Starting phenix.real_space_refine on Thu Jul 24 13:09:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k7h_22699/07_2025/7k7h_22699.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k7h_22699/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7k7h_22699/07_2025/7k7h_22699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k7h_22699/07_2025/7k7h_22699.map" model { file = "/net/cci-nas-00/data/ceres_data/7k7h_22699/07_2025/7k7h_22699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k7h_22699/07_2025/7k7h_22699.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.30, per 1000 atoms: 0.68 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: 1.19 Conformation dependent library (CDL) restraints added in 847.6 milliseconds 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: 0.85 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: 1.57 Time building geometry restraints manager: 1.45 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.240 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:17.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.930 ------------------------------------------------------------------------------- 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 : 8.54 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP B 78 HIS 0.003 0.001 HIS D 102 PHE 0.011 0.001 PHE L 77 TYR 0.020 0.001 TYR A 52 ARG 0.005 0.000 ARG L 33 Details of bonding type rmsd hydrogen bonds : bond 0.28968 ( 170) hydrogen bonds : angle 11.54725 ( 456) SS BOND : bond 0.00215 ( 8) SS BOND : angle 0.63331 ( 16) covalent geometry : bond 0.00324 ( 6480) covalent geometry : angle 0.53814 ( 8812) *********************** 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 : 0.744 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: 0.8170 (m) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.9320 time to fit residues: 259.3943 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 : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN B 88 GLN D 29 ASN D 102 HIS E 88 GLN E 115 ASN H 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.102216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.083921 restraints weight = 12112.445| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.32 r_work: 0.3056 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 6488 Z= 0.288 Angle : 0.678 5.693 8828 Z= 0.366 Chirality : 0.047 0.150 978 Planarity : 0.005 0.036 1115 Dihedral : 4.581 19.541 870 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.98 % Allowed : 21.05 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.27), residues: 800 helix: -2.45 (0.34), residues: 150 sheet: -2.25 (0.29), residues: 264 loop : -2.52 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 78 HIS 0.006 0.001 HIS B 102 PHE 0.014 0.002 PHE A 113 TYR 0.022 0.002 TYR C 91 ARG 0.005 0.001 ARG L 100 Details of bonding type rmsd hydrogen bonds : bond 0.04659 ( 170) hydrogen bonds : angle 6.53604 ( 456) SS BOND : bond 0.00319 ( 8) SS BOND : angle 1.37737 ( 16) covalent geometry : bond 0.00672 ( 6480) covalent geometry : angle 0.67651 ( 8812) *********************** 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 247 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8990 (t0) cc_final: 0.8496 (t0) REVERT: A 41 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8475 (mm-30) REVERT: A 48 ASP cc_start: 0.8108 (t70) cc_final: 0.7812 (t0) REVERT: C 33 TYR cc_start: 0.9080 (p90) cc_final: 0.8855 (p90) REVERT: C 37 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7855 (mm-30) REVERT: D 24 GLU cc_start: 0.8146 (pm20) cc_final: 0.7783 (pm20) REVERT: D 41 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7704 (mm-30) REVERT: D 74 LYS cc_start: 0.9027 (mtmt) cc_final: 0.8817 (ptpt) REVERT: L 9 SER cc_start: 0.9108 (OUTLIER) cc_final: 0.8892 (p) REVERT: L 48 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8596 (mp10) REVERT: L 51 LYS cc_start: 0.8761 (ttpt) cc_final: 0.8526 (ptmt) REVERT: L 55 TYR cc_start: 0.8677 (m-10) cc_final: 0.8464 (m-10) REVERT: L 88 ASP cc_start: 0.8222 (m-30) cc_final: 0.8020 (m-30) REVERT: H 52 ASP