Starting phenix.real_space_refine on Sat Dec 9 21:19:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wij_32531/12_2023/7wij_32531.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wij_32531/12_2023/7wij_32531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wij_32531/12_2023/7wij_32531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wij_32531/12_2023/7wij_32531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wij_32531/12_2023/7wij_32531.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wij_32531/12_2023/7wij_32531.pdb" } resolution = 3.17 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= 0.008 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 54 5.16 5 C 7950 2.51 5 N 2136 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 492": "OD1" <-> "OD2" Residue "B GLU 420": "OE1" <-> "OE2" Residue "B ASP 540": "OD1" <-> "OD2" Residue "D GLU 420": "OE1" <-> "OE2" Residue "D ASP 540": "OD1" <-> "OD2" Residue "F ASP 492": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12396 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2066 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2066 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2066 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2066 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2066 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2066 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 6.63, per 1000 atoms: 0.53 Number of scatterers: 12396 At special positions: 0 Unit cell: (115.28, 125.84, 81.84, 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 54 16.00 O 2256 8.00 N 2136 7.00 C 7950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.78 Conformation dependent library (CDL) restraints added in 2.5 seconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 0 sheets defined 82.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 404 through 411 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 433 through 453 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 476 through 495 Processing helix chain 'A' and resid 501 through 527 removed outlier: 3.523A pdb=" N ILE A 505 " --> pdb=" O LYS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 557 removed outlier: 4.856A pdb=" N LEU A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 587 Processing helix chain 'A' and resid 608 through 617 removed outlier: 3.572A pdb=" N LYS A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 635 Processing helix chain 'A' and resid 638 through 652 Processing helix chain 'A' and resid 653 through 678 removed outlier: 3.666A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 694 Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 433 through 453 Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 475 through 495 removed outlier: 3.611A pdb=" N THR B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 527 removed outlier: 3.517A pdb=" N ILE B 505 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 524 " --> pdb=" O ASP B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 557 removed outlier: 4.852A pdb=" N LEU B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 587 Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.607A pdb=" N LYS B 616 " --> pdb=" O ILE B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 635 Processing helix chain 'B' and resid 638 through 653 Processing helix chain 'B' and resid 653 through 678 removed outlier: 3.687A pdb=" N ARG B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 674 " --> pdb=" O HIS B 670 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS B 675 " --> pdb=" O ARG B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 693 Processing helix chain 'C' and resid 404 through 411 Processing helix chain 'C' and resid 417 through 427 Processing helix chain 'C' and resid 433 through 453 Processing helix chain 'C' and resid 469 through 475 Processing helix chain 'C' and resid 475 through 495 removed outlier: 3.704A pdb=" N THR C 479 " --> pdb=" O GLY C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 527 removed outlier: 3.532A pdb=" N ILE C 505 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 557 removed outlier: 4.823A pdb=" N LEU C 546 " --> pdb=" O LYS C 542 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE C 547 " --> pdb=" O THR C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 587 Processing helix chain 'C' and resid 608 through 617 removed outlier: 3.697A pdb=" N LYS C 616 " --> pdb=" O ILE C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 635 Processing helix chain 'C' and resid 638 through 652 Processing helix chain 'C' and resid 653 through 678 removed outlier: 3.735A pdb=" N ARG C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 675 " --> pdb=" O ARG C 671 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 676 " --> pdb=" O GLU C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 693 Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 417 through 427 Processing helix