Starting phenix.real_space_refine on Tue Aug 4 17:15:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6g_47564/08_2026/9e6g_47564.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6g_47564/08_2026/9e6g_47564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e6g_47564/08_2026/9e6g_47564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6g_47564/08_2026/9e6g_47564.map" model { file = "/net/cci-nas-00/data/ceres_data/9e6g_47564/08_2026/9e6g_47564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6g_47564/08_2026/9e6g_47564.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 28 5.16 5 C 3242 2.51 5 N 857 2.21 5 O 1019 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5146 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1677 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 18, 'TRANS': 192} Chain: "B" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1698 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 18, 'TRANS': 195} Chain: "C" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "D" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 813 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.37, per 1000 atoms: 0.27 Number of scatterers: 5146 At special positions: 0 Unit cell: (72.36, 88.56, 112.32, 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 28 16.00 O 1019 8.00 N 857 7.00 C 3242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 211 " distance=2.04 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 107 " distance=2.04 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 211 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 106 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 122 " 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 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG C 201 " - " ASN C 57 " " NAG C 202 " - " ASN C 63 " " NAG C 203 " - " ASN C 88 " " NAG D 201 " - " ASN D 73 " " NAG D 202 " - " ASN D 127 " " NAG E 1 " - " ASN A 83 " " NAG F 1 " - " ASN B 83 " " NAG H 1 " - " ASN D 101 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 171.3 milliseconds 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 16 sheets defined 8.6% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.669A pdb=" N HIS A 221 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 36 removed outlier: 3.565A pdb=" N THR B 36 " --> pdb=" O PRO B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 removed outlier: 3.741A pdb=" N TRP B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU B 100 " --> pdb=" O HIS B 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 100' Processing helix chain 'B' and resid 142 through 146 removed outlier: 4.184A pdb=" N THR B 145 " --> pdb=" O GLU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.600A pdb=" N TYR B 222 " --> pdb=" O HIS B 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 117 removed outlier: 3.736A pdb=" N ASN D 117 " --> pdb=" O PHE D 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 29 removed outlier: 3.739A pdb=" N THR A 46 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 89 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 137 removed outlier: 5.852A pdb=" N PHE A 190 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 168 removed outlier: 3.912A pdb=" N ALA A 164 " --> pdb=" O MET A 214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 29 removed outlier: 5.780A pdb=" N TYR B 86 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 91 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 74 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AA7, first strand: chain 'B' and resid 133 through 137 removed outlier: 6.413A pdb=" N PHE B 190 " --> pdb=" O GLY B 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 133 through 137 removed outlier: 6.413A pdb=" N PHE B 190 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE B 191 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 183 " --> pdb=" O PHE B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 172 through 173 Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 43 removed outlier: 3.880A pdb=" N ARG C 124 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 50 through 52 Processing sheet with id=AB3, first strand: chain 'C' and resid 78 through 83 removed outlier: 5.782A pdb=" N TRP C 66 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 64 " --> pdb=" O PRO