cc_start: 0.8986 (t0) cc_final: 0.8700 (t0) REVERT: H 81 MET cc_start: 0.3539 (mtt) cc_final: 0.3165 (mpt) REVERT: H 84 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.7869 (p0) REVERT: H 87 THR cc_start: 0.8664 (t) cc_final: 0.7430 (t) outliers start: 35 outliers final: 15 residues processed: 228 average time/residue: 0.9235 time to fit residues: 223.3928 Evaluate side-chains 208 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain D residue 47 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 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 88 SER 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 38 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.0070 chunk 47 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN B 31 ASN D 29 ASN E 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.107253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.088483 restraints weight = 12020.533| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.45 r_work: 0.3113 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6488 Z= 0.119 Angle : 0.579 7.554 8828 Z= 0.306 Chirality : 0.044 0.162 978 Planarity : 0.003 0.032 1115 Dihedral : 4.095 18.827 870 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.26 % Allowed : 23.04 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.28), residues: 800 helix: -1.22 (0.40), residues: 150 sheet: -1.94 (0.29), residues: 299 loop : -2.39 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 78 HIS 0.003 0.001 HIS B 43 PHE 0.011 0.001 PHE D 117 TYR 0.013 0.001 TYR E 110 ARG 0.003 0.000 ARG L 100 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 170) hydrogen bonds : angle 5.38801 ( 456) SS BOND : bond 0.00231 ( 8) SS BOND : angle 0.87109 ( 16) covalent geometry : bond 0.00266 ( 6480) covalent geometry : angle 0.57822 ( 8812) *********************** 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 249 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8429 (mm-30) REVERT: A 48 ASP cc_start: 0.8158 (t70) cc_final: 0.7802 (t0) REVERT: A 67 VAL cc_start: 0.9274 (p) cc_final: 0.8976 (m) REVERT: B 33 TYR cc_start: 0.7970 (p90) cc_final: 0.7696 (p90) REVERT: B 83 LYS cc_start: 0.8575 (tppp) cc_final: 0.8315 (tppp) REVERT: B 105 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7078 (mtpp) REVERT: B 115 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.8156 (p0) REVERT: C 33 TYR cc_start: 0.9037 (p90) cc_final: 0.8792 (p90) REVERT: C 37 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7665 (mm-30) REVERT: D 41 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7637 (mm-30) REVERT: D 97 GLN cc_start: 0.8215 (pt0) cc_final: 0.7572 (pm20) REVERT: D 132 GLN cc_start: 0.8712 (pp30) cc_final: 0.8205 (pp30) REVERT: D 133 CYS cc_start: 0.5383 (m) cc_final: 0.5177 (m) REVERT: L 6 GLN cc_start: 0.8804 (tt0) cc_final: 0.8568 (tt0) REVERT: L 55 TYR cc_start: 0.8531 (m-10) cc_final: 0.8223 (m-10) REVERT: L 88 ASP cc_start: 0.8081 (m-30) cc_final: 0.7782 (m-30) REVERT: L 96 GLN cc_start: 0.8666 (pt0) cc_final: 0.8162 (pp30) REVERT: H 52 ASP cc_start: 0.8929 (t0) cc_final: 0.8557 (t0) REVERT: H 54 TYR cc_start: 0.8992 (t80) cc_final: 0.8753 (t80) REVERT: H 81 MET cc_start: 0.3408 (mtt) cc_final: 0.3030 (mpt) REVERT: H 84 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.7781 (p0) outliers start: 37 outliers final: 11 residues processed: 223 average time/residue: 0.8506 time to fit residues: 201.5969 Evaluate side-chains 210 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 41 GLU 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 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 L residue 84 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 69 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.103736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.085337 restraints weight = 12418.135| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.42 r_work: 0.3050 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6488 Z= 0.203 Angle : 0.622 6.734 8828 Z= 0.327 Chirality : 0.046 0.161 978 Planarity : 0.003 0.028 1115 Dihedral : 4.252 18.008 