Starting phenix.real_space_refine on Wed Feb 4 01:43:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wzb_66387/02_2026/9wzb_66387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wzb_66387/02_2026/9wzb_66387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wzb_66387/02_2026/9wzb_66387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wzb_66387/02_2026/9wzb_66387.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wzb_66387/02_2026/9wzb_66387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wzb_66387/02_2026/9wzb_66387.map" } resolution = 2.67 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= 0.002 sd= 0.021 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 24 5.16 5 C 5292 2.51 5 N 1440 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8256 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.80, per 1000 atoms: 0.22 Number of scatterers: 8256 At special positions: 0 Unit cell: (84.84, 87.36, 94.92, 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 24 16.00 O 1500 8.00 N 1440 7.00 C 5292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.59 Conformation dependent library (CDL) restraints added in 201.7 milliseconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 92.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 112 through 118 removed outlier: 4.023A pdb=" N ASP A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 128 through 137 removed outlier: 4.028A pdb=" N LEU A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 154 through 164 Processing helix chain 'A' and resid 165 through 169 removed outlier: 3.513A pdb=" N ALA A 168 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 128 through 137 removed outlier: 3.980A pdb=" N LEU B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 151 Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 170 through 185 Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'C' and resid 113 through 118 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 128 through 137 removed outlier: 4.253A pdb=" N LEU C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 151 Processing helix chain 'C' and resid 154 through 164 Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 185 through 194 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 118 through 126 Processing helix chain 'D' and resid 128 through 137 removed outlier: 4.019A pdb=" N LEU D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 151 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 185 through 194 Processing helix chain 'E' and resid 113 through 118 Processing helix chain 'E' and resid 118 through 126 Processing helix chain 'E' and resid 128 through 137 removed outlier: 4.138A pdb=" N LEU E 132 " --> pdb=" O ASN E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 151 Processing helix chain 'E' and resid 154 through 164 Processing helix chain 'E' and resid 165 through 169 removed outlier: 3.503A pdb=" N ALA E 168 " --> pdb=" O PHE E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 185 Processing helix chain 'E' and resid 185 through 194 Processing helix chain 'F' and resid 113 through 118 Processing helix chain 'F' and resid 118 through 126 Processing helix chain 'F' and resid 128 through 137 removed outlier: 4.027A pdb=" N LEU F 132 " --> pdb=" O ASN F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 151 Processing helix chain 'F' and resid 154 through 164 Processing helix chain 'F' and resid 165 through 169 Processing helix chain 'F' and resid 170 through 185 Processing helix chain 'F' and resid 185 through 194 Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 118 through 126 Processing helix chain 'G' and resid 128 through 137 removed outlier: 4.008A pdb=" N LEU G 132 " --> pdb=" O ASN G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 151 Processing helix chain 'G' and resid 154 through 164 Processing helix chain 'G' and resid 165 through 169 Processing helix chain 'G' and resid 170 through 185 Processing helix chain 'G' and resid 185 through 194 Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 118 through 126 Processing helix chain 'H' and resid 128 through 137 removed outlier: 4.016A pdb=" N LEU H 132 " --> pdb=" O ASN H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 151 Processing helix chain 'H' and resid 154 through 164 Processing helix chain 'H' and resid 165 through 169 Processing helix chain 'H' and resid 170 through 185 Processing helix chain 'H' and resid 185 through 194 Processing helix