Starting phenix.real_space_refine on Sat Jun 7 03:12:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqd_29384/06_2025/8fqd_29384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqd_29384/06_2025/8fqd_29384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fqd_29384/06_2025/8fqd_29384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqd_29384/06_2025/8fqd_29384.map" model { file = "/net/cci-nas-00/data/ceres_data/8fqd_29384/06_2025/8fqd_29384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqd_29384/06_2025/8fqd_29384.cif" } resolution = 3.01 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= 0.003 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: 5 Type Number sf(0) Gaussians S 64 5.16 5 Cl 4 4.86 5 C 5332 2.51 5 N 1384 2.21 5 O 1600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8384 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2012 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2111 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.37, per 1000 atoms: 0.76 Number of scatterers: 8384 At special positions: 0 Unit cell: (121.212, 92.547, 83.538, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 64 16.00 O 1600 8.00 N 1384 7.00 C 5332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.1 seconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 42.5% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 removed outlier: 4.173A pdb=" N MET A 414 " --> pdb=" O ASN A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.627A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 420 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.822A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 436 removed outlier: 3.674A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.509A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.508A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.550A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.666A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.558A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.716A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.940A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 removed outlier: 3.528A pdb=" N TYR D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.545A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 757 Processing helix chain 'D' and resid 757 through 768 Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 399 removed outlier: 6.140A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.122A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.415A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 395 through 399 removed outlier: 6.673A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA8, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.209A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.648A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 395 through 399 Processing sheet with id=AB2, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB4, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.208A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 702 through 705 removed outlier: 4.409A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 395 through 399 removed outlier: 6.705A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.618A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC1, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.141A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.580A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2630 1.35 - 1.48: 2040 1.48 - 1.60: 3724 1.60 - 1.73: 40 1.73 - 1.85: 104 Bond restraints: 8538 Sorted by residual: bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.578 -0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " ideal model delta sigma weight residual 1.334 1.577 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C5 CYZ C1302 " pdb=" C6 CYZ C1302 " ideal model delta sigma weight residual 1.553 1.331 0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 8533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 11323 2.20 - 4.40: 125 4.40 - 6.60: 46 6.60 - 8.80: 18 8.80 - 11.00: 8 Bond angle restraints: 11520 Sorted by residual: angle pdb=" CB MET C 408 " pdb=" CG MET C 408 " pdb=" SD MET C 408 " ideal model delta sigma weight residual 112.70 123.70 -11.00 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N LYS A 410 " pdb=" CA LYS A 410 " pdb=" C LYS A 410 " ideal model delta sigma weight residual 114.75 110.36 4.39 1.26e+00 6.30e-01 1.22e+01 angle pdb=" C9 CYZ B1302 " pdb=" S1 CYZ B1302 " pdb=" N1 CYZ B1302 " ideal model delta sigma weight residual 101.75 111.45 -9.70 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C9 CYZ D1302 " pdb=" S1 CYZ D1302 " pdb=" N1 CYZ D1302 " ideal model delta sigma weight residual 101.75 111.42 -9.67 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C9 CYZ C1302 " pdb=" S1 CYZ C1302 " pdb=" N1 CYZ C1302 " ideal model delta sigma weight residual 101.75 111.40 -9.65 3.00e+00 1.11e-01 1.04e+01 ... (remaining 11515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 4719 22.84 - 45.68: 453 45.68 - 68.52: 52 68.52 - 91.36: 13 91.36 - 114.20: 11 Dihedral angle restraints: 5248 sinusoidal: 