870 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 5.97 % Allowed : 25.75 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.28), residues: 800 helix: -0.11 (0.45), residues: 120 sheet: -1.68 (0.31), residues: 265 loop : -2.25 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 78 HIS 0.003 0.001 HIS B 102 PHE 0.014 0.002 PHE E 92 TYR 0.014 0.002 TYR H 60 ARG 0.003 0.000 ARG L 100 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 170) hydrogen bonds : angle 5.25095 ( 456) SS BOND : bond 0.00241 ( 8) SS BOND : angle 1.20932 ( 16) covalent geometry : bond 0.00478 ( 6480) covalent geometry : angle 0.62042 ( 8812) *********************** 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 241 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8987 (t0) cc_final: 0.8400 (t0) REVERT: A 41 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8527 (mm-30) REVERT: A 48 ASP cc_start: 0.8340 (t70) cc_final: 0.7925 (t0) REVERT: A 67 VAL cc_start: 0.9286 (p) cc_final: 0.9025 (m) REVERT: B 33 TYR cc_start: 0.8041 (p90) cc_final: 0.7674 (p90) REVERT: B 84 GLU cc_start: 0.8480 (mp0) cc_final: 0.7996 (mp0) REVERT: B 87 ASP cc_start: 0.8492 (m-30) cc_final: 0.8217 (p0) REVERT: D 132 GLN cc_start: 0.8895 (pp30) cc_final: 0.8635 (pp30) REVERT: E 41 GLU cc_start: 0.8692 (mp0) cc_final: 0.8167 (mp0) REVERT: L 55 TYR cc_start: 0.8645 (m-10) cc_final: 0.8269 (m-10) REVERT: L 88 ASP cc_start: 0.8148 (m-30) cc_final: 0.7829 (m-30) REVERT: H 52 ASP cc_start: 0.8922 (t0) cc_final: 0.8533 (t0) REVERT: H 67 LYS cc_start: 0.9164 (ttmt) cc_final: 0.8887 (tttt) REVERT: H 81 MET cc_start: 0.3299 (mtt) cc_final: 0.2872 (mpt) REVERT: H 84 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.7565 (p0) outliers start: 42 outliers final: 21 residues processed: 214 average time/residue: 0.8710 time to fit residues: 198.2645 Evaluate side-chains 213 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU 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 114 VAL Chi-restraints excluded: chain B residue 115 ASN 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 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 84 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 87 THR Chi-restraints excluded: chain H residue 99 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 0.1980 chunk 16 optimal weight: 0.0020 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN B 132 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.107729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.088650 restraints weight = 12147.448| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.46 r_work: 0.3112 rms_B_bonded: 3.65 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 = 0.73 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 = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6488 Z= 0.124 Angle : 0.596 8.422 8828 Z= 0.310 Chirality : 0.045 0.162 978 Planarity : 0.003 0.033 1115 Dihedral : 3.981 17.869 870 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.41 % Allowed : 29.16 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.29), residues: 800 helix: -0.23 (0.44), residues: 150 sheet: -1.49 (0.29), residues: 304 loop : -2.00 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 108 HIS 0.003 0.001 HIS B 43 PHE 0.011 0.001 PHE D 117 TYR 0.011 0.001 TYR H 107 ARG 0.002 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.02952 ( 170) hydrogen bonds : angle 4.93858 ( 456) SS BOND : bond 0.00262 ( 8) SS BOND : angle 0.73120 ( 16) covalent geometry : bond 0.00289 ( 6480) covalent geometry : angle 0.59580 ( 8812) *********************** 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 226 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8304 (t70) cc_final: 0.7854 (t0) REVERT: A 67 VAL cc_start: 0.9231 (p) cc_final: 0.8993 (m) REVERT: B 33 TYR cc_start: 0.7930 (p90) cc_final: 0.7723 (p90) REVERT: B 105 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7029 (mtpp) REVERT: B 115 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.8175 (p0) REVERT: C 24 GLU cc_start: 0.8228 (pm20) cc_final: 0.7530 (pm20) REVERT: C 