chain 'I' and resid 113 through 118 Processing helix chain 'I' and resid 118 through 126 Processing helix chain 'I' and resid 128 through 137 removed outlier: 4.293A pdb=" N LEU I 132 " --> pdb=" O ASN I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 151 Processing helix chain 'I' and resid 154 through 164 Processing helix chain 'I' and resid 165 through 169 Processing helix chain 'I' and resid 170 through 185 Processing helix chain 'I' and resid 185 through 194 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 118 through 126 Processing helix chain 'J' and resid 128 through 137 removed outlier: 4.193A pdb=" N LEU J 132 " --> pdb=" O ASN J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 151 Processing helix chain 'J' and resid 154 through 164 Processing helix chain 'J' and resid 165 through 169 Processing helix chain 'J' and resid 170 through 185 Processing helix chain 'J' and resid 185 through 194 Processing helix chain 'K' and resid 113 through 118 Processing helix chain 'K' and resid 118 through 126 Processing helix chain 'K' and resid 128 through 137 removed outlier: 3.891A pdb=" N LEU K 132 " --> pdb=" O ASN K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 151 Processing helix chain 'K' and resid 154 through 164 Processing helix chain 'K' and resid 165 through 169 Processing helix chain 'K' and resid 170 through 185 Processing helix chain 'K' and resid 185 through 194 Processing helix chain 'L' and resid 113 through 118 Processing helix chain 'L' and resid 118 through 126 Processing helix chain 'L' and resid 128 through 137 removed outlier: 4.004A pdb=" N LEU L 132 " --> pdb=" O ASN L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 151 Processing helix chain 'L' and resid 154 through 164 Processing helix chain 'L' and resid 165 through 169 removed outlier: 3.507A pdb=" N ALA L 168 " --> pdb=" O PHE L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 185 Processing helix chain 'L' and resid 185 through 194 537 hydrogen bonds defined for protein. 1548 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: 0.95 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: 1.23 - 1.34: 2695 1.34 - 1.46: 1443 1.46 - 1.57: 4274 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 8448 Sorted by residual: bond pdb=" CD GLU D 183 " pdb=" OE1 GLU D 183 " ideal model delta sigma weight residual 1.249 1.235 0.014 1.90e-02 2.77e+03 5.65e-01 bond pdb=" CB GLU L 152 " pdb=" CG GLU L 152 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.62e-01 bond pdb=" N GLY F 138 " pdb=" CA GLY F 138 " ideal model delta sigma weight residual 1.463 1.448 0.015 2.01e-02 2.48e+03 5.30e-01 bond pdb=" CG GLU D 183 " pdb=" CD GLU D 183 " ideal model delta sigma weight residual 1.516 1.498 0.018 2.50e-02 1.60e+03 5.26e-01 bond pdb=" N GLY B 138 " pdb=" CA GLY B 138 " ideal model delta sigma weight residual 1.463 1.448 0.014 2.01e-02 2.48e+03 5.11e-01 ... (remaining 8443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 11323 1.95 - 3.89: 105 3.89 - 5.84: 31 5.84 - 7.78: 1 7.78 - 9.73: 12 Bond angle restraints: 11472 Sorted by residual: angle pdb=" CA LEU I 112 " pdb=" CB LEU I 112 " pdb=" CG LEU I 112 " ideal model delta sigma weight residual 116.30 126.03 -9.73 3.50e+00 8.16e-02 7.72e+00 angle pdb=" N THR F 166 " pdb=" CA THR F 166 " pdb=" C THR F 166 " ideal model delta sigma weight residual 109.81 115.75 -5.94 2.21e+00 2.05e-01 7.23e+00 angle pdb=" N THR E 166 " pdb=" CA THR E 166 " pdb=" C THR E 166 " ideal model delta sigma weight residual 109.81 115.64 -5.83 2.21e+00 2.05e-01 6.96e+00 angle pdb=" N THR D 166 " pdb=" CA THR D 166 " pdb=" C THR D 166 " ideal model delta sigma weight residual 109.81 115.57 -5.76 2.21e+00 2.05e-01 6.79e+00 angle pdb=" N THR K 166 " pdb=" CA THR K 166 " pdb=" C THR K 166 " ideal model delta sigma weight residual 109.81 115.43 -5.62 2.21e+00 2.05e-01 6.48e+00 ... (remaining 11467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 4531 15.05 - 30.10: 396 30.10 - 45.14: 115 45.14 - 60.19: 31 60.19 - 75.24: 3 Dihedral angle restraints: 5076 sinusoidal: 2088 harmonic: 2988 Sorted by residual: dihedral pdb=" CG ARG F 194 " pdb=" CD ARG F 194 " pdb=" NE ARG F 194 " pdb=" CZ ARG F 194 " ideal model delta sinusoidal sigma weight residual 90.00 41.10 48.90 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CA ASP D 143 " pdb=" CB ASP D 143 " pdb=" CG ASP D 143 " pdb=" OD1 ASP D 143 " ideal model delta sinusoidal sigma weight residual -30.00 -87.47 57.47 