Starting phenix.real_space_refine on Fri Aug 22 17:01:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k7h_22699/08_2025/7k7h_22699.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k7h_22699/08_2025/7k7h_22699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k7h_22699/08_2025/7k7h_22699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k7h_22699/08_2025/7k7h_22699.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k7h_22699/08_2025/7k7h_22699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k7h_22699/08_2025/7k7h_22699.map" } resolution = 3.0 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4019 2.51 5 N 1045 2.21 5 O 1226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 6323 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "B" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "C" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "D" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "L" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 882 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 110} Chain: "H" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "G" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 117 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Time building chain proxies: 1.42, per 1000 atoms: 0.22 Number of scatterers: 6323 At special positions: 0 Unit cell: (83, 107.07, 87.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1226 8.00 N 1045 7.00 C 4019 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 70 " distance=2.04 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 70 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 70 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 70 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 133 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 70 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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: 0.47 Conformation dependent library (CDL) restraints added in 297.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1526 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 15 sheets defined 16.7% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.541A pdb=" N TYR A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 95 " --> pdb=" O TYR A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'B' and resid 81 through 90 Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.558A pdb=" N ASN B 115 " --> pdb=" O PRO B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 81 through 96 removed outlier: 3.619A pdb=" N SER C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 117 Processing helix chain 'D' and resid 81 through 96 Processing helix chain 'D' and resid 110 through 117 removed outlier: 3.527A pdb=" N VAL D 114 " --> pdb=" O TYR D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 96 Processing helix chain 'E' and resid 110 through 115 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.045A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 241 removed outlier: 4.120A pdb=" N VAL G 235 " --> pdb=" O ASP G 231 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE G 239 " --> pdb=" O VAL G 235 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 69 removed outlier: 3.719A pdb=" N ALA A 69 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 55 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N SER A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN A 46 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR A 52 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL A 44 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N CYS A 54 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU A 42 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS A 56 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TYR A 33 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL A 103 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N SER A 35 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 101 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLN A 104 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU A 122 " --> pdb=" O GLN A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 99 through 104 removed outlier: 4.869A pdb=" N VAL B 99 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP B 36 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS B 56 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU B 42 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS B 54 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL B 44 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TYR B 52 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU B 122 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N CYS B 70 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY B 124 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 12.444A pdb=" N VAL B 72 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 123 " --> pdb=" O HIS B 102 