C 83 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 78 through 83 removed outlier: 5.782A pdb=" N TRP C 66 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 64 " --> pdb=" O PRO C 83 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN C 63 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG C 107 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 108 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN C 116 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 47 through 48 removed outlier: 4.100A pdb=" N TRP D 47 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D 66 " --> pdb=" O TRP D 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AB7, first strand: chain 'D' and resid 74 through 77 165 hydrogen bonds defined for protein. 408 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.60 Time building geometry restraints manager: 0.65 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: 1618 1.34 - 1.46: 1266 1.46 - 1.58: 2355 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 5279 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" C1 MAN F 5 " pdb=" C2 MAN F 5 " ideal model delta sigma weight residual 1.526 1.577 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" C5 MAN E 5 " pdb=" O5 MAN E 5 " ideal model delta sigma weight residual 1.418 1.467 -0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sigma weight residual 1.417 1.462 -0.045 2.00e-02 2.50e+03 5.14e+00 bond pdb=" C5 MAN E 4 " pdb=" O5 MAN E 4 " ideal model delta sigma weight residual 1.418 1.462 -0.044 2.00e-02 2.50e+03 4.94e+00 ... (remaining 5274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 7026 3.56 - 7.11: 136 7.11 - 10.67: 16 10.67 - 14.23: 1 14.23 - 17.79: 1 Bond angle restraints: 7180 Sorted by residual: angle pdb=" C GLN C 94 " pdb=" N ASN C 95 " pdb=" CA ASN C 95 " ideal model delta sigma weight residual 122.46 129.73 -7.27 1.41e+00 5.03e-01 2.66e+01 angle pdb=" CA LEU C 70 " pdb=" CB LEU C 70 " pdb=" CG LEU C 70 " ideal model delta sigma weight residual 116.30 134.09 -17.79 3.50e+00 8.16e-02 2.58e+01 angle pdb=" CA GLU D 81 " pdb=" CB GLU D 81 " pdb=" CG GLU D 81 " ideal model delta sigma weight residual 114.10 123.65 -9.55 2.00e+00 2.50e-01 2.28e+01 angle pdb=" CB MET B 214 " pdb=" CG MET B 214 " pdb=" SD MET B 214 " ideal model delta sigma weight residual 112.70 125.74 -13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" CA LYS D 62 " pdb=" CB LYS D 62 " pdb=" CG LYS D 62 " ideal model delta sigma weight residual 114.10 121.82 -7.72 2.00e+00 2.50e-01 1.49e+01 ... (remaining 7175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.88: 3151 23.88 - 47.76: 182 47.76 - 71.63: 36 71.63 - 95.51: 24 95.51 - 119.39: 21 Dihedral angle restraints: 3414 sinusoidal: 1605 harmonic: 1809 Sorted by residual: dihedral pdb=" CB CYS B 47 " pdb=" SG CYS B 47 " pdb=" SG CYS B 107 " pdb=" CB CYS B 107 " ideal model delta sinusoidal sigma weight residual 93.00 164.70 -71.70 1 1.00e+01 1.00e-02 6.59e+01 dihedral pdb=" CA LEU A 227 " pdb=" C LEU A 227 " pdb=" N SER A 228 " pdb=" CA SER A 228 " ideal model delta harmonic sigma weight residual 180.00 154.49 25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA GLN D 80 " pdb=" C GLN D 80 " pdb=" N GLU D 81 " pdb=" CA GLU D 81 " ideal model delta harmonic sigma weight residual -180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 3411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 725 0.104 - 0.208: 93 0.208 - 0.312: 6 0.312 - 0.416: 0 0.416 - 0.520: 2 Chirality restraints: 826 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN D 101 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.76e+00 chirality pdb=" C2 NAG H 1 " pdb=" C1 NAG H 1 " pdb=" C3 NAG H 1 " pdb=" N2 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.07 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 823 not shown) Planarity restraints: 912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 78 " -0.037 2.00e-02 2.50e+03 2.60e-02 1.69e+01 pdb=" CG TRP D 78 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP D 78 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP D 78 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 78 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 78 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 78 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 78 " -0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 78 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP D 78 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 167 " 0.017 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP B 167 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 167 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B 167 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 167 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 167 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 167 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 167 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 167 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP B 167 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 180 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO B 181 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " -0.041 5.00e-02 4.00e+02 ... (remaining 909 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1257 2.80 - 3.33: 4557 3.33 - 3.85: 8570 3.85 - 4.38: 9200 4.38 - 4.90: 15306 Nonbonded interactions: 38890 Sorted by model distance: nonbonded pdb=" OG1 THR B 42 " pdb=" OG1 THR B 93 " model vdw 2.281 3.040 nonbonded pdb=" O LYS A 126 " pdb=" OH TYR A 159 " model vdw 2.304 3.040 nonbonded pdb=" OE1 GLU B 58 " pdb=" NZ LYS B 112 " model vdw 2.345 3.120 nonbonded pdb=" O HIS A 54 " pdb=" OH TYR A 86 " model vdw 2.347 3.040 nonbonded pdb=" NH2 ARG B 87 " pdb=" O3 NAG F 2 " model vdw 2.360 3.120 ... (remaining 38885 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' and resid 23 through 233) } ncs_group { reference = chain 'E' 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 group one per residue 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: 7.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.310 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 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 : 0.006 0.062 5304 Z= 0.288 Angle : 1.220 17.786 7247 Z= 0.574 Chirality : 0.070 0.520 826 Planarity : 0.008 0.075 904 Dihedral : 19.448 119.389 2220 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.23 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.20 (0.31), residues: 610 helix: -3.51 (0.67), residues: 24 sheet: 0.13 (0.31), residues: 248 loop : -1.31 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 124 TYR 0.028 0.002 TYR D 120 PHE 0.021 0.002 PHE C 80 TRP 0.069 0.005 TRP D 78 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.29 ( 5279) covalent geometry : angle 1.17371 / 0.56 ( 7180) SS BOND : bond 0.00488 / 0.34 ( 8) SS BOND : angle 0.97696 / 0.67 ( 16) hydrogen bonds : bond 0.14736 / 8.74 ( 147) hydrogen bonds : angle 7.71311 / 5.47 ( 408) link_ALPHA1-3 : bond 0.00590 / 0.33 ( 2) link_ALPHA1-3 : angle 2.20852 / 1.23 ( 6) link_ALPHA1-6 : bond 0.00588 / 0.34 ( 2) link_ALPHA1-6 : angle 1.24949 / 0.78 ( 6) link_BETA1-4 : bond 0.01247 / 0.93 ( 5) link_BETA1-4 : angle 4.94593 / 2.57 ( 15) link_NAG-ASN : bond 0.00433 / 0.26 ( 8) link_NAG-ASN : angle 4.45378 / 3.13 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: B 38 MET cc_start: 0.7374 (pmm) cc_final: 0.6733 (pmm) REVERT: B 224 GLN cc_start: 0.6404 (pp30) cc_final: 0.5855 (pp30) REVERT: B 227 LEU cc_start: 0.7775 (tp) cc_final: 0.7572 (tp) REVERT: C 104 TYR cc_start: 0.8027 (m-80) cc_final: 0.7782 (m-10) REVERT: D 97 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7013 (mp0) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0571 time to fit residues: 5.5866 Evaluate side-chains 51 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN A 170 ASN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.072556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.060468 restraints weight = 33275.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.061892 restraints weight = 23274.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.062964 restraints weight = 18019.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063636 restraints weight = 14814.