pdb=" CD GLU B 571 " pdb=" OE1 GLU B 571 " ideal model delta sinusoidal sigma weight residual 0.00 -85.82 85.82 1 3.00e+01 1.11e-03 9.89e+00 dihedral pdb=" CG ARG E 565 " pdb=" CD ARG E 565 " pdb=" NE ARG E 565 " pdb=" CZ ARG E 565 " ideal model delta sinusoidal sigma weight residual 180.00 137.92 42.08 2 1.50e+01 4.44e-03 9.58e+00 ... (remaining 8499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1285 0.028 - 0.056: 549 0.056 - 0.084: 217 0.084 - 0.112: 68 0.112 - 0.140: 5 Chirality restraints: 2124 Sorted by residual: chirality pdb=" CA VAL D 439 " pdb=" N VAL D 439 " pdb=" C VAL D 439 " pdb=" CB VAL D 439 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA ILE C 447 " pdb=" N ILE C 447 " pdb=" C ILE C 447 " pdb=" CB ILE C 447 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CB VAL A 528 " pdb=" CA VAL A 528 " pdb=" CG1 VAL A 528 " pdb=" CG2 VAL A 528 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 2121 not shown) Planarity restraints: 2430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 595 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO B 596 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 596 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 596 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 645 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO E 646 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 646 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 646 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 649 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.43e+00 pdb=" C HIS C 649 " -0.027 2.00e-02 2.50e+03 pdb=" O HIS C 649 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU C 650 " 0.009 2.00e-02 2.50e+03 ... (remaining 2427 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 5501 2.92 - 3.41: 14691 3.41 - 3.91: 22316 3.91 - 4.40: 25084 4.40 - 4.90: 42591 Nonbonded interactions: 110183 Sorted by model distance: nonbonded pdb=" O TYR D 446 " pdb=" OG SER D 449 " model vdw 2.424 3.040 nonbonded pdb=" O TYR E 446 " pdb=" OG SER E 449 " model vdw 2.451 3.040 nonbonded pdb=" O TYR A 446 " pdb=" OG SER A 449 " model vdw 2.458 3.040 nonbonded pdb=" O TYR C 446 " pdb=" OG SER C 449 " model vdw 2.465 3.040 nonbonded pdb=" O GLY F 731 " pdb=" OXT LEU F 732 " model vdw 2.481 3.040 ... (remaining 110178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.160 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 : 0.003 0.028 13950 Z= 0.156 Angle : 0.573 8.767 18858 Z= 0.324 Chirality : 0.037 0.140 2124 Planarity : 0.003 0.044 2430 Dihedral : 17.176 86.077 5250 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.92 % Allowed : 17.98 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.21), residues: 1674 helix: 2.38 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -2.03 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 561 TYR 0.016 0.001 TYR B 613 PHE 0.009 0.001 PHE F 643 TRP 0.015 0.002 TRP A 466 HIS 0.005 0.001 HIS D 551 Details of bonding type rmsd covalent geometry : bond 0.00288 (13950) covalent geometry : angle 0.57336 (18858) hydrogen bonds : bond 0.14727 ( 973) hydrogen bonds : angle 4.96380 ( 2901) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 240 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 554 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7570 (mt0) REVERT: A 722 GLU cc_start: 0.6368 (mt-10) cc_final: 0.5679 (tp30) REVERT: B 474 MET cc_start: 0.7626 (mmm) cc_final: 0.7124 (mmt) REVERT: B 540 MET cc_start: 0.7529 (tpt) cc_final: 0.7326 (mmt) REVERT: B 554 GLN cc_start: 0.8136 (mt0) cc_final: 0.7819 (mt0) REVERT: B 722 GLU cc_start: 0.6407 (mt-10) cc_final: 0.5451 (tp30) REVERT: C 554 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7571 (mt0) REVERT: D 554 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7673 (mt0) REVERT: D 574 MET cc_start: 0.7924 (ttm) cc_final: 0.7648 (ttp) REVERT: D 711 ASP cc_start: 0.6975 (m-30) cc_final: 0.6749 (m-30) REVERT: E 445 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7878 (mm-30) REVERT: E 474 MET cc_start: 0.7474 (tpp) cc_final: 0.7136 (mmm) REVERT: E 554 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7576 (mt0) REVERT: E 652 ASN cc_start: 0.8079 (m-40) cc_final: 0.7383 (t0) REVERT: E 704 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7086 (mp0) REVERT: E 711 ASP cc_start: 0.7381 (m-30) cc_final: 0.7120 (m-30) REVERT: F 474 MET cc_start: 0.7721 (tpp) cc_final: 0.7519 (mmt) REVERT: F 554 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7584 (mt0) REVERT: F 618 ASP cc_start: 0.7742 (t0) cc_final: 0.7450 (t70) REVERT: F 652 ASN cc_start: 0.8029 (m-40) cc_final: 0.7327 (t0) outliers start: 14 outliers final: 11 residues processed: 253 average time/residue: 0.1142 time to fit residues: 42.6780 Evaluate side-chains 218 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 207 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain D residue 514 SER Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 726 LEU Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 599 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.0010 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN B 653 HIS C 615 GLN D 518 ASN E 465 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.214934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.179839 restraints weight = 15629.236| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 1.86 r_work: 0.3847 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13950 Z= 0.124 Angle : 0.497 8.328 18858 Z= 0.255 Chirality : 0.037 0.118 2124 Planarity : 0.004 0.044 2430 Dihedral : 3.757 39.602 1891 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.91 % Allowed : 17.59 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.21), residues: 1674 helix: 2.76 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -1.72 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 561 TYR 0.010 0.001 TYR B 613 PHE 0.014 0.001 PHE B 510 TRP 0.012 0.001 TRP A 466 HIS 0.007 0.001 HIS F 465 Details of bonding type rmsd covalent geometry : bond 0.00264 (13950) covalent geometry : angle 0.49729 (18858) hydrogen bonds : bond 0.05047 ( 973) hydrogen bonds : angle 3.80615 ( 2901) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 PHE cc_start: 0.5924 (OUTLIER) cc_final: 0.5281 (m-80) REVERT: A 554 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7608 (mt0) REVERT: A 722 GLU cc_start: 0.6353 (mt-10) cc_final: 0.5582 (tp30) REVERT: B 474 MET cc_start: 0.7581 (mmm) cc_final: 0.7190 (mmt) REVERT: B 722 GLU cc_start: 0.6457 (mt-10) cc_final: 0.5420 (tp30) REVERT: C 554 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7576 (mt0) REVERT: C 704 GLU cc_start: 0.7170 (mp0) cc_final: 0.6822 (mp0) REVERT: D 465 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6872 (t70) REVERT: D 554 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7656 (mt0) REVERT: D 574 MET cc_start: 0.7974 (ttm) cc_final: 0.7699 (ttp) REVERT: D 652 ASN cc_start: 0.7737 (m-40) cc_final: 0.7248 (t0) REVERT: D 704 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7024 (mp0) REVERT: E 550 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7865 (mp) REVERT: E 554 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7581 (mt0) REVERT: E 652 ASN cc_start: 0.7845 (m-40) cc_final: 0.7283 (t0) REVERT: E 704 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7189 (mp0) REVERT: E 711 ASP cc_start: 0.7350 (m-30) cc_final: 0.7138 (m-30) REVERT: F 554 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7589 (mt0) REVERT: F 618 ASP cc_start: 0.7792 (t0) cc_final: 0.7411 (t70) REVERT: F 652 ASN cc_start: 0.7700 (m-40) cc_final: 0.7234 (t0) REVERT: F 676 ARG cc_start: 0.5168 (OUTLIER) cc_final: 0.4937 (ttm-80) outliers start: 29 outliers final: 16 residues processed: 252 average time/residue: 0.1194 time to fit residues: 43.3666 Evaluate side-chains 229 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 465 HIS Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 602 SER Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 691 THR Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 676 ARG Chi-restraints excluded: chain F residue 691 THR Chi-restraints excluded: chain F residue 728 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 140 optimal weight: 0.0970 chunk 66 optimal weight: 0.5980 chunk 162 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 156 optimal weight: 0.0470 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 457 ASN D 464 ASN E 457 ASN E 465 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.214158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.178405 restraints weight = 15665.493| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 1.86 r_work: 0.3827 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13950 Z= 0.125 Angle : 0.490 7.212 18858 Z= 0.251 Chirality : 0.037 0.126 2124 Planarity : 0.003 0.047 2430 Dihedral : 3.237 18.354 1878 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.57 % Allowed : 18.12 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.21), residues: 