2196 harmonic: 3052 Sorted by residual: dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 166.55 -73.55 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 158.00 -65.00 1 1.00e+01 1.00e-02 5.54e+01 dihedral pdb=" N2 CYZ C1302 " pdb=" C8 CYZ C1302 " pdb=" N1 CYZ C1302 " pdb=" S1 CYZ C1302 " ideal model delta sinusoidal sigma weight residual 55.73 -58.47 114.20 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 5245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1171 0.085 - 0.170: 97 0.170 - 0.255: 0 0.255 - 0.340: 0 0.340 - 0.425: 16 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C2 CYZ A1302 " pdb=" C1 CYZ A1302 " pdb=" C3 CYZ A1302 " pdb=" C7 CYZ A1302 " both_signs ideal model delta sigma weight residual False 3.31 2.88 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" C2 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" C3 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 2.89 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C8 CYZ A1302 " pdb=" C1 CYZ A1302 " pdb=" N1 CYZ A1302 " pdb=" N2 CYZ A1302 " both_signs ideal model delta sigma weight residual False 2.20 2.63 -0.42 2.00e-01 2.50e+01 4.46e+00 ... (remaining 1281 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 736 " 0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO C 737 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 737 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 737 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 766 " 0.010 2.00e-02 2.50e+03 7.83e-03 1.53e+00 pdb=" CG TRP B 766 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP B 766 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 766 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 766 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 766 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 766 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 766 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 766 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 766 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 493 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO C 494 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 494 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 494 " -0.016 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2025 2.79 - 3.32: 7637 3.32 - 3.85: 13975 3.85 - 4.37: 16511 4.37 - 4.90: 28563 Nonbonded interactions: 68711 Sorted by model distance: nonbonded pdb=" OE1 GLU D 402 " pdb=" OH TYR D 450 " model vdw 2.264 3.040 nonbonded pdb=" O ARG B 692 " pdb=" OG SER B 696 " model vdw 2.278 3.040 nonbonded pdb=" OH TYR A 424 " pdb=" O HOH A1401 " model vdw 2.327 3.040 nonbonded pdb=" N ASP A 719 " pdb=" OD1 ASP A 719 " model vdw 2.334 3.120 nonbonded pdb=" O LEU D 639 " pdb=" NE2 GLN D 642 " model vdw 2.335 3.120 ... (remaining 68706 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 or resid 1302)) selection = (chain 'D' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 470 or (resid \ 471 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 through 506 or resid 630 through 773 or resid 1301 or resid 1302)) } 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: 3.100 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.710 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.015 0.244 8542 Z= 0.726 Angle : 0.732 11.004 11528 Z= 0.325 Chirality : 0.062 0.425 1284 Planarity : 0.003 0.036 1422 Dihedral : 17.597 114.195 3288 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.11 % Allowed : 18.57 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1044 helix: 0.79 (0.25), residues: 430 sheet: -0.75 (0.40), residues: 146 loop : -1.52 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 766 HIS 0.004 0.001 HIS C 412 PHE 0.014 0.001 PHE D 495 TYR 0.010 0.001 TYR A 702 ARG 0.008 0.001 ARG C 453 Details of bonding type rmsd hydrogen bonds : bond 0.15161 ( 322) hydrogen bonds : angle 6.48029 ( 936) SS BOND : bond 0.00110 ( 4) SS BOND : angle 0.57235 ( 8) covalent geometry : bond 0.01453 ( 8538) covalent geometry : angle 0.73202 (11520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 1.319 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.3151 time to fit residues: 60.1494 Evaluate side-chains 142 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.166256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139508 restraints weight = 10687.449| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.32 r_work: 0.3529 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8542 Z= 0.110 Angle : 0.511 6.524 11528 Z= 0.253 Chirality : 0.044 0.132 1284 Planarity : 0.004 0.036 1422 Dihedral : 10.100 92.797 1267 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.13 % Allowed : 16.44 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1044 helix: 0.81 (0.25), residues: 436 sheet: -0.59 (0.40), residues: 156 loop : -1.57 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 766 HIS 0.006 0.001 HIS C 412 PHE 0.013 0.001 PHE D 495 TYR 0.010 0.001 TYR A 702 ARG 0.005 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 322) hydrogen bonds : angle 4.83061 ( 936) SS BOND : bond 0.00173 ( 4) SS BOND : angle 0.52449 ( 8) covalent geometry : bond 0.00261 ( 8538) covalent geometry : angle 0.51109 (11520) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.994 Fit side-chains REVERT: C 443 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.8082 (p) outliers start: 19 outliers final: 10 residues processed: 157 average time/residue: 0.2899 time to fit residues: 57.7423 Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 0.0870 chunk 88 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 85 optimal weight: 0.0870 chunk 52 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 0.8338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 756 GLN ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.165404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138699 restraints weight = 10823.342| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.33 r_work: 0.3520 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8542 Z= 0.112 Angle : 0.511 7.259 11528 Z= 0.251 Chirality : 0.044 0.130 1284 Planarity : 0.004 0.041 1422 Dihedral : 9.709 87.964 1267 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.91 % Allowed : 16.67 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1044 helix: 0.84 (0.25), residues: 434 sheet: -0.49 (0.40), residues: 156 loop : -1.57 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 766 HIS 0.004 0.001 HIS C 412 PHE 0.013 0.001 PHE D 495 TYR 0.013 0.001 TYR C 702 ARG 0.004 0.000 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03088 ( 322) hydrogen bonds : angle 4.63520 ( 936) SS BOND : bond 0.00156 ( 4) SS BOND : angle 0.53409 ( 8) covalent geometry : bond 0.00268 ( 8538) covalent geometry : angle 0.51129 (11520) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.947 Fit side-chains REVERT: C 453 ARG cc_start: 0.7070 (mmm-85) cc_final: 0.6820 (mmm-85) REVERT: D 453 ARG cc_start: 0.8525 (ttm170) cc_final: 0.8109 (ttm170) outliers start: 26 outliers final: 15 residues processed: 154 average time/residue: 0.2726 time to fit residues: 53.8803 Evaluate side-chains 151 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 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 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.163711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.137412 restraints weight = 10682.901| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.28 r_work: 0.3510 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8542 Z= 0.130 Angle : 0.542 8.441 11528 Z= 0.264 Chirality : 0.045 0.147 1284 Planarity : 0.004 0.044 1422 Dihedral : 9.436 86.513 1267 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.80 % Allowed : 17.23 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1044 helix: 0.74 (0.25), residues: 434 sheet: -0.40 (0.40), residues: 156 loop : -1.59 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 766 HIS 0.004 0.001 HIS C 412 PHE 0.015 0.002 PHE A 438 TYR 0.015 0.001 TYR A 702 ARG 0.003 0.000 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 322) hydrogen bonds : angle 4.57714 ( 936) SS BOND : bond 0.00185 ( 4) SS BOND : angle 0.61616 ( 8) covalent geometry : bond 0.00315 ( 8538) covalent geometry : angle 0.54185 (11520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.994 Fit side-chains REVERT: A 657 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: B 496 MET cc_start: 0.8669 (ptt) cc_final: 0.8372 (ptp) REVERT: C 453 ARG cc_start: 0.7102 (mmm-85) cc_final: 0.6836 (mmm-85) outliers start: 25 outliers final: 16 residues processed: 150 average time/residue: 0.2744 time to fit residues: 52.6319 Evaluate side-chains 150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.158965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.133557 restraints weight = 10779.251| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.18 r_work: 0.3460 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8542 Z= 0.232 Angle : 0.651 10.124 11528 Z= 0.319 Chirality : 0.049 0.185 1284 Planarity : 0.004 0.046 1422 Dihedral : 10.676 101.532 1267 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.36 % Allowed : 18.68 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.25), residues: 1044 helix: 0.28 (0.25), residues: 428 sheet: -0.72 (0.35), residues: 192 loop : -1.58 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 766 HIS 0.003 0.001 HIS B 412 PHE 0.020 0.002 PHE D 495 TYR 0.021 0.002 TYR A 702 ARG 0.003 0.001 ARG A 715 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 322) hydrogen bonds : angle 4.82065 ( 936) SS BOND : bond 0.00383 ( 4) SS BOND : angle 1.09390 ( 8) covalent geometry : bond 0.00570 ( 8538) covalent geometry : angle 0.65048 (11520) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.942 Fit side-chains REVERT: A 657 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: A 705 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7719 (mm-30) REVERT: A 719 ASP cc_start: 0.7922 (p0) cc_final: 0.7651 (p0) REVERT: C 453 ARG cc_start: 0.7183 (mmm-85) cc_final: 0.6982 (mmm-85) outliers start: 30 outliers final: 21 residues processed: 170 average time/residue: 0.2917 time to fit residues: 62.7238 Evaluate side-chains 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 2 