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N HIS B 102 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU B 125 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG B 100 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 46 removed outlier: 6.392A pdb=" N LEU B 42 " --> pdb=" O SER E 127 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER E 127 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 44 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN B 46 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VAL E 123 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU E 122 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLN E 104 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY E 124 " --> pdb=" O HIS E 102 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS E 102 " --> pdb=" O GLY E 124 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE E 101 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER E 35 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL E 103 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR E 33 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LEU E 42 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLN E 46 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N VAL D 123 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N HIS D 102 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU D 125 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG D 100 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE D 101 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N SER D 35 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL D 103 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR D 33 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS D 56 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU D 42 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N CYS D 54 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL D 44 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR D 52 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 55 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 121 through 127 removed outlier: 6.495A pdb=" N LEU E 122 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS E 70 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N GLY E 124 " --> pdb=" O CYS E 70 " (cutoff:3.500A) removed outlier: 12.809A pdb=" N VAL E 72 " --> pdb=" O GLY E 124 " (cutoff:3.500A) removed outlier: 17.849A pdb=" N SER E 126 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE E 55 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR E 52 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL E 44 " --> pdb=" O TYR E 52 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS E 54 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU E 42 " --> pdb=" O CYS E 54 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS E 56 " --> pdb=" O SER E 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 127 through 128 removed outlier: 4.000A pdb=" N SER B 127 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE B 134 " --> pdb=" O SER B 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AA7, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.806A pdb=" N TYR C 52 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL C 44 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N CYS C 54 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU C 42 " --> pdb=" O CYS C 54 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS C 56 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TYR C 33 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL C 103 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER C 35 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE C 101 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG C 100 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU C 125 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N HIS C 102 " --> pdb=" O VAL C 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA9, first strand: chain 'L' and resid 23 through 24 removed outlier: 3.710A pdb=" N PHE L 77 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.820A pdb=" N LYS L 36 " --> pdb=" O ASN L 31 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 51 through 52 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.865A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.520A pdb=" N SER H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AB6, first strand: chain 'H' and resid 98 through 100 removed outlier: 7.181A pdb=" N GLY H 98 " --> pdb=" O PRO H 106 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR H 104 " --> pdb=" O GLU H 100 " (cutoff:3.500A) 172 hydrogen bonds defined for protein. 