Starting phenix.real_space_refine on Wed Dec 13 10:51:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5z_20659/12_2023/6u5z_20659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5z_20659/12_2023/6u5z_20659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5z_20659/12_2023/6u5z_20659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5z_20659/12_2023/6u5z_20659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5z_20659/12_2023/6u5z_20659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5z_20659/12_2023/6u5z_20659.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 126 5.16 5 C 15462 2.51 5 N 4380 2.21 5 O 4638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 545": "OE1" <-> "OE2" Residue "B GLU 545": "OE1" <-> "OE2" Residue "C GLU 545": "OE1" <-> "OE2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "E GLU 545": "OE1" <-> "OE2" Residue "F GLU 545": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 24606 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain: "B" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain: "C" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain: "D" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain: "E" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Chain: "F" Number of atoms: 4101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4101 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 25, 'TRANS': 503} Time building chain proxies: 12.27, per 1000 atoms: 0.50 Number of scatterers: 24606 At special positions: 0 Unit cell: (143.312, 133.136, 166.208, 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 126 16.00 O 4638 8.00 N 4380 7.00 C 15462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 691 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 691 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 691 " distance=2.04 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 691 " distance=2.04 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 691 " distance=2.04 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 691 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.93 Conformation dependent library (CDL) restraints added in 4.5 seconds 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 30 sheets defined 48.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.733A pdb=" N GLU A 252 " --> pdb=" O PRO A 248 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 287 through 301 removed outlier: 3.557A pdb=" N VAL A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 321 Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.969A pdb=" N ARG A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 374 Processing helix chain 'A' and resid 387 through 392 removed outlier: 4.263A pdb=" N ILE A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 Processing helix chain 'A' and resid 436 through 445 Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.532A pdb=" N PHE A 452 " --> pdb=" O ASN A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 4.062A pdb=" N ASP A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 514 Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.762A pdb=" N ILE A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 561 Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 631 through 653 removed outlier: 5.274A pdb=" N GLU A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'A' and resid 680 through 694 Processing helix chain 'A' and resid 718 through 729 Processing helix chain 'A' and resid 739 through 747 removed outlier: 4.141A pdb=" N ARG A 742 " --> pdb=" O GLU A 739 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A 745 " --> pdb=" O ARG A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE A 752 " --> pdb=" O PRO A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 771 removed outlier: 3.593A pdb=" N VAL A 766 " --> pdb=" O ARG A 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.734A pdb=" N GLU B 252 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 287 through 301 removed outlier: 3.557A pdb=" N VAL B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 321 Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.969A pdb=" N ARG B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 374 Processing helix chain 'B' and resid 387 through 392 removed outlier: 4.263A pdb=" N ILE B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 413 Processing helix chain 'B' and resid 436 through 445 Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.532A pdb=" N PHE B 452 " --> pdb=" O ASN B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 4.061A pdb=" N ASP B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 505 through 514 Processing helix chain 'B' and resid 524 through 535 removed outlier: 3.762A pdb=" N ILE B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 561 Processing helix chain 'B' and resid 575 