chain 'D' and resid 433 through 453 Processing helix chain 'D' and resid 469 through 475 Processing helix chain 'D' and resid 475 through 495 removed outlier: 3.610A pdb=" N THR D 479 " --> pdb=" O GLY D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 527 removed outlier: 3.517A pdb=" N ILE D 505 " --> pdb=" O LYS D 501 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 524 " --> pdb=" O ASP D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 557 removed outlier: 4.832A pdb=" N LEU D 546 " --> pdb=" O LYS D 542 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE D 547 " --> pdb=" O THR D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 588 Processing helix chain 'D' and resid 608 through 617 removed outlier: 3.605A pdb=" N LYS D 616 " --> pdb=" O ILE D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 635 Processing helix chain 'D' and resid 638 through 653 Processing helix chain 'D' and resid 653 through 678 removed outlier: 3.703A pdb=" N ARG D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA D 674 " --> pdb=" O HIS D 670 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 675 " --> pdb=" O ARG D 671 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 676 " --> pdb=" O GLU D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 693 Processing helix chain 'E' and resid 404 through 411 Processing helix chain 'E' and resid 417 through 427 Processing helix chain 'E' and resid 433 through 453 Processing helix chain 'E' and resid 469 through 475 Processing helix chain 'E' and resid 475 through 495 removed outlier: 3.704A pdb=" N THR E 479 " --> pdb=" O GLY E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 527 removed outlier: 3.532A pdb=" N ILE E 505 " --> pdb=" O LYS E 501 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR E 524 " --> pdb=" O ASP E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 557 removed outlier: 4.823A pdb=" N LEU E 546 " --> pdb=" O LYS E 542 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE E 547 " --> pdb=" O THR E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 587 Processing helix chain 'E' and resid 608 through 617 removed outlier: 3.672A pdb=" N LYS E 616 " --> pdb=" O ILE E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 635 Processing helix chain 'E' and resid 638 through 652 Processing helix chain 'E' and resid 653 through 678 removed outlier: 3.715A pdb=" N ARG E 659 " --> pdb=" O LEU E 655 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS E 675 " --> pdb=" O ARG E 671 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 676 " --> pdb=" O GLU E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 686 through 693 Processing helix chain 'F' and resid 404 through 411 removed outlier: 3.515A pdb=" N LEU F 410 " --> pdb=" O PRO F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 427 Processing helix chain 'F' and resid 433 through 453 Processing helix chain 'F' and resid 469 through 475 Processing helix chain 'F' and resid 476 through 495 Processing helix chain 'F' and resid 501 through 527 removed outlier: 3.523A pdb=" N ILE F 505 " --> pdb=" O LYS F 501 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR F 524 " --> pdb=" O ASP F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 557 removed outlier: 4.814A pdb=" N LEU F 546 " --> pdb=" O LYS F 542 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE F 547 " --> pdb=" O THR F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 587 Processing helix chain 'F' and resid 608 through 617 removed outlier: 3.572A pdb=" N LYS F 616 " --> pdb=" O ILE F 612 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 635 Processing helix chain 'F' and resid 638 through 652 Processing helix chain 'F' and resid 653 through 678 removed outlier: 3.661A pdb=" N ARG F 659 " --> pdb=" O LEU F 655 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS F 675 " --> pdb=" O ARG F 671 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU F 676 " --> pdb=" O GLU F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 694 952 hydrogen bonds defined for protein. 2856 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: 3.60 Time building geometry restraints manager: 5.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4020 1.34 - 1.46: 1830 1.46 - 1.57: 6636 1.57 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 12588 Sorted by residual: bond pdb=" CG1 ILE D 579 " pdb=" CD1 ILE D 579 " ideal model delta sigma weight residual 1.513 1.485 0.028 3.90e-02 6.57e+02 5.30e-01 bond pdb=" CA ILE F 579 " pdb=" C ILE F 579 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.46e-02 4.69e+03 4.54e-01 bond pdb=" C LEU A 609 " pdb=" N PRO A 610 " ideal model delta sigma weight residual 1.335 1.345 -0.009 1.36e-02 5.41e+03 4.53e-01 bond pdb=" CA ILE A 579 " pdb=" C ILE A 579 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.46e-02 4.69e+03 4.48e-01 bond pdb=" C LEU B 609 " pdb=" N PRO B 610 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 4.43e-01 ... (remaining 