37 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7477 (mt-10) REVERT: D 97 GLN cc_start: 0.8204 (pt0) cc_final: 0.7866 (pm20) REVERT: D 132 GLN cc_start: 0.8906 (pp30) cc_final: 0.8332 (pp30) REVERT: D 133 CYS cc_start: 0.5497 (m) cc_final: 0.5255 (m) REVERT: E 41 GLU cc_start: 0.8569 (mp0) cc_final: 0.8040 (mp0) REVERT: L 17 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7566 (tm-30) REVERT: L 55 TYR cc_start: 0.8495 (m-10) cc_final: 0.8065 (m-10) REVERT: L 88 ASP cc_start: 0.8178 (m-30) cc_final: 0.7864 (m-30) REVERT: L 96 GLN cc_start: 0.8640 (pt0) cc_final: 0.8227 (pp30) REVERT: H 52 ASP cc_start: 0.8944 (t0) cc_final: 0.8523 (t0) REVERT: H 54 TYR cc_start: 0.9066 (t80) cc_final: 0.8793 (t80) REVERT: H 67 LYS cc_start: 0.9136 (ttmt) cc_final: 0.8837 (tttt) REVERT: H 84 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7498 (p0) REVERT: H 87 THR cc_start: 0.8173 (p) cc_final: 0.7141 (t) outliers start: 31 outliers final: 14 residues processed: 206 average time/residue: 0.8358 time to fit residues: 183.2270 Evaluate side-chains 203 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS 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 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 19 VAL Chi-restraints excluded: chain L residue 63 VAL 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 51 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.107495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.088614 restraints weight = 12027.938| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.40 r_work: 0.3110 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- 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 = 0.70 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 = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6488 Z= 0.137 Angle : 0.613 10.209 8828 Z= 0.316 Chirality : 0.045 0.161 978 Planarity : 0.003 0.027 1115 Dihedral : 3.978 19.213 870 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.13 % Allowed : 30.58 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.29), residues: 800 helix: -0.05 (0.44), residues: 150 sheet: -1.33 (0.32), residues: 254 loop : -1.77 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 108 HIS 0.002 0.001 HIS B 43 PHE 0.011 0.001 PHE D 117 TYR 0.015 0.001 TYR H 60 ARG 0.003 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 170) hydrogen bonds : angle 4.89592 ( 456) SS BOND : bond 0.00199 ( 8) SS BOND : angle 0.80033 ( 16) covalent geometry : bond 0.00326 ( 6480) covalent geometry : angle 0.61218 ( 8812) *********************** 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 221 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8929 (t0) cc_final: 0.8311 (t0) REVERT: A 41 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8593 (mm-30) REVERT: A 48 ASP cc_start: 0.8245 (t70) cc_final: 0.7808 (t0) REVERT: A 101 ILE cc_start: 0.8962 (pt) cc_final: 0.8703 (mm) REVERT: B 33 TYR cc_start: 0.7970 (p90) cc_final: 0.7570 (p90) REVERT: C 24 GLU cc_start: 0.8225 (pm20) cc_final: 0.7548 (pm20) REVERT: C 37 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7385 (mt-10) REVERT: D 97 GLN cc_start: 0.8205 (pt0) cc_final: 0.7841 (pm20) REVERT: D 132 GLN cc_start: 0.8932 (pp30) cc_final: 0.8361 (pp30) REVERT: D 133 CYS cc_start: 0.5477 (m) cc_final: 0.5271 (m) REVERT: L 17 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7590 (tm-30) REVERT: L 55 TYR cc_start: 0.8458 (m-10) cc_final: 0.8057 (m-10) REVERT: L 88 ASP cc_start: 0.8128 (m-30) cc_final: 0.7770 (m-30) REVERT: L 96 GLN cc_start: 0.8661 (pt0) cc_final: 0.8393 (pp30) REVERT: H 52 ASP cc_start: 0.8924 (t0) cc_final: 0.8496 (t0) REVERT: H 67 LYS cc_start: 0.9130 (ttmt) cc_final: 0.8806 (tttt) REVERT: H 84 ASN cc_start: 0.8194 (m-40) cc_final: 0.7480 (p0) outliers start: 29 outliers final: 17 residues processed: 207 average time/residue: 1.1263 time to fit residues: 247.9770 Evaluate side-chains 204 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 114 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 24 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN C 