through 580 Processing helix chain 'B' and resid 631 through 653 removed outlier: 5.274A pdb=" N GLU B 650 " --> pdb=" O ARG B 646 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 661 Processing helix chain 'B' and resid 680 through 694 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 739 through 747 removed outlier: 4.140A pdb=" N ARG B 742 " --> pdb=" O GLU B 739 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU B 745 " --> pdb=" O ARG B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE B 752 " --> pdb=" O PRO B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 771 removed outlier: 3.593A pdb=" N VAL B 766 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 260 removed outlier: 3.733A pdb=" N GLU C 252 " --> pdb=" O PRO C 248 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 287 through 301 removed outlier: 3.557A pdb=" N VAL C 291 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 321 Processing helix chain 'C' and resid 329 through 341 removed outlier: 3.969A pdb=" N ARG C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 374 Processing helix chain 'C' and resid 387 through 392 removed outlier: 4.263A pdb=" N ILE C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 413 Processing helix chain 'C' and resid 436 through 445 Processing helix chain 'C' and resid 448 through 452 removed outlier: 3.533A pdb=" N PHE C 452 " --> pdb=" O ASN C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 4.062A pdb=" N ASP C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 505 through 514 Processing helix chain 'C' and resid 524 through 535 removed outlier: 3.762A pdb=" N ILE C 528 " --> pdb=" O ASP C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 561 Processing helix chain 'C' and resid 575 through 580 Processing helix chain 'C' and resid 631 through 653 removed outlier: 5.274A pdb=" N GLU C 650 " --> pdb=" O ARG C 646 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS C 651 " --> pdb=" O ALA C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 661 Processing helix chain 'C' and resid 680 through 694 Processing helix chain 'C' and resid 718 through 729 Processing helix chain 'C' and resid 739 through 747 removed outlier: 4.141A pdb=" N ARG C 742 " --> pdb=" O GLU C 739 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU C 745 " --> pdb=" O ARG C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE C 752 " --> pdb=" O PRO C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 771 removed outlier: 3.593A pdb=" N VAL C 766 " --> pdb=" O ARG C 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 260 removed outlier: 3.733A pdb=" N GLU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP D 259 " --> pdb=" O LYS D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 287 through 301 removed outlier: 3.558A pdb=" N VAL D 291 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 321 Processing helix chain 'D' and resid 329 through 341 removed outlier: 3.969A pdb=" N ARG D 333 " --> pdb=" O ARG D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 374 Processing helix chain 'D' and resid 387 through 392 removed outlier: 4.263A pdb=" N ILE D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 413 Processing helix chain 'D' and resid 436 through 445 Processing helix chain 'D' and resid 448 through 452 removed outlier: 3.533A pdb=" N PHE D 452 " --> pdb=" O ASN D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 483 removed outlier: 4.062A pdb=" N ASP D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 524 through 535 removed outlier: 3.761A pdb=" N ILE D 528 " --> pdb=" O ASP D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 561 Processing helix chain 'D' and resid 575 through 580 Processing helix chain 'D' and resid 631 through 653 removed outlier: 5.275A pdb=" N GLU D 650 " --> pdb=" O ARG D 646 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS D 651 " --> pdb=" O ALA D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 661 Processing helix chain 'D' and resid 680 through 694 Processing helix chain 'D' and resid 718 through 729 Processing helix chain 'D' and resid 739 through 747 removed outlier: 4.140A pdb=" N ARG D 742 " --> pdb=" O GLU D 739 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU D 745 " --> pdb=" O ARG D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE D 752 " --> pdb=" O PRO D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 771 removed outlier: 3.593A pdb=" N VAL D 766 " --> pdb=" O ARG D 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 260 removed outlier: 3.733A pdb=" N GLU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP E 259 " --> pdb=" O LYS E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 287 through 301 removed outlier: 3.557A pdb=" N VAL E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 321 Processing helix chain 'E' and resid 329 