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.064205 restraints weight = 12888.716| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5304 Z= 0.249 Angle : 0.857 9.470 7247 Z= 0.406 Chirality : 0.053 0.285 826 Planarity : 0.006 0.057 904 Dihedral : 18.527 105.674 1006 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.18 % Allowed : 3.94 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.33), residues: 610 helix: -2.27 (0.92), residues: 25 sheet: 0.01 (0.31), residues: 256 loop : -0.98 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 41 TYR 0.023 0.002 TYR D 120 PHE 0.019 0.002 PHE B 158 TRP 0.024 0.003 TRP D 78 HIS 0.005 0.001 HIS D 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.25 ( 5279) covalent geometry : angle 0.81508 / 0.40 ( 7180) SS BOND : bond 0.00424 / 0.27 ( 8) SS BOND : angle 1.03845 / 0.57 ( 16) hydrogen bonds : bond 0.04789 / 3.17 ( 147) hydrogen bonds : angle 6.25243 / 4.39 ( 408) link_ALPHA1-3 : bond 0.00946 / 0.57 ( 2) link_ALPHA1-3 : angle 2.97768 / 2.24 ( 6) link_ALPHA1-6 : bond 0.01234 / 0.70 ( 2) link_ALPHA1-6 : angle 2.61743 / 1.55 ( 6) link_BETA1-4 : bond 0.00438 / 0.28 ( 5) link_BETA1-4 : angle 3.61015 / 2.18 ( 15) link_NAG-ASN : bond 0.00282 / 0.20 ( 8) link_NAG-ASN : angle 3.19394 / 2.22 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 51 ASP cc_start: 0.6860 (m-30) cc_final: 0.6330 (m-30) REVERT: A 152 THR cc_start: 0.8950 (m) cc_final: 0.8642 (m) REVERT: B 38 MET cc_start: 0.7282 (pmm) cc_final: 0.6276 (pmm) REVERT: B 175 ASN cc_start: 0.7690 (p0) cc_final: 0.7444 (p0) REVERT: C 34 TRP cc_start: 0.7668 (p90) cc_final: 0.7441 (p90) REVERT: C 104 TYR cc_start: 0.8172 (m-80) cc_final: 0.7687 (m-10) REVERT: D 81 GLU cc_start: 0.5551 (tp30) cc_final: 0.5237 (tp30) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.0375 time to fit residues: 3.2779 Evaluate side-chains 45 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 14 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 44 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 53 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 = 0.3632 r_free = 0.3632 target = 0.073597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.061494 restraints weight = 32734.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.062995 restraints weight = 22703.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.064100 restraints weight = 17389.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.064833 restraints weight = 14221.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.065387 restraints weight = 12307.671| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5304 Z= 0.154 Angle : 0.804 9.303 7247 Z= 0.364 Chirality : 0.052 0.297 826 Planarity : 0.005 0.040 904 Dihedral : 16.877 93.108 1006 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.33), residues: 610 helix: -1.77 (0.94), residues: 26 sheet: -0.02 (0.31), residues: 256 loop : -0.88 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 141 TYR 0.014 0.002 TYR B 193 PHE 0.011 0.001 PHE B 158 TRP 0.016 0.002 TRP D 78 HIS 0.003 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 5279) covalent geometry : angle 0.75676 / 0.35 ( 7180) SS BOND : bond 0.00209 / 0.14 ( 8) SS BOND : angle 0.60890 / 0.35 ( 16) hydrogen bonds : bond 0.03937 / 2.56 ( 147) hydrogen bonds : angle 5.73011 / 4.04 ( 408) link_ALPHA1-3 : bond 0.01237 / 0.75 ( 2) link_ALPHA1-3 : angle 2.85792 / 1.93 ( 6) link_ALPHA1-6 : bond 0.01137 / 0.66 ( 2) link_ALPHA1-6 : angle 2.93985 / 1.78 ( 6) link_BETA1-4 : bond 0.00477 / 0.36 ( 5) link_BETA1-4 : angle 3.70919 / 2.17 ( 15) link_NAG-ASN : bond 0.00291 / 0.19 ( 8) link_NAG-ASN : angle 3.29090 / 2.32 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 199 ASP cc_start: 0.7483 (p0) cc_final: 0.7256 (p0) REVERT: A 213 VAL cc_start: 0.7551 (t) cc_final: 0.7303 (t) REVERT: B 38 MET cc_start: 0.7061 (pmm) cc_final: 0.6011 (pmm) REVERT: B 175 ASN cc_start: 0.7672 (p0) cc_final: 0.7301 (p0) REVERT: B 224 GLN cc_start: 0.6543 (pp30) cc_final: 0.6014 (pp30) REVERT: C 34 TRP cc_start: 0.7476 (p90) cc_final: 0.7207 (p90) REVERT: C 104 TYR cc_start: 0.8069 (m-80) cc_final: 0.7567 (m-10) REVERT: D 81 GLU cc_start: 0.5819 (tp30) cc_final: 0.5368 (tp30) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0576 time to fit residues: 5.6286 Evaluate side-chains 50 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 53 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 0.0170 chunk 47 optimal weight: 10.0000 chunk 55 optimal weight: 0.0000 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 52 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 53 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 = 0.3655 r_free = 0.3655 target = 0.074712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.062719 restraints weight = 32554.