1674 helix: 2.75 (0.14), residues: 1308 sheet: None (None), residues: 0 loop : -1.16 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 667 TYR 0.009 0.001 TYR A 572 PHE 0.011 0.001 PHE D 543 TRP 0.011 0.001 TRP A 466 HIS 0.005 0.001 HIS A 551 Details of bonding type rmsd covalent geometry : bond 0.00269 (13950) covalent geometry : angle 0.48991 (18858) hydrogen bonds : bond 0.05110 ( 973) hydrogen bonds : angle 3.69414 ( 2901) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.5968 (OUTLIER) cc_final: 0.5332 (m-80) REVERT: A 554 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7580 (mt0) REVERT: B 459 PHE cc_start: 0.7099 (m-80) cc_final: 0.5991 (t80) REVERT: B 474 MET cc_start: 0.7629 (mmm) cc_final: 0.7202 (mmt) REVERT: C 554 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7640 (mt0) REVERT: D 449 SER cc_start: 0.7999 (m) cc_final: 0.7501 (p) REVERT: D 540 MET cc_start: 0.7621 (mmp) cc_final: 0.7342 (mmt) REVERT: D 554 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7691 (mt0) REVERT: D 574 MET cc_start: 0.7913 (ttm) cc_final: 0.7637 (ttp) REVERT: D 652 ASN cc_start: 0.7787 (m-40) cc_final: 0.7298 (t0) REVERT: D 687 ASP cc_start: 0.7155 (m-30) cc_final: 0.6872 (m-30) REVERT: D 696 GLN cc_start: 0.6555 (mm110) cc_final: 0.6314 (mm-40) REVERT: E 550 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7830 (mp) REVERT: E 554 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7622 (mt0) REVERT: E 687 ASP cc_start: 0.7558 (m-30) cc_final: 0.7203 (m-30) REVERT: E 704 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7155 (mm-30) REVERT: E 711 ASP cc_start: 0.7348 (m-30) cc_final: 0.7118 (m-30) REVERT: F 459 PHE cc_start: 0.6439 (m-80) cc_final: 0.6060 (t80) REVERT: F 554 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7637 (mt0) REVERT: F 639 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7335 (t0) REVERT: F 652 ASN cc_start: 0.7723 (m-40) cc_final: 0.7437 (t0) REVERT: F 676 ARG cc_start: 0.5331 (OUTLIER) cc_final: 0.5122 (ttp80) outliers start: 39 outliers final: 20 residues processed: 247 average time/residue: 0.1162 time to fit residues: 41.5008 Evaluate side-chains 220 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 465 HIS Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 691 THR Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 676 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 96 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 622 ASN D 464 ASN E 465 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.210846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.175740 restraints weight = 15539.889| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.83 r_work: 0.3814 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13950 Z= 0.125 Angle : 0.492 6.955 18858 Z= 0.252 Chirality : 0.037 0.131 2124 Planarity : 0.003 0.045 2430 Dihedral : 3.224 18.489 1878 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.70 % Allowed : 18.45 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.21), residues: 1674 helix: 2.81 (0.14), residues: 1308 sheet: None (None), residues: 0 loop : -1.79 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 456 TYR 0.009 0.001 TYR B 559 PHE 0.011 0.001 PHE E 510 TRP 0.010 0.001 TRP A 466 HIS 0.005 0.001 HIS E 465 Details of bonding type rmsd covalent geometry : bond 0.00274 (13950) covalent geometry : angle 0.49160 (18858) hydrogen bonds : bond 0.05055 ( 973) hydrogen bonds : angle 3.65808 ( 2901) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.5860 (OUTLIER) cc_final: 0.5245 (m-80) REVERT: A 510 PHE cc_start: 0.6844 (OUTLIER) cc_final: 0.6288 (p90) REVERT: A 554 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7565 (mt0) REVERT: B 459 PHE cc_start: 0.7096 (m-80) cc_final: 0.5955 (t80) REVERT: B 474 MET cc_start: 0.7596 (mmm) cc_final: 0.7170 (mmt) REVERT: C 554 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7632 (mt0) REVERT: D 449 SER cc_start: 0.8123 (m) cc_final: 0.7583 (p) REVERT: D 554 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7670 (mt0) REVERT: D 574 MET cc_start: 0.7880 (ttm) cc_final: 0.7619 (ttp) REVERT: D 652 ASN cc_start: 0.7791 (m-40) cc_final: 0.7337 (t0) REVERT: D 687 ASP cc_start: 0.7118 (m-30) cc_final: 0.6732 (m-30) REVERT: E 504 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.5587 (mp10) REVERT: E 550 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7837 (mp) REVERT: E 554 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7609 (mt0) REVERT: E 711 ASP cc_start: 0.7296 (m-30) cc_final: 0.7091 (m-30) REVERT: F 459 PHE cc_start: 0.6531 (m-80) cc_final: 0.6048 (t80) REVERT: F 554 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7640 (mt0) REVERT: F 639 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7199 (t0) REVERT: F 652 ASN cc_start: 0.7736 (m-40) cc_final: 0.7456 (t0) REVERT: F 704 GLU cc_start: 0.7187 (mp0) cc_final: 0.6882 (mp0) outliers start: 41 outliers final: 23 residues processed: 240 average time/residue: 0.1191 time to fit residues: 41.3002 Evaluate side-chains 228 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 465 HIS Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain E residue 504 GLN Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain E residue 691 THR Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain F residue 639 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 30 optimal weight: 0.6980 chunk 167 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 126 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 622 ASN D 464 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.211000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.175853 restraints weight = 15667.600| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.85 r_work: 0.3815 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13950 Z= 0.121 Angle : 0.482 6.428 18858 Z= 0.247 Chirality : 0.036 0.123 2124 Planarity : 0.003 0.042 2430 Dihedral : 3.218 18.188 1878 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.96 % Allowed : 17.79 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.21), residues: 1674 helix: 2.83 (0.14), residues: 1308 sheet: None (None), residues: 0 loop : -1.78 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 561 TYR 0.012 0.001 TYR B 613 PHE 0.011 0.001 PHE D 543 TRP 0.009 0.001 TRP A 466 HIS 0.010 0.001 HIS F 465 Details of bonding type rmsd covalent geometry : bond 0.00263 (13950) covalent geometry : angle 0.48153 (18858) hydrogen bonds : bond 0.04887 ( 973) hydrogen bonds : angle 3.60383 ( 2901) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.5838 (OUTLIER) cc_final: 0.5225 (m-80) REVERT: A 510 PHE cc_start: 0.6810 (OUTLIER) cc_final: 0.6266 (p90) REVERT: A 554 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7591 (mt0) REVERT: B 474 MET cc_start: 0.7596 (mmm) cc_final: 0.7135 (mmt) REVERT: B 554 GLN cc_start: 0.8106 (mt0) cc_final: 0.7734 (mt0) REVERT: B 688 GLU cc_start: 0.7877 (tt0) cc_final: 0.7662 (mt-10) REVERT: C 554 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7643 (mt0) REVERT: D 449 SER cc_start: 0.8123 (m) cc_final: 0.7583 (p) REVERT: D 554 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7706 (mt0) REVERT: D 574 MET cc_start: 0.7879 (ttm) cc_final: 0.7624 (ttp) REVERT: D 652 ASN cc_start: 0.7852 (m-40) cc_final: 0.7373 (t0) REVERT: E 504 GLN cc_start: 0.6617 (OUTLIER) cc_final: 0.5597 (mp10) REVERT: E 510 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.6092 (p90) REVERT: E 550 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7855 (mp) REVERT: E 554 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7645 (mt0) REVERT: E 704 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7011 (mp0) REVERT: F 459 PHE cc_start: 0.6577 (m-80) cc_final: 0.6107 (t80) REVERT: F 493 ASP cc_start: 0.6515 (m-30) cc_final: 0.6207 (m-30) REVERT: F 554 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7648 (mt0) REVERT: F 639 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7171 (t0) REVERT: F 652 ASN cc_start: 0.7765 (m-40) cc_final: 0.7489 (t0) REVERT: F 704 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6943 (mp0) outliers start: 45 outliers final: 31 residues processed: 243 average time/residue: 0.1190 time to fit residues: 41.8260 Evaluate side-chains 234 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 465 HIS Chi-restraints excluded: chain D residue 510 PHE Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain E residue 504 GLN Chi-restraints excluded: chain E residue 510 PHE Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain E residue 691 THR Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 595 SER Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 704 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 164 optimal weight: 0.6980 chunk 9 optimal weight: 0.0000 chunk 87 optimal weight: 3.