456 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: 0.57 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1971 1.34 - 1.46: 1246 1.46 - 1.57: 3225 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 6480 Sorted by residual: bond pdb=" C SER C 50 " pdb=" N PRO C 51 " ideal model delta sigma weight residual 1.331 1.369 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" N TYR C 52 " pdb=" CA TYR C 52 " ideal model delta sigma weight residual 1.454 1.482 -0.029 1.23e-02 6.61e+03 5.45e+00 bond pdb=" N PHE C 53 " pdb=" CA PHE C 53 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.26e-02 6.30e+03 4.54e+00 bond pdb=" N TYR A 52 " pdb=" CA TYR A 52 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.20e-02 6.94e+03 3.34e+00 bond pdb=" N PRO C 51 " pdb=" CD PRO C 51 " ideal model delta sigma weight residual 1.473 1.493 -0.020 1.40e-02 5.10e+03 2.07e+00 ... (remaining 6475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 8499 1.26 - 2.51: 256 2.51 - 3.77: 44 3.77 - 5.02: 7 5.02 - 6.28: 6 Bond angle restraints: 8812 Sorted by residual: angle pdb=" N PRO C 51 " pdb=" CA PRO C 51 " pdb=" CB PRO C 51 " ideal model delta sigma weight residual 103.27 106.35 -3.08 9.00e-01 1.23e+00 1.17e+01 angle pdb=" C PHE C 53 " pdb=" CA PHE C 53 " pdb=" CB PHE C 53 " ideal model delta sigma weight residual 109.65 114.68 -5.03 1.75e+00 3.27e-01 8.25e+00 angle pdb=" CA PRO C 51 " pdb=" N PRO C 51 " pdb=" CD PRO C 51 " ideal model delta sigma weight residual 112.00 108.45 3.55 1.40e+00 5.10e-01 6.43e+00 angle pdb=" N ASN E 61 " pdb=" CA ASN E 61 " pdb=" C ASN E 61 " ideal model delta sigma weight residual 114.04 110.97 3.07 1.24e+00 6.50e-01 6.15e+00 angle pdb=" CA TYR C 52 " pdb=" C TYR C 52 " pdb=" O TYR C 52 " ideal model delta sigma weight residual 121.46 118.72 2.74 1.17e+00 7.31e-01 5.49e+00 ... (remaining 8807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3465 17.94 - 35.88: 294 35.88 - 53.83: 48 53.83 - 71.77: 4 71.77 - 89.71: 4 Dihedral angle restraints: 3815 sinusoidal: 1437 harmonic: 2378 Sorted by residual: dihedral pdb=" CA ASN A 61 " pdb=" C ASN A 61 " pdb=" N GLY A 62 " pdb=" CA GLY A 62 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CB LYS H 43 " pdb=" CG LYS H 43 " pdb=" CD LYS H 43 " pdb=" CE LYS H 43 " ideal model delta sinusoidal sigma weight residual 60.00 105.17 -45.17 3 1.50e+01 4.44e-03 8.12e+00 dihedral pdb=" CG ARG L 67 " pdb=" CD ARG L 67 " pdb=" NE ARG L 67 " pdb=" CZ ARG L 67 " ideal model delta sinusoidal sigma weight residual -90.00 -51.95 -38.05 2 1.50e+01 4.44e-03 8.10e+00 ... (remaining 3812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 470 0.025 - 0.049: 295 0.049 - 0.074: 117 0.074 - 0.099: 61 0.099 - 0.123: 35 Chirality restraints: 978 Sorted by residual: chirality pdb=" CA VAL B 99 " pdb=" N VAL B 99 " pdb=" C VAL B 99 " pdb=" CB VAL B 99 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA VAL E 38 " pdb=" N VAL E 38 " pdb=" C VAL E 38 " pdb=" CB VAL E 38 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA VAL E 58 " pdb=" N VAL E 58 " pdb=" C VAL E 58 " pdb=" CB VAL E 58 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 975 not shown) Planarity restraints: 1115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 52 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C TYR A 52 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR A 52 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 53 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 79 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO C 80 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 52 " 0.006 2.00e-02 2.50e+03 1.03e-02 2.13e+00 pdb=" CG TYR A 52 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR A 52 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 52 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 52 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 52 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 52 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 52 " -0.009 2.00e-02 2.50e+03 ... (remaining 1112 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1864 2.80 - 3.33: 5392 3.33 - 3.85: 10098 3.85 - 4.38: 12418 4.38 - 4.90: 22031 Nonbonded interactions: 51803 Sorted by model distance: nonbonded pdb=" O THR C 26 " pdb=" ND2 ASN C 31 " model vdw 2.281 3.120 nonbonded pdb=" OE1 GLN A 46 " pdb=" OG SER B 81 " model vdw 2.285 3.040 nonbonded pdb=" O LEU E 112 " pdb=" OG1 THR E 116 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR E 131 " pdb=" OE1 GLN E 132 " model vdw 2.305 3.040 nonbonded pdb=" OG SER C 40 " pdb=" OE1 GLU C 41 " model vdw 2.310 3.040 ... (remaining 51798 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=0.50 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: 1.810 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.030 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 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 : 0.003 0.038 6488 Z= 0.156 Angle : 0.538 6.281 8828 Z= 0.300 Chirality : 0.043 0.123 978 Planarity : 0.004 0.039 1115 Dihedral : 13.308 89.709 2265 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -5.02 (0.23), residues: 800 helix: -4.10 (0.22), residues: 125 sheet: -2.98 (0.27), residues: 