Starting phenix.real_space_refine on Thu Jul 2 06:36:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t04_40934/07_2026/8t04_40934.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t04_40934/07_2026/8t04_40934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t04_40934/07_2026/8t04_40934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t04_40934/07_2026/8t04_40934.map" model { file = "/net/cci-nas-00/data/ceres_data/8t04_40934/07_2026/8t04_40934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t04_40934/07_2026/8t04_40934.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8t04_40934/07_2026/8t04_40934.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t04_40934/07_2026/8t04_40934.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.088 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 44 5.16 5 C 4492 2.51 5 N 1092 2.21 5 O 1242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6874 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1593 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "B" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1593 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "C" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "E" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "F" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Time building chain proxies: 1.72, per 1000 atoms: 0.25 Number of scatterers: 6874 At special positions: 0 Unit cell: (72.21, 108.73, 103.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 44 16.00 P 2 15.00 O 1242 8.00 N 1092 7.00 C 4492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 59 " distance=2.04 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 59 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 462.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 180 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 184 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 184 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 180 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 43.1% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 removed outlier: 3.745A pdb=" N LEU A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 17 through 28 removed outlier: 4.144A pdb=" N THR A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 52 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 62 through 87 Processing helix chain 'A' and resid 91 through 111 Processing helix chain 'A' and resid 118 through 141 Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 153 through 170 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 175 through 195 removed outlier: 3.898A pdb=" N SER A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 14 Proline residue: B 11 - end of helix Processing helix chain 'B' and resid 17 through 28 removed outlier: 4.142A pdb=" N THR B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 52 Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 62 through 87 Processing helix chain 'B' and resid 91 through 111 removed outlier: 3.501A pdb=" N THR B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 141 Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 153 through 170 Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 175 through 195 removed outlier: 3.899A pdb=" N SER B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 65 through 67 No H-bonds generated for 'chain 'E' and resid 65 through 67' Processing helix chain 'E' and resid 88 through 91 Processing helix chain 'F' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12 removed outlier: 7.054A pdb=" N VAL C 36 " --> pdb=" O HIS C 52 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N HIS C 52 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP C 38 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.816A pdb=" N TYR C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.426A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE D 33 " --> pdb=" O HIS D 49 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N HIS D 49 