Starting phenix.real_space_refine on Mon Apr 8 03:33:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wij_32531/04_2024/7wij_32531.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wij_32531/04_2024/7wij_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_32531/04_2024/7wij_32531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wij_32531/04_2024/7wij_32531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wij_32531/04_2024/7wij_32531.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wij_32531/04_2024/7wij_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 6.65, per 1000 atoms: 0.54 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: 4.99 Conformation dependent library (CDL) restraints added in 2.4 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: 1.05 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: 3.52 Time building geometry restraints manager: 5.45 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: 4.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 24.390 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 32.810 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.730 ------------------------------------------------------------------------------- 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 : 1.508 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1928 time to fit residues: 54.1319 Evaluate side-chains 164 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.518 ------------------------------------------------------------------------------- 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 : 1.481 Fit side-chains REVERT: D 426 MET cc_start: 0.8299 (ttm) cc_final: 0.8037 (ttm) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 0.2097 time to fit residues: 54.3217 Evaluate side-chains 162 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 584 SER 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: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12588 Z= 0.250 Angle : 0.547 12.063 16986 Z= 0.272 Chirality : 0.036 0.189 2034 Planarity : 0.003 0.033 2100 Dihedral : 3.458 20.150 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 : 7.84 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 B 523 HIS 0.009 0.001 HIS B 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 175 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 1.431 Fit side-chains REVERT: B 659 ARG cc_start: 0.6786 (ttt-90) cc_final: 0.6553 (ttp-110) REVERT: D 659 ARG cc_start: 0.6739 (ttt-90) cc_final: 0.6529 (ttp-110) outliers start: 12 outliers final: 8 residues processed: 172 average time/residue: 0.2204 time to fit residues: 57.4770 Evaluate side-chains 168 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain F residue 686 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.6980 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: 0.6980 chunk 150 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8151 moved from start: 0.1108 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= 0.196 Angle : 0.504 11.385 16986 Z= 0.252 Chirality : 0.034 0.179 2034 Planarity : 0.003 0.032 2100 Dihedral : 3.400 19.911 1692 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.21 % Allowed : 9.13 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.22), residues: 1554 helix: 2.44 (0.14), residues: 1350 sheet: None (None), residues: 0 loop : -0.32 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 487 HIS 0.009 0.001 HIS D 548 PHE 0.009 0.001 PHE D 577 TYR 0.004 0.001 TYR A 535 ARG 0.002 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 181 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.498 Fit side-chains REVERT: D 426 MET cc_start: 0.8223 (ttm) cc_final: 0.8009 (ttm) outliers start: 16 outliers final: 13 residues processed: 178 average time/residue: 0.1917 time to fit residues: 53.9749 Evaluate side-chains 176 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 686 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1168 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= 0.208 Angle : 0.511 11.490 16986 Z= 0.256 Chirality : 0.035 0.182 2034 Planarity : 0.003 0.032 2100 Dihedral : 3.403 19.832 1692 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.89 % Allowed : 9.95 % Favored : 88.16 % 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: 3.20 (0.22), residues: 1554 helix: 2.50 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -0.56 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 523 HIS 0.009 0.001 HIS D 548 PHE 0.009 0.001 PHE D 577 TYR 0.004 0.001 TYR A 535 ARG 0.002 0.000 ARG B 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 190 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 1.577 Fit side-chains outliers start: 25 outliers final: 19 residues processed: 183 average time/residue: 0.1891 time to fit residues: 54.4195 Evaluate side-chains 183 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 528 GLN Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 686 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8150 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12588 Z= 0.186 Angle : 0.494 11.512 16986 Z= 0.247 Chirality : 0.034 0.178 2034 Planarity : 0.003 0.031 2100 Dihedral : 3.361 19.655 1692 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.58 % Allowed : 10.71 % Favored : 87.71 % 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: 3.31 (0.22), residues: 1554 helix: 2.54 (0.14), residues: 1350 sheet: None (None), residues: 0 loop : -0.30 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 487 HIS 0.008 0.001 HIS D 548 PHE 0.008 0.001 PHE D 577 TYR 0.004 0.001 TYR A 535 ARG 0.002 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: 21 poor density : 169 time to evaluate : 1.391 Fit side-chains outliers start: 21 outliers final: 21 residues