259 loop : -3.31 (0.25), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 33 TYR 0.020 0.001 TYR A 52 PHE 0.011 0.001 PHE L 77 TRP 0.010 0.001 TRP B 78 HIS 0.003 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6480) covalent geometry : angle 0.53814 ( 8812) SS BOND : bond 0.00215 ( 8) SS BOND : angle 0.63331 ( 16) hydrogen bonds : bond 0.28968 ( 170) hydrogen bonds : angle 11.54725 ( 456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7701 (pm20) cc_final: 0.7437 (pm20) REVERT: L 84 VAL cc_start: 0.8442 (p) cc_final: 0.8171 (m) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.3533 time to fit residues: 98.0367 Evaluate side-chains 199 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN D 29 ASN E 115 ASN H 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.106710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.088111 restraints weight = 12169.732| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.37 r_work: 0.3128 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6488 Z= 0.168 Angle : 0.605 5.515 8828 Z= 0.327 Chirality : 0.045 0.150 978 Planarity : 0.004 0.037 1115 Dihedral : 4.125 18.474 870 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.41 % Allowed : 21.05 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.78 (0.26), residues: 800 helix: -2.19 (0.37), residues: 120 sheet: -2.32 (0.29), residues: 264 loop : -2.73 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 100 TYR 0.021 0.001 TYR C 91 PHE 0.011 0.002 PHE E 53 TRP 0.011 0.001 TRP E 78 HIS 0.003 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6480) covalent geometry : angle 0.60504 ( 8812) SS BOND : bond 0.00420 ( 8) SS BOND : angle 0.81804 ( 16) hydrogen bonds : bond 0.03824 ( 170) hydrogen bonds : angle 6.32364 ( 456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8416 (mm-30) REVERT: B 105 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7096 (mtpp) REVERT: C 37 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7690 (mm-30) REVERT: C 57 THR cc_start: 0.9087 (p) cc_final: 0.8634 (p) REVERT: D 24 GLU cc_start: 0.8081 (pm20) cc_final: 0.7779 (pm20) REVERT: D 41 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7786 (mm-30) REVERT: D 74 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8749 (ptpt) REVERT: E 84 GLU cc_start: 0.9040 (mp0) cc_final: 0.8750 (mp0) REVERT: L 48 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8579 (mp10) REVERT: L 51 LYS cc_start: 0.8620 (ttpt) cc_final: 0.8394 (ptmt) REVERT: L 88 ASP cc_start: 0.8094 (m-30) cc_final: 0.7846 (m-30) REVERT: H 52 ASP cc_start: 0.8958 (t0) cc_final: 0.8673 (t0) REVERT: H 81 MET cc_start: 0.3469 (mtt) cc_final: 0.3236 (mpt) REVERT: H 84 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.7873 (p0) outliers start: 31 outliers final: 12 residues processed: 226 average time/residue: 0.3530 time to fit residues: 84.6284 Evaluate side-chains 206 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 48 GLN Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 66 optimal weight: 0.0370 chunk 67 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN B 88 GLN E 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.105075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.086737 restraints weight = 12125.931| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.33 r_work: 0.3097 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6488 Z= 0.168 Angle : 0.586 7.083 8828 Z= 0.311 Chirality : 0.044 0.147 978 Planarity : 0.003 0.033 1115 Dihedral : 4.060 18.325 870 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 5.26 % Allowed : 22.48 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.99 (0.27), residues: 800 helix: -0.82 (0.42), residues: 120 sheet: -2.01 (0.30), residues: 260 loop : -2.30 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 100 TYR 0.014 0.001 TYR E 110 PHE 0.012 0.001 PHE E 92 TRP 0.009 0.001 TRP B 78 HIS 0.002 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 6480) covalent geometry : angle 0.58512 ( 8812) SS BOND : bond 0.00150 ( 8) SS BOND : angle 0.97431 ( 16) hydrogen bonds : bond 0.03606 ( 170) hydrogen bonds : angle 5.55796 ( 456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8472 (mm-30) REVERT: A 48 ASP cc_start: 0.8091 (t70) cc_final: 0.7786 (t70) REVERT: A 67 VAL cc_start: 0.9307 (p) cc_final: 0.9005 (m) REVERT: C 37 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7690 (mm-30) REVERT: C 57 THR cc_start: 0.9153 (p) cc_final: 0.8793 (p) REVERT: D 41 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7655 (mm-30) REVERT: D 97 GLN cc_start: 0.8173 (pt0) cc_final: 0.7630 (pm20) REVERT: D 132 GLN cc_start: 0.8752 (pp30) cc_final: 0.8544 (pp30) REVERT: D 133 CYS cc_start: 0.5451 (m) cc_final: 0.5068 (m) REVERT: L 51 LYS cc_start: 0.8623 (ttpt) cc_final: 0.8387 (ptmt) REVERT: L 88 ASP cc_start: 0.8071 (m-30) cc_final: 0.7685 (m-30) REVERT: H 52 ASP cc_start: 0.8992 (t0) cc_final: 0.8663 (t0) REVERT: H 81 MET cc_start: 0.3526 (mtt) cc_final: 0.3111 (mpt) REVERT: H 84 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.7800 (p0) REVERT: H 87 THR cc_start: 0.8613 (t) cc_final: 0.7363 (t) outliers start: 37 outliers final: 13 residues processed: 218 average time/residue: 0.3801 time to fit residues: 87.9286 Evaluate side-chains 205 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN E 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.107533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.088455 restraints weight = 12112.047| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.48 r_work: 0.3115 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6488 Z= 0.127 Angle : 0.581 6.931 8828 Z= 0.305 Chirality : 0.044 0.151 978 Planarity : 0.003 0.031 1115 Dihedral : 3.929 17.431 870 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.27 % Allowed : 25.46 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.65 (0.28), residues: 800 helix: -0.01 (0.46), residues: 120 sheet: -1.68 (0.29), residues: 299 loop : -2.37 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 100 TYR 0.015 0.001 TYR H 60 PHE 0.009 0.001 PHE D 117 TRP 0.008 0.001 TRP B 78 HIS 0.002 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6480) covalent geometry : angle 0.58073 ( 8812) SS BOND : bond 0.00173 ( 8) SS BOND : angle 0.75223 ( 16) hydrogen bonds : bond 0.03010 ( 170) hydrogen bonds : angle 5.16538 ( 456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8231 (t70) cc_final: 0.7859 (t70) REVERT: A 67 VAL cc_start: 0.9271 (p) cc_final: 0.9050 (m) REVERT: B 83 LYS cc_start: 0.8611 (tppp) cc_final: 0.8335 (tppp) REVERT: B 105 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7109 (mtpp) REVERT: C 37 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7690 (mm-30) REVERT: C 57 THR cc_start: 0.9177 (p) cc_final: 0.8822 (p) REVERT: D 41 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7623 (mm-30) REVERT: D 97 GLN cc_start: 0.8183 (pt0) cc_final: 0.7790 (pm20) REVERT: D 132 GLN cc_start: 0.8837 (pp30) cc_final: 0.8572 (pp30) REVERT: E 59 LYS cc_start: 0.9169 (tppt) cc_final: 0.8877 (tppt) REVERT: L 17 GLU cc_start: 0.8117 (tp30) cc_final: 0.7843 (tm-30) REVERT: L 51 LYS cc_start: 0.8569 (ttpt) cc_final: 0.8343 (ptmt) REVERT: L 88 ASP cc_start: 0.7996 (m-30) cc_final: 0.7533 (m-30) REVERT: L 96 GLN cc_start: 0.8665 (pt0) cc_final: 0.8258 (pp30) REVERT: H 19 LYS cc_start: 0.8655 (ttpp) cc_final: 0.8327 (ttmm) REVERT: H 52 ASP cc_start: 0.8996 (t0) cc_final: 0.8621 (t0) REVERT: H 54 TYR cc_start: 0.9020 (t80) cc_final: 0.8810 (t80) REVERT: H 81 MET cc_start: 0.3513 (mtt) cc_final: 0.3152 (mpt) REVERT: H 84 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.7810 (p0) outliers start: 30 outliers final: 12 residues processed: 209 average time/residue: 0.4071 time to fit residues: 90.3754 Evaluate side-chains 206 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 84 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.107781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.088627 restraints weight = 12318.020| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.50 r_work: 0.3106 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6488 Z= 0.131 Angle : 0.590 8.510 8828 Z= 0.306 Chirality : 0.045 0.159 978 Planarity : 0.003 0.028 1115 Dihedral : 3.891 18.197 870 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.69 % Allowed : 26.17 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.38 (0.29), residues: 800 helix: 0.44 (0.47), residues: 120 sheet: -1.57 (0.29), residues: 305 loop : -2.22 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 100 TYR 0.014 0.001 TYR E 34 PHE 0.026 0.001 PHE L 68 TRP 0.011 0.001 TRP D 108 HIS 0.002 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6480) covalent geometry : angle 0.58905 ( 8812) SS BOND : bond 0.00198 ( 8) SS BOND : angle 0.81761 ( 16) hydrogen bonds : bond 0.02970 ( 170) hydrogen bonds : angle 5.06336 ( 456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8278 (t70) cc_final: 0.7894 (t70) REVERT: A 67 VAL cc_start: 0.9233 (p) cc_final: 0.9029 (m) REVERT: A 101 ILE cc_start: 0.8976 (pt) cc_final: 0.8759 (mm) REVERT: B 33 TYR cc_start: 0.7949 (p90) cc_final: 0.7676 (p90) REVERT: B 37 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8130 (mp0) REVERT: B 84 GLU cc_start: 0.8537 (mp0) cc_final: 0.7942 (mp0) REVERT: B 87 ASP cc_start: 0.8476 (m-30) cc_final: 0.8228 (p0) REVERT: C 24 GLU cc_start: 0.8293 (pm20) cc_final: 0.7672 (pm20) REVERT: C 37 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7673 (mm-30) REVERT: C 57 THR cc_start: 0.9152 (p) cc_final: 0.8794 (p) REVERT: D 41 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7508 (mm-30) REVERT: D 97 GLN cc_start: 0.8236 (pt0) cc_final: 0.7598 (pm20) REVERT: D 132 GLN cc_start: 0.8834 (pp30) cc_final: 0.8234 (pp30) REVERT: D 133 CYS cc_start: 0.5479 (m) cc_final: 0.5247 (m) REVERT: E 59 LYS cc_start: 0.9187 (tppt) cc_final: 0.8983 (tppt) REVERT: L 17 GLU cc_start: 