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.064323 restraints weight = 22383.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.065441 restraints weight = 17012.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.066192 restraints weight = 13840.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.066757 restraints weight = 11887.429| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5304 Z= 0.126 Angle : 0.789 9.591 7247 Z= 0.350 Chirality : 0.051 0.285 826 Planarity : 0.004 0.035 904 Dihedral : 15.373 79.067 1006 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.73 (0.33), residues: 610 helix: -1.75 (0.94), residues: 26 sheet: 0.09 (0.31), residues: 255 loop : -0.79 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 51 TYR 0.023 0.002 TYR B 193 PHE 0.011 0.001 PHE B 158 TRP 0.018 0.001 TRP D 78 HIS 0.001 0.000 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 5279) covalent geometry : angle 0.74260 / 0.34 ( 7180) SS BOND : bond 0.00148 / 0.10 ( 8) SS BOND : angle 0.55176 / 0.33 ( 16) hydrogen bonds : bond 0.03468 / 2.22 ( 147) hydrogen bonds : angle 5.61639 / 3.97 ( 408) link_ALPHA1-3 : bond 0.01359 / 0.82 ( 2) link_ALPHA1-3 : angle 3.23726 / 2.06 ( 6) link_ALPHA1-6 : bond 0.01693 / 1.01 ( 2) link_ALPHA1-6 : angle 3.01448 / 1.82 ( 6) link_BETA1-4 : bond 0.00713 / 0.56 ( 5) link_BETA1-4 : angle 3.61106 / 2.08 ( 15) link_NAG-ASN : bond 0.00324 / 0.21 ( 8) link_NAG-ASN : angle 3.11698 / 2.21 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 199 ASP cc_start: 0.7399 (p0) cc_final: 0.7154 (p0) REVERT: B 38 MET cc_start: 0.7085 (pmm) cc_final: 0.6102 (pmm) REVERT: B 175 ASN cc_start: 0.7779 (p0) cc_final: 0.7388 (p0) REVERT: B 224 GLN cc_start: 0.6564 (pp30) cc_final: 0.6036 (pp30) REVERT: C 34 TRP cc_start: 0.7411 (p90) cc_final: 0.7189 (p90) REVERT: C 104 TYR cc_start: 0.8064 (m-80) cc_final: 0.7614 (m-10) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0574 time to fit residues: 5.6654 Evaluate side-chains 53 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 0.0370 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 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 = 0.3614 r_free = 0.3614 target = 0.072791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.060736 restraints weight = 34028.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.062209 restraints weight = 23829.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.063273 restraints weight = 18384.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.064060 restraints weight = 15121.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.064627 restraints weight = 12994.444| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5304 Z= 0.179 Angle : 0.817 9.413 7247 Z= 0.365 Chirality : 0.051 0.271 826 Planarity : 0.004 0.033 904 Dihedral : 13.214 76.101 1006 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.70 (0.33), residues: 610 helix: -1.63 (0.94), residues: 26 sheet: -0.03 (0.31), residues: 255 loop : -0.66 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 41 TYR 0.020 0.002 TYR D 120 PHE 0.010 0.002 PHE B 158 TRP 0.017 0.002 TRP D 78 HIS 0.003 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 5279) covalent geometry : angle 0.76846 / 0.35 ( 7180) SS BOND : bond 0.00259 / 0.16 ( 8) SS BOND : angle 0.63462 / 0.36 ( 16) hydrogen bonds : bond 0.03868 / 2.48 ( 147) hydrogen bonds : angle 5.57587 / 3.94 ( 408) link_ALPHA1-3 : bond 0.01493 / 0.92 ( 2) link_ALPHA1-3 : angle 3.28134 / 2.16 ( 6) link_ALPHA1-6 : bond 0.01679 / 1.01 ( 2) link_ALPHA1-6 : angle 1.89498 / 0.90 ( 6) link_BETA1-4 : bond 0.00584 / 0.45 ( 5) link_BETA1-4 : angle 3.81317 / 2.27 ( 15) link_NAG-ASN : bond 0.00262 / 0.16 ( 8) link_NAG-ASN : angle 3.48679 / 2.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 213 VAL cc_start: 0.7612 (t) cc_final: 0.7340 (t) REVERT: B 175 ASN cc_start: 0.7859 (p0) cc_final: 0.7433 (p0) REVERT: B 224 GLN cc_start: 0.6484 (pp30) cc_final: 0.6062 (pp30) REVERT: B 227 LEU cc_start: 0.7715 (tp) cc_final: 0.7513 (tp) REVERT: C 34 TRP cc_start: 0.7748 (p90) cc_final: 0.7477 (p90) REVERT: C 104 TYR cc_start: 0.8070 (m-80) cc_final: 0.7607 (m-10) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0521 time to fit residues: 5.2164 Evaluate side-chains 50 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 43 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.0470 chunk 54 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.073223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.061190 restraints weight = 33752.