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.426A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.050A pdb=" N VAL E 36 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N HIS E 52 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP E 38 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.813A pdb=" N TYR E 109 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.423A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE F 33 " --> pdb=" O HIS F 49 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N HIS F 49 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.423A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1047 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: 1.10 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1024 1.31 - 1.44: 2033 1.44 - 1.56: 3921 1.56 - 1.69: 8 1.69 - 1.82: 72 Bond restraints: 7058 Sorted by residual: bond pdb=" C ARG B 93 " pdb=" N SER B 94 " ideal model delta sigma weight residual 1.335 1.446 -0.111 1.31e-02 5.83e+03 7.19e+01 bond pdb=" C25 LBN B 303 " pdb=" O5 LBN B 303 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C25 LBN A 303 " pdb=" O5 LBN A 303 " ideal model delta sigma weight residual 1.326 1.432 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C34 LBN A 303 " pdb=" O7 LBN A 303 " ideal model delta sigma weight residual 1.331 1.423 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C34 LBN B 303 " pdb=" O7 LBN B 303 " ideal model delta sigma weight residual 1.331 1.422 -0.091 2.00e-02 2.50e+03 2.08e+01 ... (remaining 7053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 8955 3.36 - 6.73: 584 6.73 - 10.09: 22 10.09 - 13.45: 1 13.45 - 16.82: 2 Bond angle restraints: 9564 Sorted by residual: angle pdb=" O ARG A 93 " pdb=" C ARG A 93 " pdb=" N SER A 94 " ideal model delta sigma weight residual 122.09 129.02 -6.93 1.04e+00 9.25e-01 4.45e+01 angle pdb=" O1 LBN A 303 " pdb=" P1 LBN A 303 " pdb=" O2 LBN A 303 " ideal model delta sigma weight residual 93.45 110.27 -16.82 3.00e+00 1.11e-01 3.14e+01 angle pdb=" O1 LBN B 303 " pdb=" P1 LBN B 303 " pdb=" O2 LBN B 303 " ideal model delta sigma weight residual 93.45 110.19 -16.74 3.00e+00 1.11e-01 3.12e+01 angle pdb=" N GLU B 90 " pdb=" CA GLU B 90 " pdb=" C GLU B 90 " ideal model delta sigma weight residual 110.07 103.09 6.98 1.26e+00 6.30e-01 3.07e+01 angle pdb=" N GLU A 90 " pdb=" CA GLU A 90 " pdb=" C GLU A 90 " ideal model delta sigma weight residual 110.07 103.11 6.96 1.26e+00 6.30e-01 3.06e+01 ... (remaining 9559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 4018 34.41 - 68.82: 84 68.82 - 103.23: 14 103.23 - 137.64: 2 137.64 - 172.05: 2 Dihedral angle restraints: 4120 sinusoidal: 1658 harmonic: 2462 Sorted by residual: dihedral pdb=" CA HIS F 49 " pdb=" C HIS F 49 " pdb=" N TYR F 50 " pdb=" CA TYR F 50 " ideal model delta harmonic sigma weight residual -180.00 -150.96 -29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA HIS D 49 " pdb=" C HIS D 49 " pdb=" N TYR D 50 " pdb=" CA TYR D 50 " ideal model delta harmonic sigma weight residual -180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA GLU A 90 " pdb=" C GLU A 90 " pdb=" N PRO A 91 " pdb=" CA PRO A 91 " ideal model delta harmonic sigma weight residual 0.00 26.21 -26.21 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 4117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.983: 1052 0.983 - 1.966: 0 1.966 - 2.949: 0 2.949 - 3.932: 0 3.932 - 4.915: 2 Chirality restraints: 1054 Sorted by residual: chirality pdb=" C2 LBN B 303 " pdb=" C1 LBN B 303 " pdb=" C3 LBN B 303 " pdb=" O7 LBN B 303 " both_signs ideal model delta sigma weight residual False -2.36 2.55 -4.91 2.00e-01 2.50e+01 6.04e+02 chirality pdb=" C2 LBN A 303 " pdb=" C1 LBN A 303 " pdb=" C3 LBN A 303 " pdb=" O7 LBN A 303 " both_signs ideal model delta sigma weight residual False -2.36 2.55 -4.91 2.00e-01 2.50e+01 6.03e+02 chirality pdb=" CA ILE D 21 " pdb=" N ILE D 21 " pdb=" C ILE D 21 " pdb=" CB ILE D 21 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1051 not shown) Planarity restraints: 1156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 110 " 0.021 2.00e-02 2.50e+03 1.19e-02 3.55e+00 pdb=" CG TRP C 110 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP C 110 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP C 110 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 110 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 110 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 110 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 110 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 110 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 110 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 110 " -0.021 2.00e-02 2.50e+03 1.18e-02 3.46e+00 pdb=" CG TRP E 110 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP E 110 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP E 110 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 110 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP E 110 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 110 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 110 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 110 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 110 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 93 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C ARG B 93 " 0.029 2.00e-02 2.50e+03 pdb=" O ARG B 93 " -0.011 2.00e-02 2.50e+03 pdb=" N SER B 94 " -0.009 2.00e-02 2.50e+03 ... (remaining 1153 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1240 2.84 - 3.35: 6694 3.35 - 3.87: 10820 3.87 - 4.38: 14301 4.38 - 4.90: 23575 Nonbonded interactions: 56630 Sorted by model distance: nonbonded pdb=" NH1 ARG D 61 " pdb=" OD2 ASP D 82 " model vdw 2.320 3.120 nonbonded pdb=" NH1 ARG F 61 " pdb=" OD2 ASP F 82 " model vdw 2.320 3.120 nonbonded pdb=" NH2 ARG D 61 " pdb=" OE2 GLU D 81 " model vdw 2.479 3.120 nonbonded pdb=" NH2 ARG F 61 " pdb=" OE2 GLU F 81 " model vdw 2.479 3.120 nonbonded pdb=" N GLY B 116 " pdb=" O4 LBN B 303 " model vdw 2.483 3.120 ... (remaining 56625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.680 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.220 7068 Z= 1.078 Angle : 1.828 16.817 9572 Z= 1.300 Chirality : 0.230 4.915 1054 Planarity : 0.004 0.027 1156 Dihedral : 15.866 172.049 2536 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.27 % Allowed : 6.81 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.29), residues: 840 helix: -1.11 (0.26), residues: 278 sheet: 0.01 (0.40), residues: 166 loop : -0.57 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 62 TYR 0.028 0.003 TYR D 91 PHE 0.021 0.002 PHE B 69 TRP 0.030 0.003 TRP C 110 HIS 0.007 0.002 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.01440 / 1.07 ( 7058) covalent geometry : angle 1.82850 / 1.30 ( 9564) SS BOND : bond 0.00684 / 0.34 ( 4) SS BOND : angle 1.17853 / 0.62 ( 8) hydrogen bonds : bond 0.18540 / 12.12 ( 379) hydrogen bonds : angle 8.76850 / 6.29 ( 1047) metal coordination : bond 0.11773 / 5.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.250 Fit side-chains REVERT: A 9 LEU cc_start: 0.6311 (mt) cc_final: 0.6099 (mp) REVERT: A 29 ARG cc_start: 0.6564 (mmm160) cc_final: 0.6358 (mtp180) REVERT: A 61 MET cc_start: 0.6262 (mtm) cc_final: 0.6026 (mtp) REVERT: A 87 ASP cc_start: 0.6284 (t70) cc_final: 0.6065 (t70) REVERT: A 94 SER cc_start: 0.6510 (m) cc_final: 0.6075 (p) REVERT: A 137 MET cc_start: 0.5787 (mtm) cc_final: 0.5572 (mtm) REVERT: A 170 PHE cc_start: 0.6461 (t80) cc_final: 0.6152 (t80) REVERT: B 9 LEU cc_start: 0.7564 (mt) cc_final: 0.7242 (mp) REVERT: B 83 MET cc_start: 0.8086 (mmp) cc_final: 0.7550 (mmp) REVERT: B 137 MET cc_start: 0.7561 (mtm) cc_final: 0.7157 (mtm) REVERT: B 170 PHE cc_start: 0.7342 (t80) cc_final: 0.7119 (t80) REVERT: B 189 MET cc_start: 0.7518 (tpt) cc_final: 0.7299 (mmm) REVERT: C 61 TYR cc_start: 0.7574 (m-80) cc_final: 0.7330 (m-80) REVERT: C 83 MET cc_start: 0.5581 (mmt) cc_final: 0.5237 (mmt) REVERT: C 112 GLN cc_start: 0.7255 (mt0) cc_final: 0.6928 (mm110) REVERT: D 63 SER cc_start: 0.6740 (m) cc_final: 0.6539 (p) REVERT: E 83 MET cc_start: 0.6846 (mmt) cc_final: 