0.8184 (tp30) cc_final: 0.7914 (tm-30) REVERT: L 51 LYS cc_start: 0.8538 (ttpt) cc_final: 0.8318 (ptmt) REVERT: L 88 ASP cc_start: 0.8008 (m-30) cc_final: 0.7589 (m-30) REVERT: L 96 GLN cc_start: 0.8664 (pt0) cc_final: 0.8287 (pp30) REVERT: H 52 ASP cc_start: 0.9003 (t0) cc_final: 0.8644 (t0) REVERT: H 54 TYR cc_start: 0.9113 (t80) cc_final: 0.8882 (t80) REVERT: H 67 LYS cc_start: 0.9171 (ttmt) cc_final: 0.8944 (tttt) REVERT: H 81 MET cc_start: 0.3464 (mtt) cc_final: 0.3094 (mpt) REVERT: H 84 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.7563 (p0) outliers start: 33 outliers final: 16 residues processed: 209 average time/residue: 0.4227 time to fit residues: 93.7757 Evaluate side-chains 202 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.106463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.088150 restraints weight = 12317.505| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.30 r_work: 0.3113 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6488 Z= 0.150 Angle : 0.611 11.011 8828 Z= 0.318 Chirality : 0.045 0.161 978 Planarity : 0.003 0.027 1115 Dihedral : 4.033 21.701 870 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.12 % Allowed : 27.03 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.20 (0.29), residues: 800 helix: 0.63 (0.48), residues: 120 sheet: -1.43 (0.29), residues: 305 loop : -2.15 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 67 TYR 0.016 0.001 TYR H 60 PHE 0.012 0.001 PHE L 68 TRP 0.016 0.001 TRP D 108 HIS 0.002 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6480) covalent geometry : angle 0.61078 ( 8812) SS BOND : bond 0.00206 ( 8) SS BOND : angle 0.90980 ( 16) hydrogen bonds : bond 0.03123 ( 170) hydrogen bonds : angle 5.03315 ( 456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8593 (mm-30) REVERT: A 48 ASP cc_start: 0.8311 (t70) cc_final: 0.7883 (t70) REVERT: A 101 ILE cc_start: 0.9004 (pt) cc_final: 0.8759 (mm) REVERT: B 33 TYR cc_start: 0.7955 (p90) cc_final: 0.7716 (p90) REVERT: B 105 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7067 (mtpp) REVERT: C 24 GLU cc_start: 0.8249 (pm20) cc_final: 0.7660 (pm20) REVERT: C 37 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7706 (mm-30) REVERT: C 57 THR cc_start: 0.9179 (p) cc_final: 0.8858 (p) REVERT: D 41 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7392 (mm-30) REVERT: D 61 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8479 (p0) REVERT: D 97 GLN cc_start: 0.8265 (pt0) cc_final: 0.7663 (pm20) REVERT: D 132 GLN cc_start: 0.8918 (pp30) cc_final: 0.8647 (pp30) REVERT: D 133 CYS cc_start: 0.5505 (m) cc_final: 0.5151 (m) REVERT: E 59 LYS cc_start: 0.9178 (tppt) cc_final: 0.8940 (tppt) REVERT: L 17 GLU cc_start: 0.8266 (tp30) cc_final: 0.8007 (tm-30) REVERT: L 88 ASP cc_start: 0.8127 (m-30) cc_final: 0.7660 (m-30) REVERT: L 96 GLN cc_start: 0.8652 (pt0) cc_final: 0.8327 (pp30) REVERT: H 52 ASP cc_start: 0.8988 (t0) cc_final: 0.8621 (t0) REVERT: H 54 TYR cc_start: 0.9032 (t80) cc_final: 0.8778 (t80) REVERT: H 67 LYS cc_start: 0.9148 (ttmt) cc_final: 0.8879 (tttt) REVERT: H 84 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7507 (p0) REVERT: H 87 THR cc_start: 0.8295 (p) cc_final: 0.7288 (t) outliers start: 36 outliers final: 20 residues processed: 209 average time/residue: 0.4479 time to fit residues: 99.2471 Evaluate side-chains 211 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 30.0000 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 GLN H 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.105699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.086880 restraints weight = 12301.668| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.39 r_work: 0.3108 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6488 Z= 0.150 Angle : 0.626 10.690 8828 Z= 0.324 Chirality : 0.045 0.161 978 Planarity : 0.003 0.027 1115 Dihedral : 4.032 22.038 870 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.84 % Allowed : 28.59 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.06 (0.29), residues: 800 helix: 0.75 (0.47), residues: 120 sheet: -1.31 (0.30), residues: 305 loop : -2.10 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 67 TYR 0.015 0.001 TYR E 34 PHE 0.022 0.001 PHE L 68 TRP 0.012 0.001 TRP D 108 HIS 0.002 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6480) covalent geometry : angle 0.62529 ( 8812) SS BOND : bond 0.00298 ( 8) SS BOND : angle 0.73693 ( 16) hydrogen bonds : bond 0.03082 ( 170) hydrogen bonds : angle 4.99230 ( 456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8917 (t0) cc_final: 0.8314 (t0) REVERT: A 48 ASP cc_start: 0.8323 (t70) cc_final: 0.7887 (t0) REVERT: A 101 ILE cc_start: 0.9016 (pt) cc_final: 0.8733 (mm) REVERT: B 105 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7081 (mtpp) REVERT: C 24 GLU cc_start: 0.8264 (pm20) cc_final: 0.7665 (pm20) REVERT: C 37 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7641 (mm-30) REVERT: C 41 GLU cc_start: 