processed: 181 average time/residue: 0.1960 time to fit residues: 55.1930 Evaluate side-chains 185 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 164 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 528 GLN Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 686 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.8169 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12588 Z= 0.217 Angle : 0.516 11.928 16986 Z= 0.258 Chirality : 0.035 0.184 2034 Planarity : 0.003 0.032 2100 Dihedral : 3.402 19.669 1692 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.96 % Allowed : 10.63 % Favored : 87.41 % 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: 3.20 (0.22), residues: 1554 helix: 2.50 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -0.57 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 523 HIS 0.009 0.001 HIS D 548 PHE 0.009 0.001 PHE D 577 TYR 0.004 0.001 TYR A 535 ARG 0.002 0.000 ARG D 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 191 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 1.433 Fit side-chains outliers start: 26 outliers final: 24 residues processed: 180 average time/residue: 0.2053 time to fit residues: 58.2827 Evaluate side-chains 187 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 528 GLN Chi-restraints excluded: chain D residue 555 ILE Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 686 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 136 optimal weight: 0.0170 chunk 144 optimal weight: 0.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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: 0.8102 moved from start: 0.1231 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= 0.138 Angle : 0.461 11.239 16986 Z= 0.230 Chirality : 0.033 0.168 2034 Planarity : 0.003 0.031 2100 Dihedral : 3.250 19.362 1692 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.58 % Allowed : 10.94 % Favored : 87.48 % 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: 3.55 (0.22), residues: 1554 helix: 2.68 (0.15), residues: 1356 sheet: None (None), residues: 0 loop : -0.17 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 487 HIS 0.007 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 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 193 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 1.378 Fit side-chains outliers start: 21 outliers final: 18 residues processed: 187 average time/residue: 0.1961 time to fit residues: 57.5514 Evaluate side-chains 188 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 528 GLN Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 686 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 144 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 139 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.8140 moved from start: 0.1244 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= 0.180 Angle : 0.491 11.884 16986 Z= 0.245 Chirality : 0.034 0.176 2034 Planarity : 0.003 0.031 2100 Dihedral : 3.283 19.373 1692 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.43 % Allowed : 11.24 % Favored : 87.33 % 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: 3.44 (0.22), residues: 1554 helix: 2.60 (0.14), residues: 1356 sheet: None (None), residues: 0 loop : -0.20 (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 0.008 0.001 PHE A 519 TYR 0.003 0.001 TYR F 535 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 183 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 1.570 Fit side-chains outliers start: 19 outliers final: 18 residues processed: 177 average time/residue: 0.2068 time to fit residues: 56.8097 Evaluate side-chains 181 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 528 GLN Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8142 moved from start: 0.1272 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= 0.180 Angle : 0.491 11.875 16986 Z= 0.245 Chirality : 0.034 0.177 2034 Planarity : 0.003 0.031 2100 Dihedral : 3.298 19.337 1692 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.43 % Allowed : 11.24 % Favored : 87.33 % 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: 3.43 (0.22), residues: 1554 helix: 2.60 (0.14), residues: 1356 sheet: None (None), residues: 0 loop : -0.20 (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 0.008 0.001 PHE A 519 TYR 0.004 0.001 TYR A 535 ARG 0.002 0.000 ARG B 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 185 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 1.567 Fit side-chains outliers start: 19 outliers final: 19 residues processed: 180 average time/residue: 0.1965 time to fit residues: 55.2356 Evaluate side-chains 186 residues out of total 1416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 167 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 528 GLN Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.138903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.111699 restraints weight = 13326.308| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.22 r_work: 0.2936 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1268 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= 0.190 Angle : 0.500 11.936 16986 Z= 0.250 Chirality : 0.034 0.179 2034 Planarity : 0.003 0.031 2100 Dihedral : 3.322 19.372 1692 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.51 % Allowed : 11.16 % Favored : 87.33 % 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: 3.39 (0.22), residues: 1554 helix: 2.63 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -0.49 (0.41), residues: 210 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 0.008 0.001 PHE A 519 TYR 0.004 0.001 TYR A 535 ARG 0.002 0.000 ARG D 504 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2570.63 seconds wall clock time: 48 minutes 22.20 seconds (2902.20 seconds total)