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ASP I 143 " pdb=" CB ASP I 143 " pdb=" CG ASP I 143 " pdb=" OD1 ASP I 143 " ideal model delta sinusoidal sigma weight residual -30.00 -87.09 57.09 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 5073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 854 0.027 - 0.055: 274 0.055 - 0.082: 47 0.082 - 0.110: 84 0.110 - 0.137: 13 Chirality restraints: 1272 Sorted by residual: chirality pdb=" CA THR F 166 " pdb=" N THR F 166 " pdb=" C THR F 166 " pdb=" CB THR F 166 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA THR E 166 " pdb=" N THR E 166 " pdb=" C THR E 166 " pdb=" CB THR E 166 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA THR D 166 " pdb=" N THR D 166 " pdb=" C THR D 166 " pdb=" CB THR D 166 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 1269 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 166 " 0.027 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO J 167 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO J 167 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 167 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR K 166 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO K 167 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO K 167 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO K 167 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 166 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO D 167 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 167 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 167 " -0.022 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 278 2.73 - 3.27: 8098 3.27 - 3.81: 13915 3.81 - 4.36: 15967 4.36 - 4.90: 29140 Nonbonded interactions: 67398 Sorted by model distance: nonbonded pdb=" NH2 ARG I 160 " pdb=" OE2 GLU K 144 " model vdw 2.183 3.120 nonbonded pdb=" OD1 ASN K 128 " pdb=" NE2 GLN K 185 " model vdw 2.194 3.120 nonbonded pdb=" OD2 ASP G 143 " pdb=" NE2 GLN G 147 " model vdw 2.206 3.120 nonbonded pdb=" OE2 GLU D 144 " pdb=" NH2 ARG K 160 " model vdw 2.209 3.120 nonbonded pdb=" O PHE L 163 " pdb=" OG1 THR L 166 " model vdw 2.225 3.040 ... (remaining 67393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.080 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8448 Z= 0.144 Angle : 0.591 9.727 11472 Z= 0.284 Chirality : 0.037 0.137 1272 Planarity : 0.004 0.041 1452 Dihedral : 12.844 75.240 3108 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 3.12 (0.29), residues: 972 helix: 2.81 (0.20), residues: 792 sheet: None (None), residues: 0 loop : -1.62 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 194 TYR 0.008 0.001 TYR L 146 PHE 0.009 0.001 PHE L 114 TRP 0.004 0.001 TRP K 131 HIS 0.003 0.001 HIS L 113 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8448) covalent geometry : angle 0.59074 (11472) hydrogen bonds : bond 0.14789 ( 537) hydrogen bonds : angle 4.02151 ( 1548) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.313 Fit side-chains REVERT: B 157 SER cc_start: 0.9256 (m) cc_final: 0.9049 (m) REVERT: B 179 GLN cc_start: 0.8620 (tp-100) cc_final: 0.8175 (tp40) REVERT: B 183 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7930 (mt-10) REVERT: C 128 ASN cc_start: 0.8719 (t0) cc_final: 0.8141 (p0) REVERT: C 157 SER cc_start: 0.9305 (m) cc_final: 0.9085 (m) REVERT: D 143 ASP cc_start: 0.8515 (t70) cc_final: 0.7783 (t70) REVERT: D 147 GLN cc_start: 0.9093 (mt0) cc_final: 0.8668 (mt0) REVERT: D 191 ASP cc_start: 0.9245 (t70) cc_final: 0.8959 (t0) REVERT: E 128 ASN cc_start: 0.8756 (t0) cc_final: 0.8295 (t0) REVERT: E 157 SER cc_start: 0.9321 (m) cc_final: 0.9095 (m) REVERT: F 128 ASN cc_start: 0.8740 (t0) cc_final: 0.8428 (t0) REVERT: F 157 SER cc_start: 0.9310 (m) cc_final: 0.9080 (m) REVERT: H 157 SER cc_start: 0.9277 (m) cc_final: 0.9058 (m) REVERT: I 128 ASN cc_start: 0.8723 (t0) cc_final: 0.8457 (t0) REVERT: J 128 ASN cc_start: 0.8802 (t0) cc_final: 0.8540 (t0) REVERT: K 179 GLN cc_start: 0.8782 (tp40) cc_final: 0.8243 (tp40) REVERT: L 157 SER cc_start: 0.9327 (m) cc_final: 0.9106 (m) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.6737 time to fit residues: 230.2685 Evaluate side-chains 277 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0030 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 128 ASN A 147 GLN B 128 ASN C 147 GLN D 117 GLN D 128 ASN D 185 GLN F 117 GLN F 179 GLN G 128 ASN H 128 ASN H 147 GLN I 117 GLN I 147 GLN J 147 GLN L 128 ASN L 147 