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.062723 restraints weight = 23040.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.063833 restraints weight = 17550.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.064602 restraints weight = 14308.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.065172 restraints weight = 12266.727| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5304 Z= 0.145 Angle : 0.785 9.765 7247 Z= 0.352 Chirality : 0.050 0.263 826 Planarity : 0.004 0.034 904 Dihedral : 12.029 70.777 1006 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.34), residues: 610 helix: -1.48 (0.94), residues: 27 sheet: -0.04 (0.32), residues: 258 loop : -0.54 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 141 TYR 0.017 0.002 TYR B 193 PHE 0.011 0.001 PHE B 158 TRP 0.009 0.001 TRP D 78 HIS 0.002 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 5279) covalent geometry : angle 0.74109 / 0.34 ( 7180) SS BOND : bond 0.00198 / 0.12 ( 8) SS BOND : angle 0.54589 / 0.31 ( 16) hydrogen bonds : bond 0.03593 / 2.31 ( 147) hydrogen bonds : angle 5.46758 / 3.85 ( 408) link_ALPHA1-3 : bond 0.01466 / 0.89 ( 2) link_ALPHA1-3 : angle 2.88030 / 1.86 ( 6) link_ALPHA1-6 : bond 0.01070 / 0.65 ( 2) link_ALPHA1-6 : angle 1.55346 / 0.93 ( 6) link_BETA1-4 : bond 0.00697 / 0.55 ( 5) link_BETA1-4 : angle 3.75661 / 2.20 ( 15) link_NAG-ASN : bond 0.00300 / 0.18 ( 8) link_NAG-ASN : angle 3.21010 / 2.30 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 VAL cc_start: 0.7604 (t) cc_final: 0.7392 (t) REVERT: B 175 ASN cc_start: 0.7848 (p0) cc_final: 0.7420 (p0) REVERT: B 224 GLN cc_start: 0.6543 (pp30) cc_final: 0.6026 (pp30) REVERT: C 34 TRP cc_start: 0.7676 (p90) cc_final: 0.7468 (p90) REVERT: C 104 TYR cc_start: 0.8035 (m-80) cc_final: 0.7546 (m-10) REVERT: D 81 GLU cc_start: 0.5823 (tp30) cc_final: 0.5196 (tp30) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0542 time to fit residues: 5.1927 Evaluate side-chains 51 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 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 = 0.3562 r_free = 0.3562 target = 0.070291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.058254 restraints weight = 33243.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.059650 restraints weight = 23325.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.060688 restraints weight = 18083.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061466 restraints weight = 14905.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.061989 restraints weight = 12842.587| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5304 Z= 0.229 Angle : 0.884 9.658 7247 Z= 0.400 Chirality : 0.051 0.332 826 Planarity : 0.005 0.042 904 Dihedral : 11.815 69.748 1006 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.83 (0.33), residues: 610 helix: -1.11 (1.00), residues: 25 sheet: -0.31 (0.31), residues: 267 loop : -0.62 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 41 TYR 0.028 0.002 TYR D 120 PHE 0.015 0.002 PHE B 158 TRP 0.017 0.002 TRP D 78 HIS 0.006 0.002 HIS D 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.23 ( 5279) covalent geometry : angle 0.83283 / 0.39 ( 7180) SS BOND : bond 0.00434 / 0.26 ( 8) SS BOND : angle 0.83479 / 0.55 ( 16) hydrogen bonds : bond 0.04364 / 2.82 ( 147) hydrogen bonds : angle 5.83225 / 4.14 ( 408) link_ALPHA1-3 : bond 0.01134 / 0.70 ( 2) link_ALPHA1-3 : angle 3.34638 / 2.36 ( 6) link_ALPHA1-6 : bond 0.00807 / 0.48 ( 2) link_ALPHA1-6 : angle 1.35820 / 0.90 ( 6) link_BETA1-4 : bond 0.00502 / 0.33 ( 5) link_BETA1-4 : angle 3.82452 / 2.33 ( 15) link_NAG-ASN : bond 0.00306 / 0.19 ( 8) link_NAG-ASN : angle 3.96717 / 2.83 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 214 MET cc_start: 0.7390 (mpp) cc_final: 0.7055 (mpp) REVERT: B 175 ASN cc_start: 0.7674 (p0) cc_final: 0.7223 (p0) REVERT: B 224 GLN cc_start: 0.6649 (pp30) cc_final: 0.6241 (pp30) REVERT: C 104 TYR cc_start: 0.8086 (m-80) cc_final: 0.7550 (m-10) REVERT: C 115 TYR cc_start: 0.8245 (m-80) cc_final: 0.7925 (m-80) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0463 time to fit residues: 4.1561 Evaluate side-chains 47 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 43 optimal weight: 0.0370 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 53 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 = 0.3621 r_free = 0.3621 target = 0.072923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.061086 restraints weight = 33008.