0.6255 (mmt) outliers start: 2 outliers final: 0 residues processed: 115 average time/residue: 0.4010 time to fit residues: 49.4107 Evaluate side-chains 84 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.173761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122786 restraints weight = 7110.961| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.37 r_work: 0.3281 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7068 Z= 0.186 Angle : 0.629 6.343 9572 Z= 0.326 Chirality : 0.045 0.162 1054 Planarity : 0.005 0.035 1156 Dihedral : 11.262 140.219 1006 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.54 % Allowed : 10.76 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.30), residues: 840 helix: 1.11 (0.28), residues: 288 sheet: 0.04 (0.36), residues: 230 loop : -0.10 (0.40), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 107 TYR 0.011 0.002 TYR F 91 PHE 0.021 0.002 PHE B 42 TRP 0.020 0.001 TRP E 110 HIS 0.005 0.002 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 7058) covalent geometry : angle 0.62915 / 0.33 ( 9564) SS BOND : bond 0.00109 / 0.05 ( 4) SS BOND : angle 0.59595 / 0.30 ( 8) hydrogen bonds : bond 0.04388 / 2.91 ( 379) hydrogen bonds : angle 5.32573 / 3.84 ( 1047) metal coordination : bond 0.00461 / 0.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.188 Fit side-chains REVERT: A 27 LYS cc_start: 0.7603 (ttmt) cc_final: 0.6708 (mptt) REVERT: A 138 LYS cc_start: 0.6675 (mttt) cc_final: 0.6228 (mppt) REVERT: B 27 LYS cc_start: 0.7630 (ttmt) cc_final: 0.6726 (mptt) REVERT: B 138 LYS cc_start: 0.6701 (mttt) cc_final: 0.6246 (mppt) REVERT: C 83 MET cc_start: 0.7293 (mmt) cc_final: 0.6775 (mmt) REVERT: C 107 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8717 (pmm) REVERT: D 63 SER cc_start: 0.8463 (m) cc_final: 0.8169 (p) REVERT: D 65 SER cc_start: 0.8325 (m) cc_final: 0.8026 (p) REVERT: E 83 MET cc_start: 0.7323 (mmt) cc_final: 0.6787 (mmt) REVERT: F 65 SER cc_start: 0.8217 (m) cc_final: 0.7990 (p) REVERT: F 71 TYR cc_start: 0.8459 (m-80) cc_final: 0.8258 (m-80) outliers start: 26 outliers final: 11 residues processed: 121 average time/residue: 0.4746 time to fit residues: 60.8637 Evaluate side-chains 103 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.174086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123633 restraints weight = 7021.091| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.34 r_work: 0.3286 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7068 Z= 0.165 Angle : 0.570 6.239 9572 Z= 0.296 Chirality : 0.043 0.148 1054 Planarity : 0.004 0.035 1156 Dihedral : 10.449 145.161 1006 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.00 % Allowed : 14.03 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.31), residues: 840 helix: 1.54 (0.28), residues: 296 sheet: 0.21 (0.37), residues: 230 loop : -0.12 (0.40), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 168 TYR 0.010 0.001 TYR D 91 PHE 0.019 0.002 PHE A 39 TRP 0.015 0.001 TRP E 110 HIS 0.005 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 7058) covalent geometry : angle 0.57013 / 0.30 ( 9564) SS BOND : bond 0.00071 / 0.03 ( 4) SS BOND : angle 0.33850 / 0.18 ( 8) hydrogen bonds : bond 0.04224 / 2.80 ( 379) hydrogen bonds : angle 5.03384 / 3.64 ( 1047) metal coordination : bond 0.00313 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.290 Fit side-chains REVERT: A 27 LYS cc_start: 0.7670 (ttmt) cc_final: 0.6752 (mptt) REVERT: A 138 LYS cc_start: 0.6708 (mttt) cc_final: 0.6183 (mppt) REVERT: B 27 LYS cc_start: 0.7682 (ttmt) cc_final: 0.6752 (mptt) REVERT: B 29 ARG cc_start: 0.8108 (mtp180) cc_final: 0.7895 (mtp85) REVERT: B 127 LEU cc_start: 0.7724 (tp) cc_final: 0.7521 (tp) REVERT: B 138 LYS cc_start: 0.6727 (mttt) cc_final: 0.6207 (mppt) REVERT: C 17 THR cc_start: 0.6170 (p) cc_final: 0.5793 (m) REVERT: C 83 MET cc_start: 0.7349 (mmt) cc_final: 0.7095 (mmm) REVERT: D 61 ARG cc_start: 0.7226 (ptp-170) cc_final: 0.7010 (ptp-170) REVERT: D 63 SER cc_start: 0.8367 (m) cc_final: 0.8152 (p) REVERT: E 83 MET cc_start: 0.7355 (mmt) cc_final: 0.7094 (mmm) REVERT: F 61 ARG cc_start: 0.7274 (ptp-170) cc_final: 0.7046 (ptp-170) REVERT: F 71 TYR cc_start: 0.8393 (m-80) cc_final: 0.8173 (m-80) outliers start: 22 outliers final: 7 residues processed: 112 average time/residue: 0.4902 time to fit residues: 58.1602 Evaluate side-chains 107 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 2 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.174632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.124325 restraints weight = 7057.967| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.33 r_work: 0.3286 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7068 Z= 0.144 Angle : 0.539 6.141 9572 Z= 0.279 Chirality : 0.043 0.143 1054 Planarity : 0.004 0.033 1156 Dihedral : 10.138 148.287 1006 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.45 % Allowed : 14.99 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.30), residues: 840 helix: 1.83 (0.28), residues: 296 sheet: 0.29 (0.37), residues: 230 loop : -0.16 (0.39), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 168 TYR 0.009 0.001 TYR D 91 PHE 0.018 0.002 PHE A 170 TRP 0.013 0.001 TRP E 110 HIS 0.005 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 7058) covalent geometry : angle 0.53912 / 0.28 ( 9564) SS BOND : bond 0.00044 / 0.02 ( 4) SS BOND : angle 0.39819 / 0.21 ( 8) hydrogen bonds : bond 0.03936 / 2.62 ( 379) hydrogen bonds : angle 4.86019 / 3.52 ( 1047) metal coordination : bond 0.00249 / 0.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.168 Fit side-chains REVERT: A 27 LYS cc_start: 0.7722 (ttmt) cc_final: 0.6783 (mptt) REVERT: A 29 ARG cc_start: 0.8147 (mtp180) cc_final: 0.7907 (mtp85) REVERT: A 138 LYS cc_start: 0.6759 (mttt) cc_final: 0.6262 (mppt) REVERT: B 27 LYS cc_start: 0.7709 (ttmt) cc_final: 0.6795 (mptt) REVERT: B 138 LYS cc_start: 0.6773 (mttt) cc_final: 0.6277 (mppt) REVERT: C 83 MET cc_start: 0.7359 (mmt) cc_final: 0.7118 (mmm) REVERT: D 61 ARG cc_start: 0.7240 (ptp-170) cc_final: 0.7014 (ptp-170) REVERT: E 83 MET cc_start: 0.7367 (mmt) cc_final: 0.7122 (mmm) REVERT: F 61 ARG cc_start: 0.7424 (ptp-170) cc_final: 0.7191 (ptp-170) outliers start: 18 outliers final: 9 residues processed: 114 average time/residue: 0.4394 time to fit residues: 53.0377 Evaluate side-chains 104 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 76 optimal weight: 0.0020 chunk 58 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.176968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.126462 restraints weight = 7012.724| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.35 r_work: 0.3315 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7068 Z= 0.112 Angle : 0.505 6.048 9572 Z= 0.261 Chirality : 0.041 0.139 1054 Planarity : 0.004 0.032 1156 Dihedral : 9.828 157.088 1006 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.32 % Allowed : 15.40 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.30), residues: 840 helix: 2.15 (0.28), residues: 296 sheet: 0.54 (0.38), residues: 220 loop : -0.32 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 168 TYR 0.008 0.001 TYR D 91 PHE 0.025 0.002 PHE A 42 TRP 0.011 0.001 TRP E 110 HIS 0.004 0.001 HIS E 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 7058) covalent geometry : angle 0.50552 / 0.26 ( 9564) SS BOND : bond 0.00079 / 0.04 ( 4) SS BOND : angle 0.44851 / 0.24 ( 8) hydrogen bonds : bond 0.03660 / 2.44 ( 379) hydrogen bonds : angle 4.61357 / 3.34 ( 1047) metal coordination : bond 0.00163 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.208 Fit side-chains REVERT: A 27 LYS cc_start: 0.7676 (ttmt) cc_final: 0.6795 (mptt) REVERT: A 29 ARG cc_start: 0.8169 (mtp180) cc_final: 0.7931 (mtp85) REVERT: A 138 LYS cc_start: 0.6687 (mttt) cc_final: 0.6283 (tppt) REVERT: B 23 SER cc_start: 0.7906 (p) cc_final: 0.7672 (m) REVERT: B 27 LYS cc_start: 0.7662 (ttmt) cc_final: 0.6807 (mptt) REVERT: B 138 LYS cc_start: 0.6688 (mttt) cc_final: 0.6292 (tppt) REVERT: C 83 MET cc_start: 0.7438 (mmt) cc_final: 0.7121 (mmm) REVERT: C 107 MET cc_start: 0.8962 (ptp) cc_final: 