through 341 removed outlier: 3.969A pdb=" N ARG E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 374 Processing helix chain 'E' and resid 387 through 392 removed outlier: 4.262A pdb=" N ILE E 391 " --> pdb=" O ASP E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 413 Processing helix chain 'E' and resid 436 through 445 Processing helix chain 'E' and resid 448 through 452 removed outlier: 3.531A pdb=" N PHE E 452 " --> pdb=" O ASN E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 483 removed outlier: 4.061A pdb=" N ASP E 483 " --> pdb=" O ALA E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 505 Processing helix chain 'E' and resid 505 through 514 Processing helix chain 'E' and resid 524 through 535 removed outlier: 3.762A pdb=" N ILE E 528 " --> pdb=" O ASP E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 561 Processing helix chain 'E' and resid 575 through 580 Processing helix chain 'E' and resid 631 through 653 removed outlier: 5.274A pdb=" N GLU E 650 " --> pdb=" O ARG E 646 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LYS E 651 " --> pdb=" O ALA E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 661 Processing helix chain 'E' and resid 680 through 694 Processing helix chain 'E' and resid 718 through 729 Processing helix chain 'E' and resid 739 through 747 removed outlier: 4.140A pdb=" N ARG E 742 " --> pdb=" O GLU E 739 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU E 745 " --> pdb=" O ARG E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE E 752 " --> pdb=" O PRO E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 771 removed outlier: 3.593A pdb=" N VAL E 766 " --> pdb=" O ARG E 762 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 260 removed outlier: 3.734A pdb=" N GLU F 252 " --> pdb=" O PRO F 248 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP F 259 " --> pdb=" O LYS F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 278 Processing helix chain 'F' and resid 287 through 301 removed outlier: 3.557A pdb=" N VAL F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 329 through 341 removed outlier: 3.970A pdb=" N ARG F 333 " --> pdb=" O ARG F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 374 Processing helix chain 'F' and resid 387 through 392 removed outlier: 4.262A pdb=" N ILE F 391 " --> pdb=" O ASP F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 413 Processing helix chain 'F' and resid 436 through 445 Processing helix chain 'F' and resid 448 through 452 removed outlier: 3.532A pdb=" N PHE F 452 " --> pdb=" O ASN F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 483 removed outlier: 4.062A pdb=" N ASP F 483 " --> pdb=" O ALA F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 505 Processing helix chain 'F' and resid 505 through 514 Processing helix chain 'F' and resid 524 through 535 removed outlier: 3.761A pdb=" N ILE F 528 " --> pdb=" O ASP F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 561 Processing helix chain 'F' and resid 575 through 580 Processing helix chain 'F' and resid 631 through 653 removed outlier: 5.275A pdb=" N GLU F 650 " --> pdb=" O ARG F 646 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS F 651 " --> pdb=" O ALA F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 657 through 661 Processing helix chain 'F' and resid 680 through 694 Processing helix chain 'F' and resid 718 through 729 Processing helix chain 'F' and resid 739 through 747 removed outlier: 4.141A pdb=" N ARG F 742 " --> pdb=" O GLU F 739 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU F 745 " --> pdb=" O ARG F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 753 removed outlier: 3.572A pdb=" N ILE F 752 " --> pdb=" O PRO F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 762 through 771 removed outlier: 3.592A pdb=" N VAL F 766 " --> pdb=" O ARG F 762 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 381 removed outlier: 7.363A pdb=" N VAL A 378 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ASP A 423 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET A 380 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AA3, first strand: chain 'A' and resid 597 through 602 removed outlier: 6.559A pdb=" N THR A 625 " --> pdb=" O VAL A 666 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.651A pdb=" N ALA A 702 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 734 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL A 760 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE A 736 " --> pdb=" O VAL A 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 706 through 707 removed outlier: 3.608A pdb=" N GLU A 706 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 377 through 381 removed outlier: 7.362A pdb=" N VAL B 378 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASP B 423 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET B 380 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 521 through 523 removed outlier: 6.611A pdb=" N THR B 522 " --> pdb=" O ILE B 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 597 through 602 removed outlier: 6.559A pdb=" N THR B 625 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.650A pdb=" N ALA B 702 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL B 734 " --> pdb=" O HIS B 758 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL B 760 " --> pdb=" O VAL B 734 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE B 736 " --> pdb=" O VAL B 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 706 through 707 removed outlier: 3.607A pdb=" N GLU B 706 " --> pdb=" O LEU B 714 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 377 through 381 removed outlier: 7.363A pdb=" N VAL C 378 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ASP C 423 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET C 380 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 521 through 523 Processing sheet with id=AB4, first strand: chain 'C' and resid 597 through 602 removed outlier: 6.559A pdb=" N THR C 625 " --> pdb=" O VAL C 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 701 through 703 removed outlier: 6.651A pdb=" N ALA C 702 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 734 " --> pdb=" O HIS C 758 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL C 760 " --> pdb=" O VAL C 734 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE C 736 " --> pdb=" O VAL C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 706 through 707 removed outlier: 3.608A pdb=" N GLU C 706 " --> pdb=" O LEU C 714 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 377 through 381 removed outlier: 7.363A pdb=" N VAL D 378 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ASP D 423 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET D 380 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 521 through 523 Processing sheet with id=AB9, first strand: chain 'D' and resid 597 through 602 removed outlier: 6.559A pdb=" N THR D 625 " --> pdb=" O VAL D 666 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 701 through 703 removed outlier: 6.651A pdb=" N ALA D 702 " --> pdb=" O LEU D 735 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL D 734 " --> pdb=" O HIS D 758 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N VAL D 760 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE D 736 " --> pdb=" O VAL D 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 706 through 707 removed outlier: 3.607A pdb=" N GLU D 706 " --> pdb=" O LEU D 714 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 377 through 381 removed outlier: 7.363A pdb=" N VAL E 378 " --> pdb=" O LEU E 421 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ASP E 423 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET E 380 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 521 through 523 Processing sheet with id=AC5, first strand: chain 'E' and resid 597 through 602 removed outlier: 6.558A pdb=" N THR E 625 " --> pdb=" O VAL E 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 701 through 703 removed outlier: 6.650A pdb=" N ALA E 702 " --> pdb=" O LEU E 735 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL E 734 " --> pdb=" O HIS E 758 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL E 760 " --> pdb=" O VAL E 734 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE E 736 " --> pdb=" O VAL E 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 706 through 707 removed outlier: 3.607A pdb=" N GLU E 706 " --> pdb=" O LEU E 714 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 377 through 381 removed outlier: 7.362A pdb=" N VAL F 378 " --> pdb=" O LEU F 421 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ASP F 423 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET F 380 " --> pdb=" O ASP F 423 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 521 through 523 Processing sheet with id=AD1, first strand: chain 'F' and resid 597 through 602 removed outlier: 6.558A pdb=" N THR F 625 " --> pdb=" O VAL F 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 701 through 703 removed outlier: 6.651A pdb=" N ALA F 702 " --> pdb=" O LEU F 735 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL F 734 " --> pdb=" O HIS F 758 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL F 760 " --> pdb=" O VAL F 734 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE F 736 " --> pdb=" O VAL F 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 706 through 707 removed outlier: 3.608A pdb=" N GLU F 706 " --> pdb=" O LEU F 714 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 3036 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: 8.75 Time building geometry restraints manager: 10.