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.058475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.050316 restraints weight = 18448.466| |-----------------------------------------------------------------------------| r_work (start): 0.2488 rms_B_bonded: 2.57 r_work: 0.2345 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8448 Z= 0.107 Angle : 0.534 6.192 11472 Z= 0.264 Chirality : 0.035 0.114 1272 Planarity : 0.005 0.043 1452 Dihedral : 3.235 9.856 1092 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.79 % Allowed : 12.95 % Favored : 86.26 % 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: 3.16 (0.29), residues: 972 helix: 2.77 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.51 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 194 TYR 0.010 0.001 TYR A 146 PHE 0.009 0.001 PHE I 114 TRP 0.003 0.000 TRP L 169 HIS 0.001 0.000 HIS I 113 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8448) covalent geometry : angle 0.53381 (11472) hydrogen bonds : bond 0.02961 ( 537) hydrogen bonds : angle 3.34443 ( 1548) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 304 time to evaluate : 0.343 Fit side-chains REVERT: B 147 GLN cc_start: 0.9081 (mt0) cc_final: 0.8869 (mt0) REVERT: B 179 GLN cc_start: 0.8706 (tp-100) cc_final: 0.8326 (tp40) REVERT: C 143 ASP cc_start: 0.8726 (t70) cc_final: 0.8433 (t70) REVERT: C 147 GLN cc_start: 0.9137 (mt0) cc_final: 0.8716 (mt0) REVERT: D 147 GLN cc_start: 0.9098 (mt0) cc_final: 0.8741 (mt0) REVERT: D 179 GLN cc_start: 0.8799 (tp40) cc_final: 0.8512 (tp-100) REVERT: D 183 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: F 147 GLN cc_start: 0.9093 (mt0) cc_final: 0.8863 (mt0) REVERT: H 139 LYS cc_start: 0.9592 (mtmm) cc_final: 0.9237 (mttp) REVERT: I 139 LYS cc_start: 0.9526 (mtmm) cc_final: 0.9192 (mttp) REVERT: J 179 GLN cc_start: 0.8727 (tp40) cc_final: 0.8440 (tp40) REVERT: K 146 TYR cc_start: 0.8963 (t80) cc_final: 0.8651 (t80) REVERT: K 179 GLN cc_start: 0.8919 (tp40) cc_final: 0.8508 (tp40) outliers start: 7 outliers final: 2 residues processed: 305 average time/residue: 0.7416 time to fit residues: 236.2158 Evaluate side-chains 281 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 278 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 183 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 147 GLN D 117 GLN D 128 ASN E 128 ASN E 147 GLN F 117 GLN F 128 ASN H 128 ASN H 147 GLN I 117 GLN I 128 ASN I 147 GLN J 128 ASN J 147 GLN K 147 GLN L 128 ASN L 147 GLN L 179 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.057669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2464 r_free = 0.2464 target = 0.049340 restraints weight = 18380.937| |-----------------------------------------------------------------------------| r_work (start): 0.2478 rms_B_bonded: 2.60 r_work: 0.2336 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8448 Z= 0.122 Angle : 0.547 5.437 11472 Z= 0.269 Chirality : 0.035 0.118 1272 Planarity : 0.005 0.046 1452 Dihedral : 3.157 9.726 1092 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.36 % Allowed : 13.74 % Favored : 83.90 % 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: 3.15 (0.28), residues: 972 helix: 2.74 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.44 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 194 TYR 0.010 0.001 TYR A 146 PHE 0.009 0.001 PHE I 114 TRP 0.003 0.000 TRP I 131 HIS 0.001 0.000 HIS L 113 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8448) covalent geometry : angle 0.54685 (11472) hydrogen bonds : bond 0.03020 ( 537) hydrogen bonds : angle 3.23429 ( 1548) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 283 time to evaluate : 0.347 Fit side-chains REVERT: B 147 GLN cc_start: 0.9037 (mt0) cc_final: 0.8820 (mt0) REVERT: B 179 GLN cc_start: 0.8630 (tp-100) cc_final: 0.8315 (tp40) REVERT: C 147 GLN cc_start: 0.9086 (mt0) cc_final: 0.8684 (mt0) REVERT: D 130 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6168 (tt0) REVERT: D 147 GLN cc_start: 0.9063 (mt0) cc_final: 0.8756 (mt0) REVERT: D 179 GLN cc_start: 0.8741 (tp40) cc_final: 0.8508 (tp40) REVERT: D 183 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: D 191 ASP cc_start: 0.9230 (t0) cc_final: 0.8992 (t0) REVERT: E 191 ASP cc_start: 0.9188 (t0) cc_final: 0.8915 (t0) REVERT: F 139 LYS cc_start: 0.9547 (mtmm) cc_final: 0.9289 (mttm) REVERT: F 147 GLN cc_start: 0.9001 (mt0) cc_final: 0.8759 (mt0) REVERT: G 157 SER cc_start: 0.9107 (m) cc_final: 0.8867 (p) REVERT: H 139 LYS cc_start: 