0.8724 (pmm) REVERT: D 61 ARG cc_start: 0.7301 (ptp-170) cc_final: 0.7095 (ptp-170) REVERT: E 83 MET cc_start: 0.7435 (mmt) cc_final: 0.7103 (mmm) REVERT: F 61 ARG cc_start: 0.7474 (ptp-170) cc_final: 0.7270 (ptp-170) outliers start: 17 outliers final: 11 residues processed: 106 average time/residue: 0.4348 time to fit residues: 48.6877 Evaluate side-chains 105 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 52 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.170668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119959 restraints weight = 7103.313| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.37 r_work: 0.3262 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7068 Z= 0.181 Angle : 0.569 6.325 9572 Z= 0.291 Chirality : 0.043 0.143 1054 Planarity : 0.005 0.032 1156 Dihedral : 10.032 160.686 1006 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.09 % Allowed : 15.40 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.30), residues: 840 helix: 1.96 (0.28), residues: 296 sheet: 0.47 (0.37), residues: 220 loop : -0.47 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 29 TYR 0.012 0.001 TYR D 91 PHE 0.021 0.002 PHE B 42 TRP 0.015 0.001 TRP E 110 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 ( 7058) covalent geometry : angle 0.56887 / 0.29 ( 9564) SS BOND : bond 0.00077 / 0.04 ( 4) SS BOND : angle 0.40435 / 0.21 ( 8) hydrogen bonds : bond 0.04186 / 2.77 ( 379) hydrogen bonds : angle 4.85471 / 3.50 ( 1047) metal coordination : bond 0.00295 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.257 Fit side-chains REVERT: A 27 LYS cc_start: 0.7699 (ttmt) cc_final: 0.6779 (mptt) REVERT: A 41 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8339 (ttt) REVERT: A 138 LYS cc_start: 0.6725 (mttt) cc_final: 0.6235 (mppt) REVERT: B 27 LYS cc_start: 0.7701 (ttmt) cc_final: 0.6802 (mptt) REVERT: B 138 LYS cc_start: 0.6729 (mttt) cc_final: 0.6237 (mppt) REVERT: C 83 MET cc_start: 0.7439 (mmt) cc_final: 0.7164 (mmm) REVERT: C 107 MET cc_start: 0.9007 (ptp) cc_final: 0.8710 (pmm) REVERT: D 61 ARG cc_start: 0.7430 (ptp-170) cc_final: 0.7196 (ptp-170) REVERT: E 83 MET cc_start: 0.7452 (mmt) cc_final: 0.7155 (mmm) REVERT: F 61 ARG cc_start: 0.7447 (ptp-170) cc_final: 0.7229 (ptp-170) outliers start: 30 outliers final: 15 residues processed: 118 average time/residue: 0.4057 time to fit residues: 50.9029 Evaluate side-chains 108 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 43 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.175445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.124993 restraints weight = 7038.146| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.35 r_work: 0.3296 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7068 Z= 0.133 Angle : 0.531 6.040 9572 Z= 0.272 Chirality : 0.042 0.135 1054 Planarity : 0.004 0.031 1156 Dihedral : 10.029 169.750 1006 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.54 % Allowed : 15.53 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.30), residues: 840 helix: 2.11 (0.28), residues: 296 sheet: 0.60 (0.37), residues: 220 loop : -0.50 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 29 TYR 0.009 0.001 TYR D 91 PHE 0.020 0.002 PHE B 42 TRP 0.015 0.001 TRP E 55 HIS 0.004 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 7058) covalent geometry : angle 0.53091 / 0.27 ( 9564) SS BOND : bond 0.00102 / 0.05 ( 4) SS BOND : angle 0.49783 / 0.26 ( 8) hydrogen bonds : bond 0.03834 / 2.55 ( 379) hydrogen bonds : angle 4.68328 / 3.38 ( 1047) metal coordination : bond 0.00194 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.242 Fit side-chains REVERT: A 138 LYS cc_start: 0.6717 (mttt) cc_final: 0.6240 (mppt) REVERT: B 23 SER cc_start: 0.7872 (p) cc_final: 0.7654 (m) REVERT: B 27 LYS cc_start: 0.7669 (ttmt) cc_final: 0.6784 (mptt) REVERT: B 138 LYS cc_start: 0.6719 (mttt) cc_final: 0.6244 (mppt) REVERT: C 83 MET cc_start: 0.7441 (mmt) cc_final: 0.7143 (mmm) REVERT: C 107 MET cc_start: 0.8994 (ptp) cc_final: 0.8761 (pmm) REVERT: D 61 ARG cc_start: 0.7406 (ptp-170) cc_final: 0.7197 (ptp-170) REVERT: E 83 MET cc_start: 0.7476 (mmt) cc_final: 0.7167 (mmm) outliers start: 26 outliers final: 18 residues processed: 120 average time/residue: 0.4104 time to fit residues: 52.2743 Evaluate side-chains 114 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain E residue 52 HIS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 12 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 67 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.172228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121774 restraints weight = 7151.306| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.37 r_work: 0.3285 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7068 Z= 0.142 Angle : 0.536 6.024 9572 Z= 0.277 Chirality : 0.042 0.140 1054 Planarity : 0.004 0.034 1156 Dihedral : 10.200 176.770 1006 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.41 % Allowed : 15.94 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.30), residues: 840 helix: 2.14 (0.28), residues: 296 sheet: 0.66 (0.37), residues: 220 loop : -0.54 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 29 TYR 0.011 0.001 TYR F 91 PHE 0.019 0.001 PHE A 170 TRP 0.018 0.001 TRP E 55 HIS 0.004 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 7058) covalent geometry : angle 0.53610 / 0.28 ( 9564) SS BOND : bond 0.00103 / 0.05 ( 4) SS BOND : angle 0.46238 / 0.25 ( 8) hydrogen bonds : bond 0.03919 / 2.62 ( 379) hydrogen bonds : angle 4.67499 / 3.37 ( 1047) metal coordination : bond 0.00209 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.221 Fit side-chains REVERT: A 27 LYS cc_start: 0.7687 (mtpt) cc_final: 0.6711 (mptt) REVERT: A 138 LYS cc_start: 0.6721 (mttt) cc_final: 0.6240 (mppt) REVERT: B 23 SER cc_start: 0.7911 (p) cc_final: 0.7667 (m) REVERT: B 27 LYS cc_start: 0.7658 (ttmt) cc_final: 0.6767 (mptt) REVERT: B 138 LYS cc_start: 0.6742 (mttt) cc_final: 0.6266 (mppt) REVERT: C 83 MET cc_start: 0.7466 (mmt) cc_final: 0.7183 (mmm) REVERT: C 107 MET cc_start: 0.9002 (ptp) cc_final: 0.8662 (pmm) REVERT: D 61 ARG cc_start: 0.7412 (ptp-170) cc_final: 0.7207 (ptp-170) REVERT: E 66 LYS cc_start: 0.7131 (ttpt) cc_final: 0.6925 (ttmm) REVERT: E 83 MET cc_start: 0.7485 (mmt) cc_final: 0.7195 (mmm) outliers start: 25 outliers final: 16 residues processed: 121 average time/residue: 0.4433 time to fit residues: 56.8402 Evaluate side-chains 112 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 52 HIS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 89 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 78 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 0.0030 chunk 57 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.176370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125110 restraints weight = 7026.527| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.40 r_work: 0.3315 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7068 Z= 0.115 Angle : 0.521 5.963 9572 Z= 0.269 Chirality : 0.041 0.146 1054 Planarity : 0.004 0.035 1156 Dihedral : 10.060 177.644 1006 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.27 % Allowed : 16.08 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.30), residues: 840 helix: 2.28 (0.28), residues: 296 sheet: 0.67 (0.36), residues: 230 loop : -0.45 (0.38), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 29 TYR 0.008 0.001 TYR D 91 PHE 0.023 0.001 PHE B 42 TRP 0.019 0.001 TRP E 55 HIS 0.003 0.001 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 7058) covalent geometry : angle 0.52087 / 0.27 ( 9564) SS BOND : bond 0.00120 / 0.06 ( 4) SS BOND : angle 0.50783 / 0.27 ( 8) hydrogen bonds : bond 0.03703 / 2.48 ( 379) hydrogen bonds : angle 4.53680 / 3.28 ( 1047) metal coordination : bond 0.00139 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.170 Fit side-chains REVERT: A 23 SER cc_start: 0.7890 (p) cc_final: 0.7641 (m) REVERT: A 27 LYS cc_start: 0.7702 (mtpt) cc_final: 0.6732 (mptt) REVERT: A 138 LYS cc_start: 0.6692 (mttt) cc_final: 0.6203 (mppt) REVERT: B 23 SER cc_start: 0.7892 (p) cc_final: 0.7670 (m) REVERT: B 27 LYS