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8376 1.35 - 1.47: 4717 1.47 - 1.59: 11651 1.59 - 1.71: 0 1.71 - 1.83: 222 Bond restraints: 24966 Sorted by residual: bond pdb=" N ASP A 585 " pdb=" CA ASP A 585 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.21e-02 6.83e+03 7.17e+00 bond pdb=" N ASP D 585 " pdb=" CA ASP D 585 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.90e+00 bond pdb=" N ASP B 585 " pdb=" CA ASP B 585 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.90e+00 bond pdb=" N ASP F 585 " pdb=" CA ASP F 585 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.87e+00 bond pdb=" N LYS B 416 " pdb=" CA LYS B 416 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.31e-02 5.83e+03 6.86e+00 ... (remaining 24961 not shown) Histogram of bond angle deviations from ideal: 100.50 - 107.21: 867 107.21 - 113.91: 14383 113.91 - 120.62: 9835 120.62 - 127.32: 8376 127.32 - 134.02: 223 Bond angle restraints: 33684 Sorted by residual: angle pdb=" C GLY D 326 " pdb=" N LEU D 327 " pdb=" CA LEU D 327 " ideal model delta sigma weight residual 121.54 126.22 -4.68 1.91e+00 2.74e-01 6.01e+00 angle pdb=" C GLY C 326 " pdb=" N LEU C 327 " pdb=" CA LEU C 327 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.96e+00 angle pdb=" C GLY B 326 " pdb=" N LEU B 327 " pdb=" CA LEU B 327 " ideal model delta sigma weight residual 121.54 126.18 -4.64 1.91e+00 2.74e-01 5.90e+00 angle pdb=" C GLY F 326 " pdb=" N LEU F 327 " pdb=" CA LEU F 327 " ideal model delta sigma weight residual 121.54 126.16 -4.62 1.91e+00 2.74e-01 5.86e+00 angle pdb=" C GLY E 326 " pdb=" N LEU E 327 " pdb=" CA LEU E 327 " ideal model delta sigma weight residual 121.54 126.16 -4.62 1.91e+00 2.74e-01 5.86e+00 ... (remaining 33679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.43: 14647 13.43 - 26.86: 650 26.86 - 40.29: 207 40.29 - 53.72: 54 53.72 - 67.15: 24 Dihedral angle restraints: 15582 sinusoidal: 6486 harmonic: 9096 Sorted by residual: dihedral pdb=" CA ASP F 454 " pdb=" CB ASP F 454 " pdb=" CG ASP F 454 " pdb=" OD1 ASP F 454 " ideal model delta sinusoidal sigma weight residual -30.00 -86.95 56.95 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP D 454 " pdb=" CB ASP D 454 " pdb=" CG ASP D 454 " pdb=" OD1 ASP D 454 " ideal model delta sinusoidal sigma weight residual -30.00 -86.93 56.93 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP A 454 " pdb=" CB ASP A 454 " pdb=" CG ASP A 454 " pdb=" OD1 ASP A 454 " ideal model delta sinusoidal sigma weight residual -30.00 -86.92 56.92 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 15579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2258 0.029 - 0.057: 1028 0.057 - 0.086: 348 0.086 - 0.114: 187 0.114 - 0.143: 37 Chirality restraints: 3858 Sorted by residual: chirality pdb=" CA ILE F 747 " pdb=" N ILE F 747 " pdb=" C ILE F 747 " pdb=" CB ILE F 747 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE D 747 " pdb=" N ILE D 747 " pdb=" C ILE D 747 " pdb=" CB ILE D 747 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE E 747 " pdb=" N ILE E 747 " pdb=" C ILE E 747 " pdb=" CB ILE E 747 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 3855 not shown) Planarity restraints: 4380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET F 263 " -0.027 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO F 264 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 264 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 264 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 263 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO E 264 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 264 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 264 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 263 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 264 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 264 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 264 " -0.023 5.00e-02 4.00e+02 ... (remaining 4377 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1473 2.73 - 3.28: 25104 3.28 - 3.82: 38760 3.82 - 4.36: 48541 4.36 - 4.90: 80775 Nonbonded interactions: 194653 Sorted by model distance: nonbonded pdb=" OG SER C 453 " pdb=" OD1 ASP C 460 " model vdw 2.194 2.440 nonbonded pdb=" OG SER E 453 " pdb=" OD1 ASP E 460 " model vdw 2.194 2.440 nonbonded pdb=" OG SER A 453 " pdb=" OD1 ASP A 460 " model vdw 2.194 2.440 nonbonded pdb=" OG SER D 453 " pdb=" OD1 ASP D 460 " model vdw 2.195 2.440 nonbonded pdb=" OG SER F 453 " pdb=" OD1 ASP F 460 " model vdw 2.195 2.440 ... (remaining 194648 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.350 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 64.680 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5511 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 : 0.002 0.034 24966 Z= 0.133 Angle : 0.540 5.790 33684 Z= 0.319 Chirality : 0.041 0.143 3858 