Starting phenix.real_space_refine on Fri Aug 22 22:49:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fqd_29384/08_2025/8fqd_29384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fqd_29384/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fqd_29384/08_2025/8fqd_29384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fqd_29384/08_2025/8fqd_29384.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fqd_29384/08_2025/8fqd_29384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fqd_29384/08_2025/8fqd_29384.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.37, per 1000 atoms: 0.28 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: 0.69 Conformation dependent library (CDL) restraints added in 423.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.30 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: 1.49 Time building geometry restraints manager: 0.92 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 773 or resid 1301 through 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 1302)) selection = (chain 'C' and (resid 393 through 773 or resid 1301 through 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 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: 4.270 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.920 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.940 ------------------------------------------------------------------------------- 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 : 6.49 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG C 453 TYR 0.010 0.001 TYR A 702 PHE 0.014 0.001 PHE D 495 TRP 0.021 0.001 TRP B 766 HIS 0.004 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.01453 ( 8538) covalent geometry : angle 0.73202 (11520) SS BOND : bond 0.00110 ( 4) SS BOND : angle 0.57235 ( 8) hydrogen bonds : bond 0.15161 ( 322) hydrogen bonds : angle 6.48029 ( 936) *********************** 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 : 0.348 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.1506 time to fit residues: 28.5171 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 : 0.405 ------------------------------------------------------------------------------- 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 49 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.165529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.139333 restraints weight = 10743.871| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.29 r_work: 0.3530 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8542 Z= 0.114 Angle : 0.508 6.591 11528 Z= 0.253 Chirality : 0.044 0.131 1284 Planarity : 0.004 0.037 1422 Dihedral : 10.265 94.339 1267 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.01 % Allowed : 16.78 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.25), residues: 1044 helix: 0.83 (0.25), residues: 434 sheet: -0.59 (0.40), residues: 156 loop : -1.59 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 453 TYR 0.010 0.001 TYR A 702 PHE 0.013 0.001 PHE D 495 TRP 0.012 0.001 TRP B 766 HIS 0.005 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8538) covalent geometry : angle 0.50796 (11520) SS BOND : bond 0.00169 ( 4) SS BOND : angle 0.56083 ( 8) hydrogen bonds : bond 0.03344 ( 322) hydrogen bonds : angle 4.87068 ( 936) *********************** 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 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.361 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 154 average time/residue: 0.1440 time to fit residues: 28.0906 Evaluate side-chains 148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 99 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 0.0060 chunk 38 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.164134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138270 restraints weight = 10704.368| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.26 r_work: 0.3519 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8542 Z= 0.121 Angle : 0.523 7.894 11528 Z= 0.256 Chirality : 0.044 0.134 1284 Planarity : 0.004 0.041 1422 Dihedral : 9.941 90.633 1267 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.68 % Allowed : 16.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.25), residues: 1044 helix: 0.79 (0.25), residues: 434 sheet: -0.49 (0.39), residues: 156 loop : -1.59 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 684 TYR 0.009 0.001 TYR A 702 PHE 0.013 0.001 PHE D 495 TRP 0.007 0.001 TRP B 766 HIS 0.004 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8538) covalent geometry : angle 0.52273 (11520) SS BOND : bond 0.00168 ( 4) SS BOND : angle 0.56947 ( 8) hydrogen bonds : bond 0.03231 ( 322) hydrogen bonds : angle 4.64142 ( 936) *********************** 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 166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.347 Fit side-chains REVERT: C 453 ARG cc_start: 0.7098 (mmm-85) cc_final: 0.6828 (mmm-85) outliers start: 24 outliers final: 13 residues processed: 153 average time/residue: 0.1391 time to fit residues: 27.2050 Evaluate side-chains 147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 401 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 C residue 723 VAL 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 57 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 0.0170 overall best weight: 0.9424 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.164595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.137619 restraints weight = 10930.374| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.36 r_work: 0.3493 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8542 Z= 0.120 Angle : 0.529 8.523 11528 Z= 0.257 Chirality : 0.044 0.138 1284 Planarity : 0.004 0.044 1422 Dihedral : 9.573 87.637 1267 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.91 % Allowed : 17.23 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.25), residues: 1044 helix: 0.77 (0.25), residues: 434 sheet: -0.39 (0.40), residues: 156 loop : -1.59 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 453 TYR 0.012 0.001 TYR A 702 PHE 0.014 0.001 PHE A 438 TRP 0.016 0.001 TRP B 766 HIS 0.004 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8538) covalent geometry : angle 0.52868 (11520) SS BOND : bond 0.00161 ( 4) SS BOND : angle 0.59039 ( 8) hydrogen bonds : bond 0.03089 ( 322) hydrogen bonds : angle 4.55285 ( 936) *********************** 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 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.343 Fit side-chains REVERT: A 657 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: A 719 ASP cc_start: 0.7843 (p0) cc_final: 0.7551 (p0) REVERT: C 453 ARG cc_start: 0.7135 (mmm-85) cc_final: 0.6888 (mmm-85) REVERT: D 414 MET cc_start: 0.6330 (OUTLIER) cc_final: 0.6082 (pmm) outliers start: 26 outliers final: 17 residues processed: 152 average time/residue: 0.1444 time to fit residues: 27.9244 Evaluate side-chains 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 631 SER 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 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 414 MET 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 12 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 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 = 0.3889 r_free = 0.3889 target = 0.161049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.135156 restraints weight = 10858.178| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.26 r_work: 0.3478 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8542 Z= 0.170 Angle : 0.590 9.524 11528 Z= 0.288 Chirality : 0.047 0.179 1284 Planarity : 0.004 0.046 1422 Dihedral : 9.904 93.898 1267 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.24 % Allowed : 18.34 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.25), residues: 1044 helix: 0.51 (0.25), residues: 434 sheet: -0.55 (0.36), residues: 190 loop : -1.58 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 715 TYR 0.015 0.002 TYR A 702 PHE 0.017 0.002 PHE B 495 TRP 0.015 0.001 TRP B 766 HIS 0.004 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8538) covalent geometry : angle 0.59025 (11520) SS BOND : bond 0.00312 ( 4) SS BOND : angle 0.85297 ( 8) hydrogen bonds : bond 0.03706 ( 322) hydrogen bonds : angle 4.64992 ( 936) *********************** 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 177 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.442 Fit side-chains REVERT: A 657 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8239 (mp0) REVERT: A 705 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7624 (mm-30) REVERT: A 719 ASP cc_start: 0.7891 (p0) cc_final: 0.7622 (p0) outliers start: 29 outliers final: 18 residues processed: 164 average time/residue: 0.1465 time to fit residues: 30.4290 Evaluate side-chains 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 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 498 LEU Chi-restraints excluded: chain B residue 631 SER 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 102 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.162962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.136897 restraints weight = 10736.578| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.27 r_work: 0.3495 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8542 Z= 0.119 Angle : 0.547 10.627 11528 Z= 0.267 Chirality : 0.045 0.204 1284 Planarity : 0.004 0.046 1422 Dihedral : 9.292 91.547 1267 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.02 % Allowed : 19.13 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.25), residues: 1044 helix: 0.65 (0.25), residues: 434 sheet: -0.38 (0.37), residues: 186 loop : -1.63 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 453 TYR 0.010 0.001 TYR A 702 PHE 0.015 0.001 PHE D 495 TRP 0.013 0.001 TRP D 766 HIS 0.007 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8538) covalent geometry : angle 0.54688 (11520) SS BOND : bond 0.00156 ( 4) SS BOND : angle 0.64187 ( 8) hydrogen bonds : bond 0.03019 ( 322) hydrogen bonds : angle 4.52683 ( 936) *********************** 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 171 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.339 Fit side-chains REVERT: A 657 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8263 (mp0) REVERT: A 719 ASP cc_start: 0.7858 (p0) cc_final: 0.7658 (p0) outliers start: 27 outliers final: 15 residues processed: 160 average time/residue: 0.1432 time to fit residues: 28.9661 Evaluate side-chains 155 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 401 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 723 VAL 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 69 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 28 optimal weight: 0.0170 chunk 76 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.7624 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.159992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135108 restraints weight = 10815.011| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.14 r_work: 0.3482 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8542 Z= 0.186 Angle : 0.608 9.662 11528 Z= 0.299 Chirality : 0.048 0.214 1284 Planarity : 0.004 0.047 1422 Dihedral : 9.749 98.018 1267 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.80 % Allowed : 20.13 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.25), residues: 1044 helix: 0.38 (0.25), residues: 434 sheet: -0.57 (0.36), residues: 190 loop : -1.68 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 453 TYR 0.024 0.002 TYR A 702 PHE 0.018 0.002 PHE D 495 TRP 0.018 0.001 TRP D 766 HIS 0.006 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 8538) covalent geometry : angle 0.60785 (11520) SS BOND : bond 0.00293 ( 4) SS BOND : angle 0.92256 ( 8) hydrogen bonds : bond 0.03761 ( 322) hydrogen bonds : angle 4.67964 ( 936) *********************** 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 175 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.349 Fit side-chains REVERT: A 657 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: A 705 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7640 (mm-30) outliers start: 25 outliers final: 19 residues processed: 164 average time/residue: 0.1314 time to fit residues: 27.2294 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 : 0.298 ------------------------------------------------------------------------------- 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 401 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 498 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.161589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136165 restraints weight = 10579.447| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.21 