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.212545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.177879 restraints weight = 15620.681| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.83 r_work: 0.3834 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13950 Z= 0.111 Angle : 0.469 6.404 18858 Z= 0.239 Chirality : 0.036 0.122 2124 Planarity : 0.003 0.040 2430 Dihedral : 3.175 17.998 1878 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.83 % Allowed : 17.65 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.21), residues: 1674 helix: 2.91 (0.14), residues: 1308 sheet: None (None), residues: 0 loop : -1.76 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 561 TYR 0.009 0.001 TYR B 613 PHE 0.012 0.001 PHE D 543 TRP 0.009 0.001 TRP D 466 HIS 0.008 0.001 HIS F 465 Details of bonding type rmsd covalent geometry : bond 0.00237 (13950) covalent geometry : angle 0.46860 (18858) hydrogen bonds : bond 0.04456 ( 973) hydrogen bonds : angle 3.52046 ( 2901) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 214 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 PHE cc_start: 0.5796 (OUTLIER) cc_final: 0.5213 (m-80) REVERT: A 510 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6298 (p90) REVERT: A 554 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7596 (mt0) REVERT: B 474 MET cc_start: 0.7565 (mmm) cc_final: 0.7147 (mmt) REVERT: B 688 GLU cc_start: 0.7788 (tt0) cc_final: 0.7574 (mt-10) REVERT: C 450 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6886 (mp) REVERT: C 554 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7631 (mt0) REVERT: D 449 SER cc_start: 0.8108 (m) cc_final: 0.7570 (p) REVERT: D 554 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7688 (mt0) REVERT: D 574 MET cc_start: 0.7875 (ttm) cc_final: 0.7619 (ttp) REVERT: D 652 ASN cc_start: 0.7830 (m-40) cc_final: 0.7353 (t0) REVERT: E 504 GLN cc_start: 0.6585 (OUTLIER) cc_final: 0.5625 (mp10) REVERT: E 510 PHE cc_start: 0.6654 (OUTLIER) cc_final: 0.6114 (p90) REVERT: E 554 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7628 (mt0) REVERT: F 459 PHE cc_start: 0.6656 (m-80) cc_final: 0.6184 (t80) REVERT: F 493 ASP cc_start: 0.6457 (m-30) cc_final: 0.6090 (m-30) REVERT: F 554 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7596 (mt0) REVERT: F 639 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7067 (t0) REVERT: F 652 ASN cc_start: 0.7773 (m-40) cc_final: 0.7504 (t0) REVERT: F 704 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6933 (mp0) outliers start: 43 outliers final: 29 residues processed: 246 average time/residue: 0.1235 time to fit residues: 43.6407 Evaluate side-chains 237 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 510 PHE Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain E residue 504 GLN Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 510 PHE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 602 SER Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain E residue 691 THR Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 595 SER Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 704 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 167 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.210907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.176383 restraints weight = 15548.115| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 1.80 r_work: 0.3816 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13950 Z= 0.131 Angle : 0.514 12.339 18858 Z= 0.260 Chirality : 0.037 0.146 2124 Planarity : 0.003 0.039 2430 Dihedral : 3.243 18.223 1878 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.83 % Allowed : 17.92 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.21), residues: 1674 helix: 2.81 (0.14), residues: 1308 sheet: None (None), residues: 0 loop : -1.81 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 561 TYR 0.010 0.001 TYR A 572 PHE 0.012 0.001 PHE E 510 TRP 0.008 0.001 TRP A 466 HIS 0.007 0.001 HIS F 465 Details of bonding type rmsd covalent geometry : bond 0.00293 (13950) covalent geometry : angle 0.51364 (18858) hydrogen bonds : bond 0.05156 ( 973) hydrogen bonds : angle 3.63028 ( 2901) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.5814 (OUTLIER) cc_final: 0.5253 (m-80) REVERT: A 510 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.6237 (p90) REVERT: A 554 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7621 (mt0) REVERT: A 704 GLU cc_start: 0.7525 (tt0) cc_final: 0.7054 (tm-30) REVERT: B 474 MET cc_start: 0.7554 (mmm) cc_final: 0.7114 (mmt) REVERT: B 554 GLN cc_start: 0.8112 (mt0) cc_final: 0.7745 (mt0) REVERT: B 688 GLU cc_start: 0.7862 (tt0) cc_final: 0.7648 (mt-10) REVERT: C 450 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7037 (mp) REVERT: C 554 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7692 (mt0) REVERT: C 722 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5532 (tp30) REVERT: D 449 SER cc_start: 0.8156 (m) cc_final: 0.7631 (p) REVERT: D 554 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7744 (mt0) REVERT: D 574 MET cc_start: 0.7945 (ttm) cc_final: 0.7687 (ttp) REVERT: D 652 ASN cc_start: 0.7949 (m-40) cc_final: 0.7420 (t0) REVERT: E 504 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.6435 (mm-40) REVERT: E 510 PHE cc_start: 0.6703 (OUTLIER) cc_final: 0.6124 (p90) REVERT: E 554 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7629 (mt0) REVERT: E 704 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7022 (mp0) REVERT: F 450 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7091 (mp) REVERT: F 459 PHE cc_start: 0.6698 (m-80) cc_final: 0.6176 (t80) REVERT: F 493 ASP cc_start: 0.6650 (m-30) cc_final: 0.6278 (m-30) REVERT: F 554 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7620 (mt0) REVERT: F 639 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7044 (t0) REVERT: F 652 ASN cc_start: 0.7796 (m-40) cc_final: 0.7524 (t0) REVERT: F 704 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6938 (mp0) outliers start: 43 outliers final: 29 residues processed: 230 average time/residue: 0.1223 time to fit residues: 40.7120 Evaluate side-chains 238 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 510 PHE Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain E residue 504 GLN Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 510 PHE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 602 SER Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain E residue 691 THR Chi-restraints excluded: chain F residue 450 LEU Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 595 SER Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 704 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 15 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.210809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.176368 restraints weight = 15523.657| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.79 r_work: 0.3812 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13950 Z= 0.132 Angle : 0.512 11.423 18858 Z= 0.260 Chirality : 0.037 0.123 2124 Planarity : 0.004 0.038 2430 Dihedral : 3.267 18.315 1878 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.83 % Allowed : 18.25 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.21), residues: 1674 helix: 2.76 (0.14), residues: 1308 sheet: None (None), residues: 0 loop : -1.82 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 708 TYR 0.012 0.001 TYR B 613 PHE 0.012 0.001 PHE E 510 TRP 0.009 0.001 TRP D 466 HIS 0.006 0.001 HIS F 465 Details of bonding type rmsd covalent geometry : bond 0.00295 (13950) covalent geometry : angle 0.51199 (18858) hydrogen bonds : bond 0.05147 ( 973) hydrogen bonds : angle 3.64000 ( 2901) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.5831 (OUTLIER) cc_final: 0.5258 (m-80) REVERT: A 510 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.6273 (p90) REVERT: A 554 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7619 (mt0) REVERT: A 704 GLU cc_start: 0.7547 (tt0) cc_final: 0.7064 (tm-30) REVERT: B 474 MET cc_start: 0.7513 (mmm) cc_final: 0.7228 (mmt) REVERT: B 688 GLU cc_start: 0.7852 (tt0) cc_final: 0.7640 (mt-10) REVERT: C 450 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7062 (mp) REVERT: C 554 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7694 (mt0) REVERT: C 722 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.5539 (tp30) REVERT: D 449 SER cc_start: 0.8157 (m) cc_final: 0.7635 (p) REVERT: D 554 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7756 (mt0) REVERT: D 574 MET cc_start: 0.7905 (ttm) cc_final: 0.7659 (ttp) REVERT: E 450 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6891 (mp) REVERT: E 504 GLN cc_start: 0.6649 (OUTLIER) cc_final: 0.6428 (mm-40) REVERT: E 510 PHE cc_start: 0.6709 (OUTLIER) cc_final: 0.6146 (p90) REVERT: E 554 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7646 (mt0) REVERT: F 450 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7076 (mp) REVERT: F 459 PHE cc_start: 0.6727 (m-80) cc_final: 0.6179 (t80) REVERT: F 493 ASP cc_start: 0.6650 (m-30) cc_final: 0.6281 (m-30) REVERT: F 554 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7626 (mt0) REVERT: F 639 