Planarity : 0.004 0.042 4380 Dihedral : 9.077 67.151 9720 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 3162 helix: -0.07 (0.14), residues: 1242 sheet: -1.03 (0.19), residues: 474 loop : -1.91 (0.14), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 303 HIS 0.001 0.000 HIS E 324 PHE 0.003 0.001 PHE F 420 TYR 0.006 0.001 TYR C 377 ARG 0.002 0.000 ARG D 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.4197 time to fit residues: 329.1121 Evaluate side-chains 267 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 2.525 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 chunk 131 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 244 optimal weight: 10.0000 chunk 94 optimal weight: 0.4980 chunk 148 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 0.0770 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS A 510 GLN A 597 GLN C 510 GLN C 667 HIS C 712 GLN D 635 GLN D 712 GLN E 251 ASN ** E 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 473 ASN F 455 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24966 Z= 0.199 Angle : 0.587 8.855 33684 Z= 0.294 Chirality : 0.043 0.171 3858 Planarity : 0.004 0.054 4380 Dihedral : 2.930 17.601 3456 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.53 % Allowed : 9.62 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3162 helix: 1.11 (0.14), residues: 1248 sheet: -0.52 (0.22), residues: 432 loop : -1.14 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 303 HIS 0.005 0.001 HIS A 505 PHE 0.016 0.001 PHE E 658 TYR 0.024 0.001 TYR B 337 ARG 0.007 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 310 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 29 residues processed: 355 average time/residue: 0.3625 time to fit residues: 202.2882 Evaluate side-chains 276 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 247 time to evaluate : 2.756 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2245 time to fit residues: 16.0242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 283 optimal weight: 0.9990 chunk 306 optimal weight: 20.0000 chunk 252 optimal weight: 0.4980 chunk 281 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN A 635 GLN ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 HIS C 591 ASN ** E 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 635 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24966 Z= 0.173 Angle : 0.547 8.966 33684 Z= 0.274 Chirality : 0.042 0.177 3858 Planarity : 0.004 0.058 4380 Dihedral : 3.184 23.150 3456 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.32 % Allowed : 11.54 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3162 helix: 1.52 (0.15), residues: 1248 sheet: -0.15 (0.21), residues: 474 loop : -1.12 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 303 HIS 0.002 0.000 HIS D 567 PHE 0.012 0.001 PHE E 658 TYR 0.012 0.001 TYR B 337 ARG 0.007 0.000 ARG C 594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 283 time to evaluate : 2.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 15 residues processed: 303 average time/residue: 0.3778 time to fit residues: 183.6051 Evaluate side-chains 245 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 230 time to evaluate : 2.526 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2840 time to fit residues: 11.3917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 284 optimal weight: 0.9990 chunk 301 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 269 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN D 591 ASN ** E 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24966 Z= 0.189 Angle : 0.549 11.576 33684 Z= 0.276 Chirality : 0.042 0.197 3858 Planarity : 0.004 0.057 4380 Dihedral : 3.393 26.356 3456 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.36 % Allowed : 12.90 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3162 helix: 1.76 (0.15), residues: 1236 sheet: -0.11 (0.21), residues: 516 loop : -1.07 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 303 HIS 0.003 0.001 HIS C 727 PHE 0.011 0.001 PHE E 658 TYR 0.012 0.001 TYR B 337 ARG 0.007 0.000 ARG C 594 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 262 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 13 residues processed: 285 average time/residue: 0.3556 time to fit residues: 161.9903 Evaluate side-chains 243 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 230 time to evaluate : 2.637 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2110 time to fit residues: 9.2525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.0050 chunk 171 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 257 optimal weight: 4.9990 chunk 208 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 153 optimal weight: 3.9990 chunk 270 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 HIS C 510 GLN C 576 HIS D 341 GLN D 455 HIS ** D 