0.9564 (mtmm) cc_final: 0.9218 (mttp) REVERT: I 130 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6253 (tt0) REVERT: J 179 GLN cc_start: 0.8709 (tp40) cc_final: 0.8421 (tp40) REVERT: K 147 GLN cc_start: 0.9113 (mt0) cc_final: 0.8903 (mt0) outliers start: 21 outliers final: 9 residues processed: 298 average time/residue: 0.6860 time to fit residues: 214.1401 Evaluate side-chains 283 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 271 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain K residue 157 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 78 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 0.0070 chunk 90 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 147 GLN C 128 ASN C 185 GLN D 117 GLN E 128 ASN E 147 GLN E 179 GLN F 117 GLN F 128 ASN F 179 GLN H 179 GLN I 128 ASN I 147 GLN J 128 ASN J 147 GLN K 179 GLN L 147 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.058797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.050317 restraints weight = 18964.048| |-----------------------------------------------------------------------------| r_work (start): 0.2484 rms_B_bonded: 2.53 r_work: 0.2348 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8448 Z= 0.110 Angle : 0.549 10.099 11472 Z= 0.267 Chirality : 0.035 0.115 1272 Planarity : 0.005 0.046 1452 Dihedral : 3.083 9.707 1092 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.93 % Allowed : 15.09 % Favored : 81.98 % 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: 3.16 (0.28), residues: 972 helix: 2.74 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.38 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 194 TYR 0.010 0.001 TYR K 146 PHE 0.009 0.001 PHE I 114 TRP 0.002 0.000 TRP A 169 HIS 0.002 0.000 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8448) covalent geometry : angle 0.54922 (11472) hydrogen bonds : bond 0.02607 ( 537) hydrogen bonds : angle 3.16905 ( 1548) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 284 time to evaluate : 0.362 Fit side-chains REVERT: B 143 ASP cc_start: 0.8706 (t70) cc_final: 0.8471 (t70) REVERT: B 147 GLN cc_start: 0.9136 (mt0) cc_final: 0.8917 (mt0) REVERT: B 179 GLN cc_start: 0.8737 (tp-100) cc_final: 0.8449 (tp40) REVERT: C 147 GLN cc_start: 0.9154 (mt0) cc_final: 0.8718 (mt0) REVERT: D 147 GLN cc_start: 0.9162 (mt0) cc_final: 0.8815 (mt0) REVERT: D 179 GLN cc_start: 0.8824 (tp40) cc_final: 0.8546 (tp-100) REVERT: D 183 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: F 139 LYS cc_start: 0.9588 (mtmm) cc_final: 0.9329 (mttm) REVERT: F 147 GLN cc_start: 0.9091 (mt0) cc_final: 0.8796 (mt0) REVERT: F 182 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8584 (ttp-170) REVERT: H 139 LYS cc_start: 0.9597 (mtmm) cc_final: 0.9240 (mttp) REVERT: H 147 GLN cc_start: 0.9175 (mt0) cc_final: 0.8966 (mt0) REVERT: I 130 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6360 (tt0) REVERT: I 139 LYS cc_start: 0.9567 (mtmm) cc_final: 0.9331 (mttp) REVERT: J 179 GLN cc_start: 0.8807 (tp40) cc_final: 0.8539 (tp40) REVERT: K 146 TYR cc_start: 0.9118 (t80) cc_final: 0.8820 (t80) REVERT: K 147 GLN cc_start: 0.9208 (mt0) cc_final: 0.8940 (mt0) REVERT: K 179 GLN cc_start: 0.8958 (tp40) cc_final: 0.8602 (tp40) outliers start: 26 outliers final: 10 residues processed: 306 average time/residue: 0.5896 time to fit residues: 189.2025 Evaluate side-chains 287 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 274 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 157 SER Chi-restraints excluded: chain K residue 157 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 14 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN C 128 ASN C 185 GLN D 117 GLN E 128 ASN E 147 GLN F 117 GLN F 185 GLN G 117 GLN H 179 GLN H 185 GLN I 147 GLN J 147 GLN L 147 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.056499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.048122 restraints weight = 18635.723| |-----------------------------------------------------------------------------| r_work (start): 0.2448 rms_B_bonded: 2.62 r_work: 0.2305 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8448 Z= 0.154 Angle : 0.608 10.422 11472 Z= 0.292 Chirality : 0.037 0.134 1272 Planarity : 0.005 0.047 1452 Dihedral : 3.254 9.406 1092 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.48 % Allowed : 16.22 % Favored : 81.31 % 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: 3.12 (0.28), residues: 972 helix: 2.73 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.50 