12583 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.44: 285 106.44 - 113.33: 7226 113.33 - 120.22: 4294 120.22 - 127.11: 5055 127.11 - 134.00: 126 Bond angle restraints: 16986 Sorted by residual: angle pdb=" CA LEU D 550 " pdb=" CB LEU D 550 " pdb=" CG LEU D 550 " ideal model delta sigma weight residual 116.30 126.36 -10.06 3.50e+00 8.16e-02 8.26e+00 angle pdb=" CA LEU A 550 " pdb=" CB LEU A 550 " pdb=" CG LEU A 550 " ideal model delta sigma weight residual 116.30 126.07 -9.77 3.50e+00 8.16e-02 7.79e+00 angle pdb=" CA LEU B 550 " pdb=" CB LEU B 550 " pdb=" CG LEU B 550 " ideal model delta sigma weight residual 116.30 126.00 -9.70 3.50e+00 8.16e-02 7.68e+00 angle pdb=" CA LEU F 550 " pdb=" CB LEU F 550 " pdb=" CG LEU F 550 " ideal model delta sigma weight residual 116.30 125.84 -9.54 3.50e+00 8.16e-02 7.44e+00 angle pdb=" C PHE E 547 " pdb=" N HIS E 548 " pdb=" CA HIS E 548 " ideal model delta sigma weight residual 122.06 117.06 5.00 1.86e+00 2.89e-01 7.24e+00 ... (remaining 16981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6879 17.96 - 35.91: 621 35.91 - 53.87: 106 53.87 - 71.82: 32 71.82 - 89.78: 6 Dihedral angle restraints: 7644 sinusoidal: 3006 harmonic: 4638 Sorted by residual: dihedral pdb=" CA HIS E 548 " pdb=" C HIS E 548 " pdb=" N LEU E 549 " pdb=" CA LEU E 549 " ideal model delta harmonic sigma weight residual 180.00 159.42 20.58 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA HIS C 548 " pdb=" C HIS C 548 " pdb=" N LEU C 549 " pdb=" CA LEU C 549 " ideal model delta harmonic sigma weight residual 180.00 159.42 20.58 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA HIS B 548 " pdb=" C HIS B 548 " pdb=" N LEU B 549 " pdb=" CA LEU B 549 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 7641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1463 0.034 - 0.069: 481 0.069 - 0.103: 78 0.103 - 0.137: 6 0.137 - 0.172: 6 Chirality restraints: 2034 Sorted by residual: chirality pdb=" CA HIS F 548 " pdb=" N HIS F 548 " pdb=" C HIS F 548 " pdb=" CB HIS F 548 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA HIS A 548 " pdb=" N HIS A 548 " pdb=" C HIS A 548 " pdb=" CB HIS A 548 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA HIS C 548 " pdb=" N HIS C 548 " pdb=" C HIS C 548 " pdb=" CB HIS C 548 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 2031 not shown) Planarity restraints: 2100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 548 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C HIS A 548 " 0.027 2.00e-02 2.50e+03 pdb=" O HIS A 548 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 549 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS F 548 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" C HIS F 548 " -0.027 2.00e-02 2.50e+03 pdb=" O HIS F 548 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU F 549 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS E 548 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C HIS E 548 " -0.027 2.00e-02 2.50e+03 pdb=" O HIS E 548 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU E 549 " 0.009 2.00e-02 2.50e+03 ... (remaining 2097 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2287 2.77 - 3.31: 12023 3.31 - 3.84: 20224 3.84 - 4.37: 22294 4.37 - 4.90: 40388 Nonbonded interactions: 97216 Sorted by model distance: nonbonded pdb=" OE1 GLU A 509 " pdb=" NE2 HIS A 548 " model vdw 2.243 2.520 nonbonded pdb=" OE1 GLU B 509 " pdb=" NE2 HIS B 548 " model vdw 2.244 2.520 nonbonded pdb=" OE1 GLU F 509 " pdb=" NE2 HIS F 548 " model vdw 2.244 2.520 nonbonded pdb=" OE1 GLU D 509 " pdb=" NE2 HIS D 548 " model vdw 2.244 2.520 nonbonded pdb=" OE1 GLU E 509 " pdb=" NE2 HIS E 548 " model vdw 2.246 2.520 ... (remaining 97211 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 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: 3.020 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: 14.140 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 34.140 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 0.028 12588 Z= 0.157 Angle : 0.503 10.058 16986 Z= 0.251 Chirality : 0.034 0.172 2034 Planarity : 0.003 0.025 2100 Dihedral : 14.486 89.778 4620 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.22), residues: 1554 helix: 2.24 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -0.68 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 487 HIS 0.008 0.001 HIS E 548 PHE 0.007 0.001 PHE B 577 TYR 0.004 0.001 TYR A 535 ARG 0.001 0.000 ARG F 504 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.453 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1959 time to fit residues: 55.0736 Evaluate side-chains 164 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.402 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0670 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 122 optimal weight: 0.0970 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12588 Z= 0.194 Angle : 0.516 11.033 16986 Z= 0.257 Chirality : 0.035 0.179 2034 Planarity : 