0.8633 (mp0) cc_final: 0.8371 (mp0) REVERT: C 57 THR cc_start: 0.9160 (p) cc_final: 0.8787 (p) REVERT: D 97 GLN cc_start: 0.8237 (pt0) cc_final: 0.7629 (pm20) REVERT: D 132 GLN cc_start: 0.8954 (pp30) cc_final: 0.8682 (pp30) REVERT: D 133 CYS cc_start: 0.5542 (m) cc_final: 0.5222 (m) REVERT: E 59 LYS cc_start: 0.9184 (tppt) cc_final: 0.8905 (tppt) REVERT: L 9 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8631 (p) REVERT: L 17 GLU cc_start: 0.8321 (tp30) cc_final: 0.8023 (tm-30) REVERT: L 88 ASP cc_start: 0.8028 (m-30) cc_final: 0.7631 (m-30) REVERT: L 96 GLN cc_start: 0.8648 (pt0) cc_final: 0.8328 (pp30) REVERT: H 52 ASP cc_start: 0.8990 (t0) cc_final: 0.8599 (t0) REVERT: H 67 LYS cc_start: 0.9173 (ttmt) cc_final: 0.8867 (tttt) REVERT: H 84 ASN cc_start: 0.8191 (m-40) cc_final: 0.7498 (p0) outliers start: 27 outliers final: 19 residues processed: 206 average time/residue: 0.4617 time to fit residues: 100.8549 Evaluate side-chains 208 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN D 61 ASN H 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.106931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.088103 restraints weight = 12203.104| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.38 r_work: 0.3124 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6488 Z= 0.132 Angle : 0.632 11.063 8828 Z= 0.328 Chirality : 0.045 0.222 978 Planarity : 0.003 0.028 1115 Dihedral : 3.971 22.310 870 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.70 % Allowed : 29.59 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.92 (0.29), residues: 800 helix: 0.89 (0.47), residues: 120 sheet: -1.21 (0.29), residues: 305 loop : -2.03 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 67 TYR 0.017 0.001 TYR H 60 PHE 0.026 0.001 PHE L 68 TRP 0.013 0.001 TRP D 108 HIS 0.002 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6480) covalent geometry : angle 0.63139 ( 8812) SS BOND : bond 0.00264 ( 8) SS BOND : angle 0.69519 ( 16) hydrogen bonds : bond 0.02907 ( 170) hydrogen bonds : angle 4.92639 ( 456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8923 (t0) cc_final: 0.8316 (t0) REVERT: B 105 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7051 (mtpp) REVERT: C 24 GLU cc_start: 0.8239 (pm20) cc_final: 0.7633 (pm20) REVERT: C 37 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7627 (mm-30) REVERT: C 41 GLU cc_start: 0.8627 (mp0) cc_final: 0.8298 (mp0) REVERT: C 57 THR cc_start: 0.9168 (p) cc_final: 0.8813 (p) REVERT: D 97 GLN cc_start: 0.8195 (pt0) cc_final: 0.7590 (pm20) REVERT: D 132 GLN cc_start: 0.8970 (pp30) cc_final: 0.8689 (pp30) REVERT: E 59 LYS cc_start: 0.9193 (tppt) cc_final: 0.8981 (tppt) REVERT: L 9 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8644 (p) REVERT: L 17 GLU cc_start: 0.8305 (tp30) cc_final: 0.7999 (tm-30) REVERT: L 58 SER cc_start: 0.8926 (p) cc_final: 0.8698 (m) REVERT: L 88 ASP cc_start: 0.8008 (m-30) cc_final: 0.7614 (m-30) REVERT: H 52 ASP cc_start: 0.8996 (t0) cc_final: 0.8223 (t0) REVERT: H 54 TYR cc_start: 0.9132 (t80) cc_final: 0.8923 (t80) REVERT: H 67 LYS cc_start: 0.9167 (ttmt) cc_final: 0.8864 (tttt) REVERT: H 73 ASP cc_start: 0.8028 (t0) cc_final: 0.7598 (t0) REVERT: H 84 ASN cc_start: 0.8147 (m-40) cc_final: 0.7397 (p0) outliers start: 26 outliers final: 17 residues processed: 207 average time/residue: 0.4570 time to fit residues: 100.2378 Evaluate side-chains 208 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.0060 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN D 61 ASN D 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.106449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.087483 restraints weight = 12454.005| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.41 r_work: 0.3112 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6488 Z= 0.142 Angle : 0.646 10.986 8828 Z= 0.337 Chirality : 0.045 0.158 978 Planarity : 0.003 0.027 1115 Dihedral : 3.955 22.326 870 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.99 % Allowed : 32.15 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.85 (0.29), residues: 800 helix: 1.04 (0.47), residues: 120 sheet: -1.20 (0.29), residues: 315 loop : -1.99 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 67 TYR 0.015 0.001 TYR E 34 PHE 0.024 0.001 PHE L 68 TRP 0.010 0.001 TRP D 108 HIS 0.002 0.001 HIS L 98 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6480) covalent geometry : angle 0.64538 ( 8812) SS BOND : bond 0.00412 ( 8) SS BOND : angle 1.04736 ( 16) hydrogen bonds : bond 0.02902 ( 170) hydrogen bonds : angle 4.94069 ( 456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8938 (t0) cc_final: 0.8304 (t0) REVERT: B 105 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7053 (mtpp) REVERT: C 24 GLU cc_start: 0.8242 (pm20) cc_final: 0.7621 (pm20) REVERT: C 37 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7680 (mm-30) REVERT: C 41 GLU cc_start: 0.8644 (mp0) cc_final: 0.8279 (mp0) REVERT: C 57 THR cc_start: 