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.161578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136030 restraints weight = 10609.250| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.23 r_work: 0.3505 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8542 Z= 0.112 Angle : 0.546 10.869 11528 Z= 0.267 Chirality : 0.045 0.171 1284 Planarity : 0.004 0.046 1422 Dihedral : 9.767 94.315 1267 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.68 % Allowed : 19.57 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.25), residues: 1044 helix: 0.59 (0.25), residues: 434 sheet: -0.47 (0.37), residues: 186 loop : -1.70 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 766 HIS 0.009 0.001 HIS A 412 PHE 0.015 0.001 PHE D 495 TYR 0.010 0.001 TYR A 702 ARG 0.005 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 322) hydrogen bonds : angle 4.54586 ( 936) SS BOND : bond 0.00132 ( 4) SS BOND : angle 0.65452 ( 8) covalent geometry : bond 0.00265 ( 8538) covalent geometry : angle 0.54544 (11520) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.917 Fit side-chains REVERT: A 657 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: A 719 ASP cc_start: 0.7805 (p0) cc_final: 0.7411 (p0) REVERT: C 453 ARG cc_start: 0.7175 (mmm-85) cc_final: 0.6962 (mmm-85) outliers start: 24 outliers final: 12 residues processed: 160 average time/residue: 0.2899 time to fit residues: 58.5094 Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 503 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 0.0670 chunk 98 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.162877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136909 restraints weight = 10767.069| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.28 r_work: 0.3499 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8542 Z= 0.115 Angle : 0.538 7.978 11528 Z= 0.266 Chirality : 0.045 0.204 1284 Planarity : 0.004 0.045 1422 Dihedral : 9.205 90.631 1267 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.57 % Allowed : 21.03 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.25), residues: 1044 helix: 0.69 (0.25), residues: 434 sheet: -0.45 (0.37), residues: 186 loop : -1.70 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 766 HIS 0.005 0.001 HIS A 412 PHE 0.014 0.001 PHE D 495 TYR 0.010 0.001 TYR A 702 ARG 0.006 0.000 ARG A 715 Details of bonding type rmsd hydrogen bonds : bond 0.02956 ( 322) hydrogen bonds : angle 4.49068 ( 936) SS BOND : bond 0.00152 ( 4) SS BOND : angle 0.60202 ( 8) covalent geometry : bond 0.00275 ( 8538) covalent geometry : angle 0.53835 (11520) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.929 Fit side-chains REVERT: A 657 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: A 719 ASP cc_start: 0.7848 (p0) cc_final: 0.7515 (p0) REVERT: B 674 MET cc_start: 0.8590 (mtm) cc_final: 0.8117 (mtm) REVERT: C 420 ARG cc_start: 0.8374 (ptt90) cc_final: 0.8089 (ptt90) REVERT: C 453 ARG cc_start: 0.7161 (mmm-85) cc_final: 0.6951 (mmm-85) REVERT: D 765 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7677 (pptt) outliers start: 23 outliers final: 16 residues processed: 155 average time/residue: 0.2740 time to fit residues: 54.0032 Evaluate side-chains 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 765 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 91 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 21 optimal weight: 0.0070 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.161166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135916 restraints weight = 10821.234| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.18 r_work: 0.3489 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8542 Z= 0.156 Angle : 0.583 11.477 11528 Z= 0.286 Chirality : 0.047 0.224 1284 Planarity : 0.004 0.046 1422 Dihedral : 9.463 93.843 1267 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.46 % Allowed : 21.14 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.25), residues: 1044 helix: 0.55 (0.25), residues: 434 sheet: -0.53 (0.36), residues: 188 loop : -1.74 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 766 HIS 0.004 0.001 HIS C 412 PHE 0.016 0.002 PHE D 495 TYR 0.012 0.001 TYR A 702 ARG 0.006 0.001 ARG A 715 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 322) hydrogen bonds : angle 4.57784 ( 936) SS BOND : bond 0.00307 ( 4) SS BOND : angle 0.79051 ( 8) covalent geometry : bond 0.00380 ( 8538) covalent geometry : angle 0.58313 (11520) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 1.002 Fit side-chains REVERT: A 657 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8260 (mp0) REVERT: A 705 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7560 (mm-30) REVERT: A 719 ASP cc_start: 0.7879 (p0) cc_final: 0.7566 (p0) REVERT: B 674 MET cc_start: 0.8657 (mtm) cc_final: 0.8269 (mtm) REVERT: C 453 ARG cc_start: 0.7238 (mmm-85) cc_final: 0.6986 (mmm-85) REVERT: D 454 ASP cc_start: 0.7488 (t70) cc_final: 0.7142 (t0) outliers start: 22 outliers final: 17 residues processed: 158 average time/residue: 0.3125 time to fit residues: 63.2390 Evaluate side-chains 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 675 ARG Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 503 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 