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 758 HIS ** E 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 24966 Z= 0.402 Angle : 0.781 11.212 33684 Z= 0.399 Chirality : 0.049 0.229 3858 Planarity : 0.006 0.050 4380 Dihedral : 4.681 29.444 3456 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.51 % Favored : 93.45 % Rotamer: Outliers : 2.30 % Allowed : 13.35 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3162 helix: 0.65 (0.14), residues: 1320 sheet: -0.24 (0.24), residues: 468 loop : -2.08 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP E 303 HIS 0.007 0.002 HIS D 727 PHE 0.021 0.002 PHE A 658 TYR 0.020 0.002 TYR C 534 ARG 0.008 0.001 ARG C 728 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 312 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 26 residues processed: 354 average time/residue: 0.3693 time to fit residues: 202.1718 Evaluate side-chains 269 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 243 time to evaluate : 2.516 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2208 time to fit residues: 14.3619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 0.5980 chunk 271 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 301 optimal weight: 9.9990 chunk 250 optimal weight: 0.0670 chunk 139 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 712 GLN D 558 GLN D 635 GLN E 473 ASN E 758 HIS ** F 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 24966 Z= 0.177 Angle : 0.587 11.440 33684 Z= 0.295 Chirality : 0.042 0.218 3858 Planarity : 0.004 0.072 4380 Dihedral : 4.045 33.069 3456 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.28 % Allowed : 15.01 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 3162 helix: 1.25 (0.14), residues: 1302 sheet: -0.28 (0.22), residues: 546 loop : -1.76 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 303 HIS 0.003 0.001 HIS B 667 PHE 0.016 0.001 PHE A 658 TYR 0.030 0.001 TYR E 659 ARG 0.010 0.000 ARG F 396 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 277 time to evaluate : 2.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 11 residues processed: 301 average time/residue: 0.3578 time to fit residues: 171.1099 Evaluate side-chains 252 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 241 time to evaluate : 2.598 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2125 time to fit residues: 8.3720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 300 optimal weight: 0.9980 chunk 188 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 ASN D 591 ASN E 758 HIS ** F 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.6464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 24966 Z= 0.277 Angle : 0.646 10.298 33684 Z= 0.325 Chirality : 0.045 0.181 3858 Planarity : 0.005 0.062 4380 Dihedral : 4.220 32.062 3456 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.47 % Allowed : 15.91 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3162 helix: 1.02 (0.14), residues: 1320 sheet: -0.30 (0.24), residues: 498 loop : -1.90 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 303 HIS 0.004 0.001 HIS D 667 PHE 0.012 0.001 PHE A 658 TYR 0.032 0.002 TYR E 659 ARG 0.010 0.001 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 255 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 18 residues processed: 277 average time/residue: 0.3522 time to fit residues: 157.0805 Evaluate side-chains 258 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 240 time to evaluate : 2.616 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2327 time to fit residues: 12.1451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 90 optimal weight: 0.0870 chunk 59 optimal weight: 9.9990 chunk 58 optimal weight: 0.0980 chunk 191 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 236 optimal weight: 7.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 635 GLN ** F 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 24966 Z= 0.162 Angle : 0.569 10.347 33684 Z= 0.283 Chirality : 0.042 0.182 3858 Planarity : 0.004 0.054 4380 Dihedral : 3.943 28.450 3456 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.83 % Allowed : 16.44 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 3162 helix: 1.51 (0.15), residues: 1266 sheet: -0.14 (0.24), residues: 498 loop : -1.46 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 303 HIS 0.003 0.000 HIS E 324 PHE 0.012 0.001 PHE A 658 TYR 0.021 0.001 TYR E 659 ARG 0.007 0.000 ARG C 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 266 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 278 average time/residue: 0.3614 time to fit residues: 161.4664 Evaluate side-chains 254 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 243 time to evaluate : 2.629 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2330 time to fit residues: 8.5621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 9.9990 chunk 288 