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.106591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.087421 restraints weight = 12089.597| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.44 r_work: 0.3104 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6488 Z= 0.143 Angle : 0.626 10.649 8828 Z= 0.323 Chirality : 0.045 0.162 978 Planarity : 0.003 0.027 1115 Dihedral : 3.963 19.311 870 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.84 % Allowed : 31.01 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.29), residues: 800 helix: 0.07 (0.44), residues: 150 sheet: -1.14 (0.30), residues: 299 loop : -1.85 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 108 HIS 0.002 0.001 HIS B 43 PHE 0.012 0.001 PHE D 117 TYR 0.011 0.001 TYR H 32 ARG 0.002 0.000 ARG D 90 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 170) hydrogen bonds : angle 4.90581 ( 456) SS BOND : bond 0.00226 ( 8) SS BOND : angle 0.87368 ( 16) covalent geometry : bond 0.00339 ( 6480) covalent geometry : angle 0.62507 ( 8812) *********************** 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 224 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8945 (t0) cc_final: 0.8334 (t0) REVERT: A 41 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8573 (mm-30) REVERT: A 101 ILE cc_start: 0.8971 (pt) cc_final: 0.8692 (mm) REVERT: B 33 TYR cc_start: 0.7955 (p90) cc_final: 0.7551 (p90) REVERT: B 105 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7029 (mtpp) REVERT: C 24 GLU cc_start: 0.8235 (pm20) cc_final: 0.7558 (pm20) REVERT: C 37 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7408 (mt-10) REVERT: C 41 GLU cc_start: 0.8579 (mp0) cc_final: 0.8230 (mp0) REVERT: D 97 GLN cc_start: 0.8179 (pt0) cc_final: 0.7802 (pm20) REVERT: D 132 GLN cc_start: 0.8945 (pp30) cc_final: 0.8361 (pp30) REVERT: L 55 TYR cc_start: 0.8461 (m-10) cc_final: 0.8038 (m-10) REVERT: L 88 ASP cc_start: 0.8122 (m-30) cc_final: 0.7748 (m-30) REVERT: L 96 GLN cc_start: 0.8767 (pt0) cc_final: 0.8414 (pp30) REVERT: H 52 ASP cc_start: 0.8949 (t0) cc_final: 0.8488 (t0) REVERT: H 54 TYR cc_start: 0.9134 (t80) cc_final: 0.8914 (t80) REVERT: H 67 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8823 (tttt) REVERT: H 73 ASP cc_start: 0.7938 (t0) cc_final: 0.7454 (t0) REVERT: H 84 ASN cc_start: 0.8184 (m-40) cc_final: 0.7468 (p0) outliers start: 27 outliers final: 18 residues processed: 206 average time/residue: 1.0522 time to fit residues: 230.2530 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 : 0.794 ------------------------------------------------------------------------------- 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 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 L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 84 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 60 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.105443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.086778 restraints weight = 12165.627| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.39 r_work: 0.3078 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6488 Z= 0.173 Angle : 0.656 10.804 8828 Z= 0.339 Chirality : 0.046 0.211 978 Planarity : 0.003 0.025 1115 Dihedral : 4.084 20.075 870 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.41 % Allowed : 32.72 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.29), residues: 800 helix: 0.82 (0.47), residues: 120 sheet: -1.10 (0.32), residues: 265 loop : -1.83 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 108 HIS 0.002 0.001 HIS B 102 PHE 0.017 0.001 PHE D 117 TYR 0.015 0.001 TYR H 60 ARG 0.003 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 170) hydrogen bonds : angle 5.02569 ( 456) SS BOND : bond 0.00276 ( 8) SS BOND : angle 0.97174 ( 16) covalent geometry : bond 0.00408 ( 6480) covalent geometry : angle 0.65504 ( 8812) *********************** 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 217 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8991 (t0) cc_final: 0.8356 (t0) REVERT: A 41 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8600 (mm-30) REVERT: A 48 ASP cc_start: 0.8193 (t70) cc_final: 0.7772 (t0) REVERT: B 33 TYR cc_start: 0.7974 (p90) cc_final: 0.7561 (p90) REVERT: C 24 GLU cc_start: 0.8252 (pm20) cc_final: 0.7586 (pm20) REVERT: C 37 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7577 (mt-10) REVERT: C 41 GLU cc_start: 0.8692 (mp0) cc_final: 0.8358 (mp0) REVERT: D 97 GLN cc_start: 0.8218 (pt0) cc_final: 0.7808 (pm20) REVERT: D 132 GLN cc_start: 0.8985 (pp30) cc_final: 0.8449 (pp30) REVERT: L 55 TYR cc_start: 0.8488 (m-10) cc_final: 0.8096 (m-10) REVERT: L 88 ASP cc_start: 0.8167 (m-30) cc_final: 0.7839 (m-30) REVERT: L 96 GLN cc_start: 0.8816 (pt0) cc_final: 0.8469 (pp30) REVERT: H 52 ASP cc_start: 0.8950 (t0) cc_final: 0.8577 (t0) REVERT: H 67 LYS cc_start: 0.9148 (ttmt) cc_final: 0.8799 (tttt) REVERT: H 73 ASP cc_start: 0.8006 (t0) cc_final: 0.7500 (t0) REVERT: H 84 ASN cc_start: 0.8150 (m-40) cc_final: 0.7417 (p0) outliers start: 24 outliers final: 17 residues processed: 205 average time/residue: 1.1933 time to fit residues: 260.2363 Evaluate side-chains 206 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 84 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.107619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.088477 restraints weight = 12182.582| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.44 r_work: 0.3113 rms_B_bonded: 3.64 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 = 0.64 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 = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4318 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= 0.139 Angle : 0.688 11.328 8828 Z= 0.354 Chirality : 0.046 0.244 978 Planarity : 0.003 0.026 1115 Dihedral : 4.012 19.693 870 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.56 % Allowed : 33.71 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.29), residues: 800 helix: 0.99 (0.47), residues: 120 sheet: -1.10 (0.30), residues: 309 loop : -1.97 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 25 HIS 0.002 0.001 HIS B 43 PHE 0.014 0.001 PHE D 117 TYR 0.013 0.001 TYR H 32 ARG 0.003 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.02906 ( 170) hydrogen bonds : angle 4.94209 ( 456) SS BOND : bond 0.00682 ( 8) SS BOND : angle 2.41485 ( 16) covalent geometry : bond 0.00326 ( 6480) covalent geometry : angle 0.68044 ( 8812) *********************** 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 213 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8949 (t0) cc_final: 0.8326 (t0) REVERT: A 41 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8551 (mm-30) REVERT: A 48 ASP cc_start: 0.8205 (t70) cc_final: 0.7782 (t0) REVERT: B 33 TYR cc_start: 0.7972 (p90) cc_final: 0.7586 (p90) REVERT: B 105 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7060 (mtpp) REVERT: C 24 GLU cc_start: 0.8247 (pm20) cc_final: 0.7567 (pm20) REVERT: C 37 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7353 (mt-10) REVERT: C 41 GLU cc_start: 0.8609 (mp0) cc_final: 0.8202 (mp0) REVERT: D 97 GLN cc_start: 0.8220 (pt0) cc_final: 0.7812 (pm20) REVERT: D 132 GLN cc_start: 0.8974 (pp30) cc_final: 0.8416 (pp30) REVERT: E 41 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8463 (mm-30) REVERT: L 55 TYR cc_start: 0.8385 (m-10) cc_final: 0.7974 (m-10) REVERT: L 88 ASP cc_start: 0.8128 (m-30) cc_final: 0.7783 (m-30) REVERT: L 96 GLN cc_start: 0.8775 (pt0) cc_final: 0.8388 (pp30) REVERT: H 52 ASP cc_start: 0.8938 (t0) cc_final: 0.8050 (t0) REVERT: H 67 LYS cc_start: 0.9172 (ttmt) cc_final: 0.8819 (tttt) REVERT: H 73 ASP cc_start: 0.7966 (t0) cc_final: 0.7482 (t0) REVERT: H 84 ASN cc_start: 0.8122 (m-40) cc_final: 0.7377 (p0) outliers start: 18 outliers final: 13 residues processed: 201 average time/residue: 1.5993 time to fit residues: 342.2847 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 : 1.479 ------------------------------------------------------------------------------- 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 105 LYS 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 L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 84 