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7010 (t0) REVERT: F 652 ASN cc_start: 0.7835 (m-40) cc_final: 0.7559 (t0) REVERT: F 704 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7022 (mp0) outliers start: 43 outliers final: 31 residues processed: 232 average time/residue: 0.1211 time to fit residues: 40.7785 Evaluate side-chains 230 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain D residue 510 PHE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 504 GLN Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 510 PHE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 602 SER Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain E residue 691 THR Chi-restraints excluded: chain F residue 450 LEU Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 595 SER Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 704 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 56 optimal weight: 0.9980 chunk 80 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 97 optimal weight: 0.2980 chunk 142 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.212670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.178894 restraints weight = 15443.763| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.78 r_work: 0.3841 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13950 Z= 0.113 Angle : 0.485 10.133 18858 Z= 0.247 Chirality : 0.036 0.115 2124 Planarity : 0.003 0.038 2430 Dihedral : 3.191 17.814 1878 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.44 % Allowed : 18.77 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.06 (0.21), residues: 1674 helix: 2.83 (0.14), residues: 1308 sheet: None (None), residues: 0 loop : -1.19 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 561 TYR 0.009 0.001 TYR B 613 PHE 0.014 0.001 PHE E 643 TRP 0.009 0.001 TRP D 466 HIS 0.006 0.001 HIS F 465 Details of bonding type rmsd covalent geometry : bond 0.00243 (13950) covalent geometry : angle 0.48544 (18858) hydrogen bonds : bond 0.04411 ( 973) hydrogen bonds : angle 3.55028 ( 2901) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.5829 (OUTLIER) cc_final: 0.5262 (m-80) REVERT: A 510 PHE cc_start: 0.6816 (OUTLIER) cc_final: 0.6288 (p90) REVERT: A 554 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7622 (mt0) REVERT: A 704 GLU cc_start: 0.7492 (tt0) cc_final: 0.7038 (tm-30) REVERT: B 474 MET cc_start: 0.7467 (mmm) cc_final: 0.7032 (mmt) REVERT: B 554 GLN cc_start: 0.8106 (mt0) cc_final: 0.7739 (mt0) REVERT: B 688 GLU cc_start: 0.7836 (tt0) cc_final: 0.7620 (mt-10) REVERT: C 554 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7671 (mt0) REVERT: C 704 GLU cc_start: 0.7215 (mp0) cc_final: 0.7011 (mp0) REVERT: C 722 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5522 (tp30) REVERT: D 449 SER cc_start: 0.8140 (m) cc_final: 0.7630 (p) REVERT: D 554 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7707 (mt0) REVERT: D 574 MET cc_start: 0.7907 (ttm) cc_final: 0.7658 (ttp) REVERT: E 450 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6848 (mp) REVERT: E 493 ASP cc_start: 0.6543 (m-30) cc_final: 0.6260 (m-30) REVERT: E 510 PHE cc_start: 0.6702 (OUTLIER) cc_final: 0.6181 (p90) REVERT: E 554 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7608 (mt0) REVERT: E 704 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7197 (mp0) REVERT: F 450 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7078 (mp) REVERT: F 459 PHE cc_start: 0.6681 (m-80) cc_final: 0.6168 (t80) REVERT: F 493 ASP cc_start: 0.6580 (m-30) cc_final: 0.6159 (m-30) REVERT: F 540 MET cc_start: 0.7802 (mmp) cc_final: 0.7139 (mmt) REVERT: F 554 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7607 (mt0) REVERT: F 639 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.6999 (t0) REVERT: F 652 ASN cc_start: 0.7772 (m-40) cc_final: 0.7514 (t0) REVERT: F 704 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6979 (mp0) outliers start: 37 outliers final: 25 residues processed: 236 average time/residue: 0.1140 time to fit residues: 39.1410 Evaluate side-chains 236 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain D residue 510 PHE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 595 SER Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 510 PHE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain E residue 691 THR Chi-restraints excluded: chain F residue 450 LEU Chi-restraints excluded: chain F residue 506 VAL Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 704 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 161 