cc_start: 0.7684 (ttmt) cc_final: 0.6774 (mptt) REVERT: B 138 LYS cc_start: 0.6723 (mttt) cc_final: 0.6243 (mppt) REVERT: C 66 LYS cc_start: 0.7619 (ttmm) cc_final: 0.6855 (ttmm) REVERT: C 83 MET cc_start: 0.7459 (mmt) cc_final: 0.7154 (mmm) REVERT: C 117 THR cc_start: 0.8981 (p) cc_final: 0.8531 (t) REVERT: E 83 MET cc_start: 0.7468 (mmt) cc_final: 0.7152 (mmm) outliers start: 24 outliers final: 12 residues processed: 124 average time/residue: 0.4318 time to fit residues: 57.0501 Evaluate side-chains 110 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 89 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 42 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.174791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122741 restraints weight = 7049.505| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.44 r_work: 0.3291 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7068 Z= 0.143 Angle : 0.550 6.035 9572 Z= 0.283 Chirality : 0.042 0.146 1054 Planarity : 0.004 0.034 1156 Dihedral : 9.966 176.515 1006 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.04 % Allowed : 18.26 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.30), residues: 840 helix: 2.05 (0.28), residues: 308 sheet: 0.70 (0.36), residues: 230 loop : -0.54 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 29 TYR 0.011 0.001 TYR D 91 PHE 0.019 0.002 PHE A 46 TRP 0.023 0.001 TRP E 55 HIS 0.004 0.001 HIS F 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 7058) covalent geometry : angle 0.55000 / 0.28 ( 9564) SS BOND : bond 0.00119 / 0.06 ( 4) SS BOND : angle 0.46114 / 0.25 ( 8) hydrogen bonds : bond 0.03903 / 2.60 ( 379) hydrogen bonds : angle 4.63249 / 3.34 ( 1047) metal coordination : bond 0.00200 / 0.12 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.253 Fit side-chains REVERT: A 23 SER cc_start: 0.7930 (p) cc_final: 0.7667 (m) REVERT: A 27 LYS cc_start: 0.7714 (mtpt) cc_final: 0.6755 (mptt) REVERT: A 138 LYS cc_start: 0.6695 (mttt) cc_final: 0.6210 (mppt) REVERT: B 23 SER cc_start: 0.7909 (p) cc_final: 0.7685 (m) REVERT: B 27 LYS cc_start: 0.7684 (ttmt) cc_final: 0.6801 (mptt) REVERT: B 138 LYS cc_start: 0.6715 (mttt) cc_final: 0.6237 (mppt) REVERT: C 66 LYS cc_start: 0.7622 (ttmm) cc_final: 0.6802 (ttmm) REVERT: C 83 MET cc_start: 0.7529 (mmt) cc_final: 0.7254 (mmm) REVERT: C 117 THR cc_start: 0.8993 (p) cc_final: 0.8577 (t) REVERT: D 61 ARG cc_start: 0.7194 (ptp-170) cc_final: 0.6977 (ttp-170) REVERT: E 66 LYS cc_start: 0.7637 (ttmm) cc_final: 0.6820 (ttmm) REVERT: E 83 MET cc_start: 0.7468 (mmt) cc_final: 0.7168 (mmm) REVERT: E 117 THR cc_start: 0.8963 (p) cc_final: 0.8505 (t) outliers start: 15 outliers final: 11 residues processed: 121 average time/residue: 0.4297 time to fit residues: 55.3827 Evaluate side-chains 113 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 3 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.175571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123811 restraints weight = 7034.697| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.42 r_work: 0.3301 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7068 Z= 0.131 Angle : 0.539 5.997 9572 Z= 0.278 Chirality : 0.042 0.147 1054 Planarity : 0.004 0.034 1156 Dihedral : 9.474 164.313 1006 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.77 % Allowed : 18.80 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.30), residues: 840 helix: 2.09 (0.28), residues: 308 sheet: 0.81 (0.37), residues: 220 loop : -0.64 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 29 TYR 0.010 0.001 TYR C 109 PHE 0.022 0.002 PHE B 42 TRP 0.026 0.001 TRP E 55 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 7058) covalent geometry : angle 0.53866 / 0.28 ( 9564) SS BOND : bond 0.00124 / 0.06 ( 4) SS BOND : angle 0.48090 / 0.26 ( 8) hydrogen bonds : bond 0.03829 / 2.56 ( 379) hydrogen bonds : angle 4.59947 / 3.32 ( 1047) metal coordination : bond 0.00178 / 0.11 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1977.03 seconds wall clock time: 34 minutes 29.85 seconds (2069.85 seconds total)