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.062675 restraints weight = 22497.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.063794 restraints weight = 16993.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.064615 restraints weight = 13773.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.065158 restraints weight = 11729.042| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5304 Z= 0.138 Angle : 0.823 10.026 7247 Z= 0.366 Chirality : 0.050 0.286 826 Planarity : 0.004 0.040 904 Dihedral : 11.524 68.673 1006 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.73 (0.34), residues: 610 helix: -1.11 (1.00), residues: 25 sheet: -0.25 (0.31), residues: 269 loop : -0.53 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 51 TYR 0.017 0.002 TYR B 193 PHE 0.011 0.001 PHE B 158 TRP 0.051 0.002 TRP C 34 HIS 0.011 0.001 HIS D 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 5279) covalent geometry : angle 0.77487 / 0.36 ( 7180) SS BOND : bond 0.00290 / 0.19 ( 8) SS BOND : angle 0.69412 / 0.46 ( 16) hydrogen bonds : bond 0.03705 / 2.30 ( 147) hydrogen bonds : angle 5.60261 / 3.95 ( 408) link_ALPHA1-3 : bond 0.01311 / 0.79 ( 2) link_ALPHA1-3 : angle 2.83046 / 1.83 ( 6) link_ALPHA1-6 : bond 0.00865 / 0.53 ( 2) link_ALPHA1-6 : angle 1.45435 / 0.97 ( 6) link_BETA1-4 : bond 0.00749 / 0.61 ( 5) link_BETA1-4 : angle 3.73312 / 2.17 ( 15) link_NAG-ASN : bond 0.00228 / 0.15 ( 8) link_NAG-ASN : angle 3.63473 / 2.62 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 213 VAL cc_start: 0.7667 (t) cc_final: 0.7446 (t) REVERT: B 38 MET cc_start: 0.7215 (pmm) cc_final: 0.5958 (pmm) REVERT: B 175 ASN cc_start: 0.7856 (p0) cc_final: 0.7406 (p0) REVERT: B 224 GLN cc_start: 0.6615 (pp30) cc_final: 0.6061 (pp30) REVERT: C 104 TYR cc_start: 0.8046 (m-80) cc_final: 0.7437 (m-10) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0489 time to fit residues: 4.6654 Evaluate side-chains 45 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 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 = 0.3600 r_free = 0.3600 target = 0.071946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.060046 restraints weight = 32831.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061523 restraints weight = 22843.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.062521 restraints weight = 17478.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.063329 restraints weight = 14412.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.063876 restraints weight = 12362.984| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5304 Z= 0.164 Angle : 0.829 9.892 7247 Z= 0.371 Chirality : 0.050 0.278 826 Planarity : 0.004 0.038 904 Dihedral : 11.241 68.269 1006 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.74 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.74 (0.34), residues: 610 helix: -0.87 (1.04), residues: 25 sheet: -0.30 (0.31), residues: 269 loop : -0.51 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 41 TYR 0.019 0.002 TYR B 193 PHE 0.013 0.002 PHE C 80 TRP 0.032 0.002 TRP C 34 HIS 0.005 0.001 HIS D 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 5279) covalent geometry : angle 0.78469 / 0.36 ( 7180) SS BOND : bond 0.00261 / 0.16 ( 8) SS BOND : angle 0.74273 / 0.46 ( 16) hydrogen bonds : bond 0.03816 / 2.42 ( 147) hydrogen bonds : angle 5.50118 / 3.86 ( 408) link_ALPHA1-3 : bond 0.01192 / 0.72 ( 2) link_ALPHA1-3 : angle 2.81721 / 1.90 ( 6) link_ALPHA1-6 : bond 0.00755 / 0.46 ( 2) link_ALPHA1-6 : angle 1.41449 / 0.93 ( 6) link_BETA1-4 : bond 0.00664 / 0.53 ( 5) link_BETA1-4 : angle 3.70499 / 2.20 ( 15) link_NAG-ASN : bond 0.00237 / 0.14 ( 8) link_NAG-ASN : angle 3.43287 / 2.45 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: B 38 MET cc_start: 0.7137 (pmm) cc_final: 0.5860 (pmm) REVERT: B 175 ASN cc_start: 0.7847 (p0) cc_final: 0.7396 (p0) REVERT: B 224 GLN cc_start: 0.6500 (pp30) cc_final: 0.6132 (pp30) REVERT: C 104 TYR cc_start: 0.8045 (m-80) cc_final: 0.7471 (m-10) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0397 time to fit residues: 3.5237 Evaluate side-chains 44 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 40 optimal weight: 0.0370 chunk 35 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 25 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 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 = 0.3636 r_free = 0.3636 target = 0.073566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.061651 restraints weight = 33129.