0.003 0.032 2100 Dihedral : 3.402 20.105 1692 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 0.08 % Allowed : 6.03 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.22), residues: 1554 helix: 2.45 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -0.70 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 523 HIS 0.008 0.001 HIS D 548 PHE 0.009 0.001 PHE D 577 TYR 0.004 0.001 TYR F 685 ARG 0.002 0.000 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.401 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 0.1991 time to fit residues: 51.6916 Evaluate side-chains 162 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.404 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1053 time to fit residues: 2.1982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 517 GLN E 517 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12588 Z= 0.251 Angle : 0.548 12.122 16986 Z= 0.273 Chirality : 0.036 0.189 2034 Planarity : 0.003 0.033 2100 Dihedral : 3.459 20.096 1692 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.90 % Allowed : 7.77 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.22), residues: 1554 helix: 2.31 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -0.60 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 523 HIS 0.009 0.001 HIS D 548 PHE 0.012 0.002 PHE D 577 TYR 0.005 0.001 TYR F 685 ARG 0.002 0.000 ARG D 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 1.460 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 173 average time/residue: 0.2179 time to fit residues: 57.0823 Evaluate side-chains 168 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.453 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1146 time to fit residues: 3.7301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 ASN C 517 GLN E 517 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12588 Z= 0.167 Angle : 0.485 11.187 16986 Z= 0.242 Chirality : 0.034 0.173 2034 Planarity : 0.003 0.032 2100 Dihedral : 3.357 19.796 1692 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.75 % Allowed : 9.28 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.22), residues: 1554 helix: 2.51 (0.14), residues: 1350 sheet: None (None), residues: 0 loop : -0.27 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 487 HIS 0.008 0.001 HIS D 548 PHE 0.007 0.001 PHE D 577 TYR 0.004 0.001 TYR A 535 ARG 0.001 0.000 ARG F 504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 174 time to evaluate : 1.506 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 180 average time/residue: 0.1951 time to fit residues: 54.8761 Evaluate side-chains 181 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 174 time to evaluate : 1.501 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1073 time to fit residues: 3.4031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 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 585 ASN B 585 ASN C 517 GLN E 517 GLN F 585 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12588 Z= 0.168 Angle : 0.489 11.234 16986 Z= 0.242 Chirality : 0.034 0.174 2034 Planarity : 0.003 0.030 2100 Dihedral : 3.318 19.623 1692 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.45 % Allowed : 10.63 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.22), residues: 1554 helix: 2.61 (0.14), residues: 1350 sheet: None (None), residues: 0 loop : -0.26 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 429 HIS 0.008 0.001 HIS B 548 PHE 0.008 0.001 PHE A 519 TYR 0.003 0.001 TYR A 535 ARG 0.002 0.000 ARG F 504 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 172 time to evaluate : 1.453 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 174 average time/residue: 0.2043 time to fit residues: 55.5032 Evaluate side-chains 175 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1279 time to fit residues: 2.9646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.2980 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 ASN C 517 GLN E 517 GLN F 585 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12588 Z= 0.145 Angle : 0.470 11.358 16986 Z= 0.232 Chirality : 0.033 0.170 2034 Planarity : 0.003 0.029 2100 Dihedral : 3.244 19.325 1692 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.13 % Allowed : 11.09 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.22), residues: 1554 helix: 2.73 (0.14), residues: 1350 sheet: None (None), residues: 0 loop : -0.21 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 487 HIS 0.008 0.001 HIS D 548 PHE 0.007 0.001 PHE A 519 TYR 0.003 0.001 TYR A 535 ARG 0.001 0.000 ARG F 504 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 175 time to evaluate : 1.494 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 188 average time/residue: 0.1961 time to fit residues: 58.2235 Evaluate side-chains 183 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 173 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1162 time to fit residues: 4.1972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 150 