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 622 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.208845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.173904 restraints weight = 15694.022| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.84 r_work: 0.3784 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13950 Z= 0.152 Angle : 0.547 10.779 18858 Z= 0.278 Chirality : 0.039 0.133 2124 Planarity : 0.004 0.038 2430 Dihedral : 3.352 18.576 1878 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.44 % Allowed : 18.91 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.21), residues: 1674 helix: 2.61 (0.14), residues: 1308 sheet: None (None), residues: 0 loop : -1.86 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 708 TYR 0.013 0.001 TYR B 613 PHE 0.017 0.002 PHE E 643 TRP 0.009 0.002 TRP B 466 HIS 0.011 0.001 HIS F 465 Details of bonding type rmsd covalent geometry : bond 0.00351 (13950) covalent geometry : angle 0.54704 (18858) hydrogen bonds : bond 0.05689 ( 973) hydrogen bonds : angle 3.74852 ( 2901) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 459 PHE cc_start: 0.5773 (OUTLIER) cc_final: 0.5218 (m-80) REVERT: A 510 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6333 (p90) REVERT: A 554 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7568 (mt0) REVERT: A 704 GLU cc_start: 0.7547 (tt0) cc_final: 0.7064 (tm-30) REVERT: B 474 MET cc_start: 0.7548 (mmm) cc_final: 0.7260 (mmt) REVERT: B 554 GLN cc_start: 0.8089 (mt0) cc_final: 0.7696 (mt0) REVERT: B 688 GLU cc_start: 0.7896 (tt0) cc_final: 0.7682 (mt-10) REVERT: C 450 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7080 (mp) REVERT: C 554 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7692 (mt0) REVERT: D 449 SER cc_start: 0.8123 (m) cc_final: 0.7582 (p) REVERT: D 554 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7685 (mt0) REVERT: D 574 MET cc_start: 0.7926 (ttm) cc_final: 0.7693 (ttp) REVERT: E 450 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6855 (mp) REVERT: E 510 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.6180 (p90) REVERT: E 554 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7615 (mt0) REVERT: E 704 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7183 (mp0) REVERT: F 450 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7079 (mp) REVERT: F 493 ASP cc_start: 0.6666 (m-30) cc_final: 0.6252 (m-30) REVERT: F 554 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7671 (mt0) REVERT: F 639 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7015 (t0) REVERT: F 704 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6932 (mp0) outliers start: 37 outliers final: 25 residues processed: 224 average time/residue: 0.1225 time to fit residues: 39.2658 Evaluate side-chains 227 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain D residue 510 PHE Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain E residue 450 LEU Chi-restraints excluded: chain E residue 506 VAL Chi-restraints excluded: chain E residue 510 PHE Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 602 SER Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain E residue 691 THR Chi-restraints excluded: chain F residue 450 LEU Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 704 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 139 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 152 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.211803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.177401 restraints weight = 15769.766| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.84 r_work: 0.3819 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13950 Z= 0.122 Angle : 0.506 9.984 18858 Z= 0.258 Chirality : 0.037 0.121 2124 Planarity : 0.004 0.038 2430 Dihedral : 3.285 17.887 1878 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.37 % Allowed : 18.84 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.21), residues: 1674 helix: 2.71 (0.14), residues: 1308 sheet: None (None), residues: 0 loop : -1.87 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 561 TYR 0.010 0.001 TYR B 613 PHE 0.015 0.001 PHE E 643 TRP 0.010 0.001 TRP D 466 HIS 0.011 0.001 HIS F 465 Details of bonding type rmsd covalent geometry : bond 0.00266 (13950) covalent geometry : angle 0.50566 (18858) hydrogen bonds : bond 0.04763 ( 973) hydrogen bonds : angle 3.63482 ( 2901) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2973.46 seconds wall clock time: 51 minutes 37.91 seconds (3097.91 seconds total)