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 280 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 253 optimal weight: 7.9990 chunk 265 optimal weight: 8.9990 chunk 279 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 GLN B 758 HIS ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 ASN D 635 GLN E 758 HIS F 665 HIS ** F 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.7685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.120 24966 Z= 0.539 Angle : 0.893 12.244 33684 Z= 0.455 Chirality : 0.053 0.254 3858 Planarity : 0.006 0.070 4380 Dihedral : 5.322 38.285 3456 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.56 % Favored : 92.38 % Rotamer: Outliers : 0.90 % Allowed : 17.08 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3162 helix: 0.03 (0.14), residues: 1344 sheet: -0.51 (0.24), residues: 486 loop : -2.15 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 603 HIS 0.009 0.002 HIS B 505 PHE 0.070 0.004 PHE B 420 TYR 0.029 0.003 TYR C 377 ARG 0.009 0.001 ARG C 489 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 264 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 273 average time/residue: 0.3655 time to fit residues: 161.1583 Evaluate side-chains 244 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 229 time to evaluate : 2.954 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2325 time to fit residues: 10.5651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.8980 chunk 296 optimal weight: 6.9990 chunk 180 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 205 optimal weight: 0.6980 chunk 310 optimal weight: 9.9990 chunk 286 optimal weight: 2.9990 chunk 247 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 191 optimal weight: 0.0980 chunk 151 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 ASN B 635 GLN B 758 HIS D 591 ASN D 635 GLN ** F 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.7543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24966 Z= 0.190 Angle : 0.644 15.041 33684 Z= 0.322 Chirality : 0.044 0.172 3858 Planarity : 0.004 0.056 4380 Dihedral : 4.461 36.676 3456 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.26 % Allowed : 18.02 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3162 helix: 1.14 (0.15), residues: 1260 sheet: -0.40 (0.24), residues: 498 loop : -1.67 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 603 HIS 0.004 0.001 HIS E 324 PHE 0.014 0.001 PHE A 658 TYR 0.020 0.001 TYR E 659 ARG 0.006 0.000 ARG A 396 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 250 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 255 average time/residue: 0.3517 time to fit residues: 144.8003 Evaluate side-chains 240 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 236 time to evaluate : 2.710 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2193 time to fit residues: 5.7491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.7183 > 50: distance: 47 - 51: 3.344 distance: 83 - 85: 21.982 distance: 85 - 86: 38.265 distance: 86 - 89: 50.044 distance: 87 - 88: 39.966 distance: 87 - 94: 57.304 distance: 88 - 148: 41.339 distance: 89 - 90: 11.503 distance: 94 - 95: 56.630 distance: 95 - 96: 39.485 distance: 95 - 98: 56.525 distance: 96 - 102: 46.399 distance: 98 - 99: 57.432 distance: 98 - 100: 57.068 distance: 102 - 103: 14.030 distance: 103 - 104: 54.794 distance: 103 - 106: 43.157 distance: 104 - 105: 25.600 distance: 104 - 109: 28.258 distance: 106 - 107: 20.744 distance: 106 - 108: 40.853 distance: 109 - 110: 16.014 distance: 110 - 111: 30.059 distance: 110 - 113: 15.264 distance: 111 - 112: 24.631 distance: 111 - 117: 62.438 distance: 113 - 114: 42.839 distance: 114 - 115: 39.688 distance: 114 - 116: 44.980 distance: 117 - 118: 40.857 distance: 118 - 119: 34.360 distance: 118 - 121: 40.743 distance: 119 - 120: 39.317 distance: 119 - 128: 5.375 distance: 121 - 122: 28.413 distance: 122 - 123: 17.290 distance: 123 - 124: 29.370 distance: 124 - 125: 13.877 distance: 125 - 126: 12.210 distance: 125 - 127: 27.951 distance: 128 - 129: 14.409 distance: 129 - 130: 10.692 distance: 130 - 131: 37.972 distance: 130 - 132: 35.421 distance: 132 - 133: 37.010 distance: 133 - 134: 3.339 distance: 133 - 136: 42.456 distance: 134 - 135: 39.854 distance: 136 - 137: 47.004 distance: 138 - 139: 20.498 distance: 138 - 140: 40.902 distance: 142 - 143: 50.158 distance: 143 - 144: 50.684 distance: 143 - 148: 41.617 distance: 145 - 146: 40.763 distance: 145 - 147: 40.884 distance: 148 - 149: 39.523 distance: 149 - 152: 56.578 distance: 150 - 151: 40.127 distance: 150 - 156: 42.289 distance: 152 - 153: 57.172 distance: 153 - 155: 39.363 distance: 156 - 157: 43.739 distance: 156 - 162: 12.271 distance: 157 - 158: 34.989 distance: 157 - 160: 22.547 distance: 158 - 159: 19.896 distance: 158 - 163: 24.851 distance: 160 - 161: 28.450 distance: 161 - 162: 32.839