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 69 optimal weight: 0.0570 chunk 93 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 517 GLN E 517 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12588 Z= 0.157 Angle : 0.478 11.493 16986 Z= 0.237 Chirality : 0.033 0.172 2034 Planarity : 0.003 0.029 2100 Dihedral : 3.254 19.326 1692 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.45 % Allowed : 11.69 % 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: 3.56 (0.22), residues: 1554 helix: 2.69 (0.14), residues: 1356 sheet: None (None), residues: 0 loop : -0.18 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 523 HIS 0.008 0.001 HIS D 548 PHE 0.007 0.001 PHE A 519 TYR 0.003 0.001 TYR A 535 ARG 0.001 0.000 ARG F 504 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 169 time to evaluate : 1.561 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 173 average time/residue: 0.2014 time to fit residues: 54.3517 Evaluate side-chains 169 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 1.529 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1104 time to fit residues: 2.7017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.0770 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 14 optimal weight: 0.0970 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 517 GLN E 517 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12588 Z= 0.166 Angle : 0.490 11.787 16986 Z= 0.240 Chirality : 0.034 0.174 2034 Planarity : 0.003 0.029 2100 Dihedral : 3.270 19.331 1692 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.30 % Allowed : 11.92 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.22), residues: 1554 helix: 2.67 (0.14), residues: 1356 sheet: None (None), residues: 0 loop : -0.19 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 429 HIS 0.008 0.001 HIS D 548 PHE 0.007 0.001 PHE A 519 TYR 0.003 0.001 TYR A 535 ARG 0.002 0.000 ARG F 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 161 time to evaluate : 1.434 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 163 average time/residue: 0.2018 time to fit residues: 51.2583 Evaluate side-chains 161 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 1.505 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1137 time to fit residues: 2.5389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 140 optimal weight: 0.5980 chunk 144 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12588 Z= 0.184 Angle : 0.504 11.907 16986 Z= 0.248 Chirality : 0.034 0.178 2034 Planarity : 0.003 0.030 2100 Dihedral : 3.312 19.374 1692 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.08 % Allowed : 11.99 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.22), residues: 1554 helix: 2.64 (0.14), residues: 1350 sheet: None (None), residues: 0 loop : -0.27 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 523 HIS 0.008 0.001 HIS D 548 PHE 0.008 0.001 PHE D 577 TYR 0.003 0.001 TYR F 685 ARG 0.002 0.000 ARG F 504 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.581 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 162 average time/residue: 0.2439 time to fit residues: 62.0443 Evaluate side-chains 161 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.682 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1220 time to fit residues: 3.0476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.0970 chunk 90 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12588 Z= 0.164 Angle : 0.491 11.685 16986 Z= 0.241 Chirality : 0.034 0.174 2034 Planarity : 0.003 0.029 2100 Dihedral : 3.288 19.328 1692 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.22), residues: 1554 helix: 2.66 (0.14), residues: 1356 sheet: None (None), residues: 0 loop : -0.18 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 429 HIS 0.008 0.001 HIS D 548 PHE 0.008 0.001 PHE A 519 TYR 0.003 0.001 TYR A 535 ARG 0.002 0.000 ARG F 504 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.454 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2071 time to fit residues: 53.6871 Evaluate side-chains 165 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.139070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.112097 restraints weight = 13338.075| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.22 r_work: 0.2948 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12588 Z= 0.202 Angle : 0.514 12.074 16986 Z= 0.254 Chirality : 0.035 0.180 2034 Planarity : 0.003 0.030 2100 Dihedral : 3.348 19.383 1692 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.08 % Allowed : 12.29 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.22), residues: 1554 helix: 2.62 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -0.51 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 523 HIS 0.008 0.001 HIS D 548 PHE 0.009 0.001 PHE D 577 TYR 0.004 0.001 TYR A 685 ARG 0.002 0.000 ARG B 504 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2569.67 seconds wall clock time: 47 minutes 39.34 seconds (2859.34 seconds total)