r_work: 0.3504 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1762 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= 0.120 Angle : 0.553 11.531 11528 Z= 0.271 Chirality : 0.045 0.184 1284 Planarity : 0.004 0.046 1422 Dihedral : 9.184 93.629 1267 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.46 % Allowed : 20.69 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.25), residues: 1044 helix: 0.63 (0.25), residues: 434 sheet: -0.42 (0.37), residues: 186 loop : -1.72 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 453 TYR 0.015 0.001 TYR A 702 PHE 0.015 0.001 PHE D 495 TRP 0.018 0.001 TRP D 766 HIS 0.005 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8538) covalent geometry : angle 0.55264 (11520) SS BOND : bond 0.00143 ( 4) SS BOND : angle 0.63704 ( 8) hydrogen bonds : bond 0.03008 ( 322) hydrogen bonds : angle 4.51682 ( 936) *********************** 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 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.357 Fit side-chains REVERT: A 657 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8233 (mp0) outliers start: 22 outliers final: 16 residues processed: 155 average time/residue: 0.1404 time to fit residues: 27.2119 Evaluate side-chains 158 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 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 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 76 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 98 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.164472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138621 restraints weight = 10687.408| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.27 r_work: 0.3520 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8542 Z= 0.103 Angle : 0.534 7.565 11528 Z= 0.264 Chirality : 0.044 0.215 1284 Planarity : 0.004 0.045 1422 Dihedral : 8.323 85.467 1267 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.83 % Favored : 96.07 % Rotamer: Outliers : 1.90 % Allowed : 21.14 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.25), residues: 1044 helix: 0.81 (0.26), residues: 434 sheet: -0.41 (0.37), residues: 186 loop : -1.68 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 453 TYR 0.012 0.001 TYR A 702 PHE 0.013 0.001 PHE D 495 TRP 0.012 0.001 TRP D 766 HIS 0.005 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8538) covalent geometry : angle 0.53398 (11520) SS BOND : bond 0.00133 ( 4) SS BOND : angle 0.55118 ( 8) hydrogen bonds : bond 0.02712 ( 322) hydrogen bonds : angle 4.44085 ( 936) *********************** 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 167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.347 Fit side-chains REVERT: A 644 GLU cc_start: 0.6032 (tm-30) cc_final: 0.5684 (pp20) REVERT: A 657 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: D 454 ASP cc_start: 0.7483 (t70) cc_final: 0.7135 (t0) outliers start: 17 outliers final: 15 residues processed: 159 average time/residue: 0.1399 time to fit residues: 28.2854 Evaluate side-chains 159 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 736 THR 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 90 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 0.0170 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.160355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.134779 restraints weight = 10765.713| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.22 r_work: 0.3473 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8542 Z= 0.191 Angle : 0.632 12.486 11528 Z= 0.310 Chirality : 0.048 0.239 1284 Planarity : 0.005 0.061 1422 Dihedral : 9.078 94.868 1267 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 2.46 % Allowed : 21.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.25), residues: 1044 helix: 0.43 (0.25), residues: 434 sheet: -0.52 (0.37), residues: 188 loop : -1.71 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 684 TYR 0.021 0.002 TYR A 702 PHE 0.018 0.002 PHE B 495 TRP 0.033 0.002 TRP B 766 HIS 0.004 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 8538) covalent geometry : angle 0.63167 (11520) SS BOND : bond 0.00272 ( 4) SS BOND : angle 0.92125 ( 8) hydrogen bonds : bond 0.03758 ( 322) hydrogen bonds : angle 4.66463 ( 936) ********************** 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 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.354 Fit side-chains REVERT: A 657 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: A 670 MET cc_start: 0.7608 (mtm) cc_final: 0.7366 (mtm) REVERT: A 705 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7630 (mm-30) REVERT: C 684 ARG cc_start: 0.7941 (ttm110) cc_final: 0.7198 (ttp80) REVERT: C 755 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: D 454 ASP cc_start: 0.7433 (t70) cc_final: 0.7061 (t0) outliers start: 22 outliers final: 16 residues processed: 154 average time/residue: 0.1465 time to fit residues: 28.4350 Evaluate side-chains 165 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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 C residue 755 GLU 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 37 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.160280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.134832 restraints weight = 10647.543| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.21 r_work: 0.3474 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8542 Z= 0.180 Angle : 0.612 9.388 11528 Z= 0.303 Chirality : 0.048 0.239 1284 Planarity : 0.004 0.051 1422 Dihedral : 9.135 98.728 1267 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.31 % Favored : 95.59 % Rotamer: Outliers : 2.24 % Allowed : 21.14 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.25), residues: 1044 helix: 0.36 (0.25), residues: 434 sheet: -0.54 (0.37), residues: 188 loop : -1.72 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 684 TYR 0.019 0.002 TYR A 702 PHE 0.018 0.002 PHE B 495 TRP 0.031 0.002 TRP B 766 HIS 0.004 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8538) covalent geometry : angle 0.61159 (11520) SS BOND : bond 0.00242 ( 4) SS BOND : angle 0.90414 ( 8) hydrogen bonds : bond 0.03607 ( 322) hydrogen bonds : angle 4.65305 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2489.34 seconds wall clock time: 43 minutes 30.77 seconds (2610.77 seconds total)