32 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.161580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137003 restraints weight = 10774.677| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.13 r_work: 0.3498 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8542 Z= 0.150 Angle : 0.575 8.870 11528 Z= 0.285 Chirality : 0.046 0.200 1284 Planarity : 0.004 0.046 1422 Dihedral : 9.581 95.935 1267 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.21 % Favored : 95.69 % Rotamer: Outliers : 2.35 % Allowed : 21.25 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.25), residues: 1044 helix: 0.55 (0.25), residues: 434 sheet: -0.51 (0.37), residues: 188 loop : -1.76 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 766 HIS 0.005 0.001 HIS C 412 PHE 0.017 0.002 PHE D 495 TYR 0.012 0.001 TYR A 702 ARG 0.005 0.000 ARG A 715 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 322) hydrogen bonds : angle 4.57406 ( 936) SS BOND : bond 0.00183 ( 4) SS BOND : angle 0.75959 ( 8) covalent geometry : bond 0.00364 ( 8538) covalent geometry : angle 0.57490 (11520) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.008 Fit side-chains REVERT: A 657 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8214 (mp0) REVERT: A 705 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7570 (mm-30) REVERT: A 719 ASP cc_start: 0.7896 (p0) cc_final: 0.7585 (p0) REVERT: B 674 MET cc_start: 0.8656 (mtm) cc_final: 0.8277 (mtm) REVERT: C 420 ARG cc_start: 0.8366 (ptt90) cc_final: 0.8109 (ptt90) REVERT: C 453 ARG cc_start: 0.7191 (mmm-85) cc_final: 0.6951 (mmm-85) REVERT: D 414 MET cc_start: 0.6300 (OUTLIER) cc_final: 0.5847 (pmm) REVERT: D 454 ASP cc_start: 0.7425 (t70) cc_final: 0.7054 (t0) outliers start: 21 outliers final: 18 residues processed: 157 average time/residue: 0.3240 time to fit residues: 64.0707 Evaluate side-chains 164 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 675 ARG Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 503 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 0.0970 chunk 82 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.162542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137189 restraints weight = 10534.797| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.21 r_work: 0.3520 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8542 Z= 0.109 Angle : 0.545 12.458 11528 Z= 0.268 Chirality : 0.045 0.165 1284 Planarity : 0.004 0.045 1422 Dihedral : 9.055 89.521 1267 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.16 % Favored : 96.74 % Rotamer: Outliers : 2.13 % Allowed : 21.59 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.25), residues: 1044 helix: 0.79 (0.25), residues: 434 sheet: -0.46 (0.37), residues: 186 loop : -1.73 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 766 HIS 0.005 0.001 HIS C 412 PHE 0.014 0.001 PHE D 495 TYR 0.010 0.001 TYR C 647 ARG 0.007 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.02820 ( 322) hydrogen bonds : angle 4.44651 ( 936) SS BOND : bond 0.00109 ( 4) SS BOND : angle 0.55049 ( 8) covalent geometry : bond 0.00258 ( 8538) covalent geometry : angle 0.54538 (11520) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.950 Fit side-chains REVERT: A 634 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6753 (mm-30) REVERT: A 644 GLU cc_start: 0.6162 (tm-30) cc_final: 0.5821 (pp20) REVERT: A 657 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: A 719 ASP cc_start: 0.7845 (p0) cc_final: 0.7529 (p0) REVERT: B 674 MET cc_start: 0.8663 (mtm) cc_final: 0.8305 (mtm) REVERT: C 453 ARG cc_start: 0.7186 (mmm-85) cc_final: 0.6984 (mmm-85) REVERT: D 414 MET cc_start: 0.6309 (OUTLIER) cc_final: 0.5864 (pmm) REVERT: D 454 ASP cc_start: 0.7412 (t70) cc_final: 0.7035 (t0) outliers start: 19 outliers final: 17 residues processed: 157 average time/residue: 0.2858 time to fit residues: 56.9035 Evaluate side-chains 161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 675 ARG Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 503 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.160847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.135110 restraints weight = 10850.875| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.24 r_work: 0.3462 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8542 Z= 0.172 Angle : 0.616 12.555 11528 Z= 0.303 Chirality : 0.047 0.209 1284 Planarity : 0.004 0.060 1422 Dihedral : 9.619 94.753 1267 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 2.13 % Allowed : 21.81 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1044 helix: 0.52 (0.25), residues: 434 sheet: -0.56 (0.37), residues: 188 loop : -1.75 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 766 HIS 0.003 0.001 HIS C 412 PHE 0.017 0.002 PHE D 495 TYR 0.025 0.002 TYR A 702 ARG 0.012 0.001 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 322) hydrogen bonds : angle 4.61339 ( 936) SS BOND : bond 0.00218 ( 4) SS BOND : angle 0.83023 ( 8) covalent geometry : bond 0.00422 ( 8538) covalent geometry : angle 0.61539 (11520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5396.31 seconds wall clock time: 94 minutes 24.83 seconds (5664.83 seconds total)