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 194 TYR 0.010 0.001 TYR K 146 PHE 0.008 0.001 PHE L 114 TRP 0.004 0.000 TRP I 131 HIS 0.003 0.001 HIS L 113 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8448) covalent geometry : angle 0.60775 (11472) hydrogen bonds : bond 0.03178 ( 537) hydrogen bonds : angle 3.25712 ( 1548) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 283 time to evaluate : 0.297 Fit side-chains REVERT: B 143 ASP cc_start: 0.8697 (t70) cc_final: 0.8463 (t70) REVERT: B 147 GLN cc_start: 0.9039 (mt0) cc_final: 0.8795 (mt0) REVERT: B 179 GLN cc_start: 0.8638 (tp-100) cc_final: 0.8338 (tp40) REVERT: C 147 GLN cc_start: 0.9081 (mt0) cc_final: 0.8653 (mt0) REVERT: D 130 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6157 (tm-30) REVERT: D 143 ASP cc_start: 0.8566 (t70) cc_final: 0.8093 (t70) REVERT: D 147 GLN cc_start: 0.9035 (mt0) cc_final: 0.8756 (mt0) REVERT: D 179 GLN cc_start: 0.8743 (tp40) cc_final: 0.8483 (tp40) REVERT: F 182 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8457 (ttp-170) REVERT: H 147 GLN cc_start: 0.9074 (mt0) cc_final: 0.8873 (mt0) REVERT: I 139 LYS cc_start: 0.9510 (mtmm) cc_final: 0.9108 (mttp) REVERT: J 179 GLN cc_start: 0.8717 (tp40) cc_final: 0.8415 (tp40) REVERT: K 147 GLN cc_start: 0.9130 (mt0) cc_final: 0.8897 (mt0) REVERT: K 179 GLN cc_start: 0.8936 (tp40) cc_final: 0.8580 (tp40) REVERT: K 183 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8227 (mt-10) REVERT: K 191 ASP cc_start: 0.9174 (t0) cc_final: 0.8909 (t0) REVERT: L 157 SER cc_start: 0.9159 (m) cc_final: 0.8678 (p) outliers start: 22 outliers final: 10 residues processed: 300 average time/residue: 0.6307 time to fit residues: 197.9360 Evaluate side-chains 284 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 272 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain I residue 157 SER Chi-restraints excluded: chain J residue 186 SER Chi-restraints excluded: chain K residue 157 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 4 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN C 128 ASN C 185 GLN D 117 GLN E 128 ASN E 147 GLN E 179 GLN F 117 GLN F 147 GLN F 179 GLN F 185 GLN H 179 GLN H 185 GLN I 147 GLN J 128 ASN J 147 GLN L 147 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.057004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.048755 restraints weight = 18818.880| |-----------------------------------------------------------------------------| r_work (start): 0.2454 rms_B_bonded: 2.46 r_work: 0.2316 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2197 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8448 Z= 0.138 Angle : 0.604 10.099 11472 Z= 0.290 Chirality : 0.036 0.121 1272 Planarity : 0.005 0.054 1452 Dihedral : 3.208 9.520 1092 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.48 % Allowed : 16.55 % Favored : 80.97 % 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: 3.12 (0.28), residues: 972 helix: 2.74 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.53 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 194 TYR 0.013 0.001 TYR K 146 PHE 0.009 0.001 PHE I 114 TRP 0.002 0.000 TRP A 169 HIS 0.002 0.001 HIS L 113 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8448) covalent geometry : angle 0.60373 (11472) hydrogen bonds : bond 0.02932 ( 537) hydrogen bonds : angle 3.23046 ( 1548) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 273 time to evaluate : 0.328 Fit side-chains REVERT: B 143 ASP cc_start: 0.8842 (t70) cc_final: 0.8608 (t70) REVERT: B 147 GLN cc_start: 0.9173 (mt0) cc_final: 0.8950 (mt0) REVERT: B 179 GLN cc_start: 0.8798 (tp-100) cc_final: 0.8523 (tp40) REVERT: C 147 GLN cc_start: 0.9211 (mt0) cc_final: 0.8802 (mt0) REVERT: D 130 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6407 (tm-30) REVERT: D 147 GLN cc_start: 0.9166 (mt0) cc_final: 0.8859 (mt0) REVERT: D 179 GLN cc_start: 0.8935 (tp40) cc_final: 0.8586 (tp-100) REVERT: F 147 GLN cc_start: 0.9142 (mt0) cc_final: 0.8878 (mt0) REVERT: F 182 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8603 (ttp-170) REVERT: G 191 ASP cc_start: 0.9357 (t0) cc_final: 0.9079 (t0) REVERT: H 147 GLN cc_start: 0.9203 (mt0) cc_final: 0.8998 (mt0) REVERT: I 139 LYS cc_start: 0.9579 (mtmm) cc_final: 0.9222 (mttp) REVERT: J 179 GLN cc_start: 0.8840 (tp40) cc_final: 0.8630 (tp40) REVERT: K 130 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6234 (tt0) REVERT: K 143 ASP cc_start: 0.8831 (t70) cc_final: 0.8617 (t70) REVERT: K 179 GLN cc_start: 0.9067 (tp40) cc_final: 0.8716 (tp40) REVERT: K 191 ASP cc_start: 0.9200 (t0) cc_final: 0.8925 (t0) REVERT: L 157 SER cc_start: 0.9311 (m) cc_final: 0.8830 (p) outliers start: 22 outliers final: 11 residues processed: 288 average time/residue: 0.6367 time to fit residues: 191.8995 Evaluate side-chains 282 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 268 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain I residue 157 SER Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 157 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 16 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.0370 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN C 185 GLN D 117 GLN E 147 GLN F 117 GLN F 179 GLN F 185 GLN H 179 GLN H 185 GLN I 147 GLN J 147 GLN K 147 GLN L 147 GLN L 179 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.057972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.049195 restraints weight = 18292.003| |-----------------------------------------------------------------------------| r_work (start): 0.2484 rms_B_bonded: 2.66 r_work: 0.2336 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8448 Z= 0.138 Angle : 0.611 9.056 11472 Z= 0.293 Chirality : 0.036 0.120 1272 Planarity : 0.005 0.056 1452 Dihedral : 3.205 9.387 1092 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.59 % Allowed : 17.12 % Favored : 80.29 % 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: 3.13 (0.28), residues: 972 helix: 2.74 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.53 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 194 TYR 0.012 0.001 TYR K 146 PHE 0.009 0.001 PHE I 114 TRP 0.002 0.000 TRP A 169 HIS 0.002 0.001 HIS L 113 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8448) covalent geometry : angle 0.61066 (11472) hydrogen bonds : bond 0.02909 ( 537) hydrogen bonds : angle 3.23221 ( 1548) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 274 time to evaluate : 0.257 Fit side-chains REVERT: B 143 ASP cc_start: 0.8677 (t70) cc_final: 0.8421 (t70) REVERT: B 147 GLN cc_start: 0.9009 (mt0) cc_final: 0.8768 (mt0) REVERT: B 179 GLN cc_start: 0.8590 (tp-100) cc_final: 0.8297 (tp40) REVERT: C 147 GLN cc_start: 0.9016 (mt0) cc_final: 0.8588 (mt0) REVERT: D 130 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6199 (tm-30) REVERT: D 147 GLN cc_start: 0.8981 (mt0) cc_final: 0.8641 (mt0) REVERT: D 179 GLN cc_start: 0.8773 (tp40) cc_final: 0.8442 (tp-100) REVERT: D 183 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: D 191 ASP cc_start: 0.9138 (t0) cc_final: 0.8849 (t0) REVERT: E 191 ASP cc_start: 0.9090 (t0) cc_final: 0.8872 (t0) REVERT: F 147 GLN cc_start: 0.8991 (mt0) cc_final: 0.8732 (mt0) REVERT: F 182 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8410 (ttp-170) REVERT: H 147 GLN cc_start: 0.9018 (mt0) cc_final: 0.8797 (mt0) REVERT: I 139 LYS cc_start: 0.9501 (mtmm) cc_final: 0.9206 (mttp) REVERT: I 179 GLN cc_start: 0.8669 (tp40) cc_final: 0.8359 (tp40) REVERT: J 179 GLN cc_start: 0.8669 (tp40) cc_final: 0.8451 (tp40) REVERT: K 130 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.5970 (tt0) REVERT: K 147 GLN cc_start: 0.9068 (mt0) cc_final: 0.8864 (mt0) REVERT: K 179 GLN cc_start: 0.8929 (tp40) cc_final: 0.8589 (tp40) outliers start: 23 outliers final: 12 residues processed: 288 average time/residue: 0.6462 time to fit residues: 194.6576 Evaluate side-chains 284 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 268 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain G residue 157 SER Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain I residue 157 SER Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 157 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 5.9990 chunk 36 optimal weight: 0.0970 chunk 27 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 185 GLN C 185 GLN D 117 GLN E 147 GLN E 179 GLN F 117 GLN F 179 GLN F 185 GLN H 179 GLN H 185 GLN I 147 GLN L 147 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.056780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.048409 restraints weight = 19008.631| |-----------------------------------------------------------------------------| r_work (start): 0.2437 rms_B_bonded: 2.50 r_work: 0.2297 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2173 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8448 Z= 0.166 Angle : 0.635 8.892 11472 Z= 0.305 Chirality : 0.037 0.124 1272 Planarity : 0.005 0.065 1452 