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.063216 restraints weight = 22857.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.064333 restraints weight = 17336.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.065132 restraints weight = 14043.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.065586 restraints weight = 11966.778| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5304 Z= 0.124 Angle : 0.812 10.081 7247 Z= 0.358 Chirality : 0.050 0.290 826 Planarity : 0.004 0.035 904 Dihedral : 10.924 66.580 1006 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.41 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.34), residues: 610 helix: -0.92 (1.04), residues: 26 sheet: -0.15 (0.31), residues: 263 loop : -0.50 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.013 0.001 TYR B 105 PHE 0.009 0.001 PHE B 158 TRP 0.024 0.002 TRP C 34 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 5279) covalent geometry : angle 0.76842 / 0.35 ( 7180) SS BOND : bond 0.00238 / 0.16 ( 8) SS BOND : angle 0.59433 / 0.38 ( 16) hydrogen bonds : bond 0.03441 / 2.14 ( 147) hydrogen bonds : angle 5.32973 / 3.77 ( 408) link_ALPHA1-3 : bond 0.01308 / 0.79 ( 2) link_ALPHA1-3 : angle 2.57539 / 1.66 ( 6) link_ALPHA1-6 : bond 0.00779 / 0.48 ( 2) link_ALPHA1-6 : angle 1.41133 / 0.95 ( 6) link_BETA1-4 : bond 0.00842 / 0.69 ( 5) link_BETA1-4 : angle 3.70408 / 2.14 ( 15) link_NAG-ASN : bond 0.00331 / 0.21 ( 8) link_NAG-ASN : angle 3.38947 / 2.43 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 118 ILE cc_start: 0.8566 (pt) cc_final: 0.8296 (mm) REVERT: B 38 MET cc_start: 0.7001 (pmm) cc_final: 0.5760 (pmm) REVERT: B 175 ASN cc_start: 0.7825 (p0) cc_final: 0.7358 (p0) REVERT: B 224 GLN cc_start: 0.6401 (pp30) cc_final: 0.5969 (pp30) REVERT: C 104 TYR cc_start: 0.8027 (m-80) cc_final: 0.7411 (m-10) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0527 time to fit residues: 4.8585 Evaluate side-chains 46 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 0.0040 chunk 42 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 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 = 0.3628 r_free = 0.3628 target = 0.073195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.061315 restraints weight = 33719.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.062815 restraints weight = 23046.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.063978 restraints weight = 17421.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.064779 restraints weight = 14068.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.065320 restraints weight = 11950.801| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5304 Z= 0.138 Angle : 0.825 10.088 7247 Z= 0.364 Chirality : 0.050 0.291 826 Planarity : 0.004 0.035 904 Dihedral : 10.753 65.843 1006 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.57 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.34), residues: 610 helix: -0.54 (1.10), residues: 26 sheet: -0.22 (0.31), residues: 268 loop : -0.53 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 124 TYR 0.023 0.002 TYR A 135 PHE 0.010 0.001 PHE C 80 TRP 0.015 0.002 TRP D 78 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 5279) covalent geometry : angle 0.78343 / 0.35 ( 7180) SS BOND : bond 0.00205 / 0.12 ( 8) SS BOND : angle 0.55461 / 0.36 ( 16) hydrogen bonds : bond 0.03510 / 2.20 ( 147) hydrogen bonds : angle 5.30896 / 3.74 ( 408) link_ALPHA1-3 : bond 0.01164 / 0.70 ( 2) link_ALPHA1-3 : angle 2.55280 / 1.69 ( 6) link_ALPHA1-6 : bond 0.00758 / 0.46 ( 2) link_ALPHA1-6 : angle 1.41410 / 0.95 ( 6) link_BETA1-4 : bond 0.00835 / 0.68 ( 5) link_BETA1-4 : angle 3.66450 / 2.14 ( 15) link_NAG-ASN : bond 0.00310 / 0.19 ( 8) link_NAG-ASN : angle 3.35764 / 2.39 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1010.93 seconds wall clock time: 18 minutes 11.54 seconds (1091.54 seconds total)