0.9164 (p) cc_final: 0.8823 (p) REVERT: D 97 GLN cc_start: 0.8192 (pt0) cc_final: 0.7586 (pm20) REVERT: D 132 GLN cc_start: 0.8948 (pp30) cc_final: 0.8347 (pp30) REVERT: D 133 CYS cc_start: 0.5439 (m) cc_final: 0.5236 (m) REVERT: E 59 LYS cc_start: 0.9181 (tppt) cc_final: 0.8955 (tppt) REVERT: L 17 GLU cc_start: 0.8321 (tp30) cc_final: 0.7998 (tm-30) REVERT: L 88 ASP cc_start: 0.7994 (m-30) cc_final: 0.7556 (m-30) REVERT: L 96 GLN cc_start: 0.8931 (pp30) cc_final: 0.8479 (pp30) REVERT: H 10 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8531 (mm-30) REVERT: H 52 ASP cc_start: 0.8879 (t0) cc_final: 0.8503 (t0) REVERT: H 55 ASN cc_start: 0.8205 (p0) cc_final: 0.7845 (p0) REVERT: H 67 LYS cc_start: 0.9182 (ttmt) cc_final: 0.8884 (tttt) REVERT: H 73 ASP cc_start: 0.8081 (t0) cc_final: 0.7637 (t0) REVERT: H 84 ASN cc_start: 0.8136 (m-40) cc_final: 0.7408 (p0) outliers start: 21 outliers final: 17 residues processed: 203 average time/residue: 0.4395 time to fit residues: 94.8380 Evaluate side-chains 205 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain H residue 72 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.106842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088436 restraints weight = 12324.126| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.30 r_work: 0.3124 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6488 Z= 0.146 Angle : 0.700 12.554 8828 Z= 0.364 Chirality : 0.046 0.234 978 Planarity : 0.004 0.061 1115 Dihedral : 4.086 25.707 870 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.84 % Allowed : 32.43 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.79 (0.29), residues: 800 helix: 1.09 (0.47), residues: 120 sheet: -1.09 (0.29), residues: 309 loop : -2.02 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 67 TYR 0.015 0.001 TYR H 60 PHE 0.023 0.001 PHE L 68 TRP 0.007 0.001 TRP B 78 HIS 0.002 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6480) covalent geometry : angle 0.69042 ( 8812) SS BOND : bond 0.00793 ( 8) SS BOND : angle 2.82879 ( 16) hydrogen bonds : bond 0.02961 ( 170) hydrogen bonds : angle 4.96548 ( 456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8935 (t0) cc_final: 0.8304 (t0) REVERT: A 48 ASP cc_start: 0.8256 (t70) cc_final: 0.7832 (t0) REVERT: B 105 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7078 (mtpp) REVERT: B 112 LEU cc_start: 0.7849 (tm) cc_final: 0.7558 (tt) REVERT: C 24 GLU cc_start: 0.8245 (pm20) cc_final: 0.7635 (pm20) REVERT: C 37 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7680 (mm-30) REVERT: C 41 GLU cc_start: 0.8628 (mp0) cc_final: 0.8214 (mp0) REVERT: C 57 THR cc_start: 0.9179 (p) cc_final: 0.8837 (p) REVERT: D 97 GLN cc_start: 0.8167 (pt0) cc_final: 0.7571 (pm20) REVERT: D 132 GLN cc_start: 0.8964 (pp30) cc_final: 0.8350 (pp30) REVERT: D 133 CYS cc_start: 0.5432 (m) cc_final: 0.5227 (m) REVERT: E 59 LYS cc_start: 0.9171 (tppt) cc_final: 0.8941 (tppt) REVERT: L 17 GLU cc_start: 0.8315 (tp30) cc_final: 0.7929 (tm-30) REVERT: L 85 GLN cc_start: 0.8987 (mm110) cc_final: 0.8673 (mp-120) REVERT: L 88 ASP cc_start: 0.7889 (m-30) cc_final: 0.7536 (m-30) REVERT: L 96 GLN cc_start: 0.9059 (pp30) cc_final: 0.8588 (pp30) REVERT: H 10 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8565 (mm-30) REVERT: H 52 ASP cc_start: 0.8861 (t0) cc_final: 0.8599 (t0) REVERT: H 55 ASN cc_start: 0.8273 (p0) cc_final: 0.8048 (p0) REVERT: H 67 LYS cc_start: 0.9171 (ttmt) cc_final: 0.8851 (tttt) REVERT: H 73 ASP cc_start: 0.8120 (t0) cc_final: 0.7673 (t0) REVERT: H 84 ASN cc_start: 0.8136 (m-40) cc_final: 0.7412 (p0) outliers start: 20 outliers final: 18 residues processed: 203 average time/residue: 0.4412 time to fit residues: 95.0927 Evaluate side-chains 206 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 105 LYS Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.102407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.084722 restraints weight = 12629.829| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.22 r_work: 0.3089 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 6488 Z= 0.276 Angle : 0.779 13.135 8828 Z= 0.409 Chirality : 0.050 0.263 978 Planarity : 0.005 0.089 1115 Dihedral : 4.601 29.076 870 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.27 % Allowed : 32.72 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.85 (0.28), residues: 800 helix: 0.68 (0.46), residues: 120 sheet: -1.21 (0.30), residues: 275 loop : -1.82 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 100 TYR 0.017 0.002 TYR E 34 PHE 0.024 0.002 PHE L 68 TRP 0.010 0.002 TRP D 78 HIS 0.005 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00643 ( 6480) covalent geometry : angle 0.76853 ( 8812) SS BOND : bond 0.00863 ( 8) SS BOND : angle 3.07247 ( 16) hydrogen bonds : bond 0.03819 ( 170) hydrogen bonds : angle 5.38018 ( 456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2345.47 seconds wall clock time: 40 minutes 59.67 seconds (2459.67 seconds total)