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.107001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.087923 restraints weight = 12227.968| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.47 r_work: 0.3104 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6488 Z= 0.143 Angle : 0.676 11.333 8828 Z= 0.350 Chirality : 0.046 0.191 978 Planarity : 0.003 0.026 1115 Dihedral : 4.017 20.165 870 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.84 % Allowed : 33.57 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.29), residues: 800 helix: 1.00 (0.48), residues: 120 sheet: -0.98 (0.30), residues: 309 loop : -1.94 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 108 HIS 0.002 0.001 HIS B 43 PHE 0.015 0.001 PHE D 117 TYR 0.016 0.001 TYR E 34 ARG 0.003 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 170) hydrogen bonds : angle 4.94348 ( 456) SS BOND : bond 0.00686 ( 8) SS BOND : angle 2.03972 ( 16) covalent geometry : bond 0.00337 ( 6480) covalent geometry : angle 0.67121 ( 8812) ********************** 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 : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8966 (t0) cc_final: 0.8348 (t0) REVERT: A 41 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8578 (mm-30) REVERT: A 48 ASP cc_start: 0.8289 (t70) cc_final: 0.7850 (t0) REVERT: B 33 TYR cc_start: 0.7965 (p90) cc_final: 0.7559 (p90) REVERT: B 105 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7069 (mtpp) REVERT: C 24 GLU cc_start: 0.8246 (pm20) cc_final: 0.7647 (pm20) REVERT: C 37 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7526 (mt-10) REVERT: C 41 GLU cc_start: 0.8625 (mp0) cc_final: 0.8160 (mp0) REVERT: D 97 GLN cc_start: 0.8221 (pt0) cc_final: 0.7817 (pm20) REVERT: D 132 GLN cc_start: 0.8963 (pp30) cc_final: 0.8427 (pp30) REVERT: E 41 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8501 (mm-30) REVERT: L 17 GLU cc_start: 0.8395 (pt0) cc_final: 0.8096 (pm20) REVERT: L 55 TYR cc_start: 0.8395 (m-10) cc_final: 0.7964 (m-10) REVERT: L 88 ASP cc_start: 0.8098 (m-30) cc_final: 0.7738 (m-30) REVERT: L 96 GLN cc_start: 0.8788 (pt0) cc_final: 0.8418 (pp30) REVERT: H 52 ASP cc_start: 0.8820 (t0) cc_final: 0.8388 (t0) REVERT: H 67 LYS cc_start: 0.9160 (ttmt) cc_final: 0.8809 (tttt) REVERT: H 73 ASP cc_start: 0.8043 (t0) cc_final: 0.7562 (t0) REVERT: H 84 ASN cc_start: 0.8124 (m-40) cc_final: 0.7400 (p0) outliers start: 20 outliers final: 14 residues processed: 200 average time/residue: 1.0310 time to fit residues: 218.5877 Evaluate side-chains 200 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 105 LYS Chi-restraints excluded: chain B residue 114 VAL 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 L residue 19 VAL Chi-restraints excluded: chain L residue 59 THR Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 84 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 38 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.109481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.090344 restraints weight = 12302.107| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.46 r_work: 0.3138 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4548 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= 0.129 Angle : 0.665 10.879 8828 Z= 0.345 Chirality : 0.045 0.159 978 Planarity : 0.003 0.025 1115 Dihedral : 3.925 19.778 870 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.42 % Allowed : 34.00 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.29), residues: 800 helix: 1.10 (0.48), residues: 120 sheet: -0.94 (0.30), residues: 309 loop : -1.93 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 108 HIS 0.002 0.001 HIS B 43 PHE 0.016 0.001 PHE B 113 TYR 0.013 0.001 TYR H 32 ARG 0.003 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.02738 ( 170) hydrogen bonds : angle 4.87338 ( 456) SS BOND : bond 0.00605 ( 8) SS BOND : angle 1.66913 ( 16) covalent geometry : bond 0.00302 ( 6480) covalent geometry : angle 0.66216 ( 8812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6512.10 seconds wall clock time: 118 minutes 4.78 seconds (7084.78 seconds total)