Dihedral : 3.304 10.255 1092 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.93 % Allowed : 17.12 % Favored : 79.95 % 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: 3.06 (0.29), residues: 972 helix: 2.71 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.69 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 194 TYR 0.009 0.001 TYR C 146 PHE 0.009 0.001 PHE I 114 TRP 0.003 0.000 TRP A 169 HIS 0.002 0.001 HIS J 113 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8448) covalent geometry : angle 0.63454 (11472) hydrogen bonds : bond 0.03195 ( 537) hydrogen bonds : angle 3.28651 ( 1548) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 273 time to evaluate : 0.237 Fit side-chains REVERT: B 143 ASP cc_start: 0.8909 (t70) cc_final: 0.8680 (t70) REVERT: B 147 GLN cc_start: 0.9235 (mt0) cc_final: 0.9014 (mt0) REVERT: B 179 GLN cc_start: 0.8883 (tp-100) cc_final: 0.8596 (tp40) REVERT: C 147 GLN cc_start: 0.9306 (mt0) cc_final: 0.8895 (mt0) REVERT: D 130 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6456 (tm-30) REVERT: D 147 GLN cc_start: 0.9186 (mt0) cc_final: 0.8861 (mt0) REVERT: D 179 GLN cc_start: 0.8958 (tp40) cc_final: 0.8597 (tp40) REVERT: F 182 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8647 (ttp-170) REVERT: I 139 LYS cc_start: 0.9591 (mtmm) cc_final: 0.9372 (mttp) REVERT: J 179 GLN cc_start: 0.8893 (tp40) cc_final: 0.8680 (tp40) REVERT: K 179 GLN cc_start: 0.9083 (tp40) cc_final: 0.8754 (tp40) REVERT: L 157 SER cc_start: 0.9369 (m) cc_final: 0.8898 (p) outliers start: 26 outliers final: 12 residues processed: 292 average time/residue: 0.6591 time to fit residues: 201.3013 Evaluate side-chains 285 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 271 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain I residue 157 SER Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain J residue 186 SER Chi-restraints excluded: chain K residue 157 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 9 optimal weight: 0.0670 chunk 95 optimal weight: 5.9990 chunk 14 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 179 GLN C 185 GLN D 117 GLN E 128 ASN E 147 GLN F 117 GLN F 147 GLN F 179 GLN F 185 GLN H 179 GLN H 185 GLN I 147 GLN I 179 GLN J 147 GLN K 147 GLN L 147 GLN L 179 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.059437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.050975 restraints weight = 18622.662| |-----------------------------------------------------------------------------| r_work (start): 0.2501 rms_B_bonded: 2.56 r_work: 0.2363 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8448 Z= 0.119 Angle : 0.623 8.123 11472 Z= 0.299 Chirality : 0.035 0.116 1272 Planarity : 0.006 0.070 1452 Dihedral : 3.090 11.212 1092 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.69 % Allowed : 19.14 % Favored : 79.17 % 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: 3.09 (0.29), residues: 972 helix: 2.70 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.48 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 194 TYR 0.009 0.001 TYR A 146 PHE 0.009 0.001 PHE I 114 TRP 0.003 0.000 TRP A 169 HIS 0.003 0.001 HIS I 113 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8448) covalent geometry : angle 0.62337 (11472) hydrogen bonds : bond 0.02494 ( 537) hydrogen bonds : angle 3.19830 ( 1548) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 279 time to evaluate : 0.362 Fit side-chains REVERT: B 143 ASP cc_start: 0.8664 (t70) cc_final: 0.8394 (t70) REVERT: B 147 GLN cc_start: 0.9095 (mt0) cc_final: 0.8845 (mt0) REVERT: B 179 GLN cc_start: 0.8650 (tp40) cc_final: 0.8289 (tp40) REVERT: C 147 GLN cc_start: 0.9099 (mt0) cc_final: 0.8713 (mt0) REVERT: D 130 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6271 (tt0) REVERT: D 143 ASP cc_start: 0.8450 (t70) cc_final: 0.8034 (t70) REVERT: D 147 GLN cc_start: 0.9014 (mt0) cc_final: 0.8691 (mt0) REVERT: D 179 GLN cc_start: 0.8794 (tp40) cc_final: 0.8485 (tp-100) REVERT: D 183 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: E 191 ASP cc_start: 0.9118 (t0) cc_final: 0.8889 (t0) REVERT: F 139 LYS cc_start: 0.9582 (mtmm) cc_final: 0.9380 (mttm) REVERT: F 182 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8483 (ttp-170) REVERT: I 139 LYS cc_start: 0.9540 (mtmm) cc_final: 0.9155 (mttp) REVERT: I 179 GLN cc_start: 0.8653 (tp40) cc_final: 0.8401 (tp40) REVERT: K 179 GLN cc_start: 0.8966 (tp40) cc_final: 0.8565 (tp40) outliers start: 15 outliers final: 8 residues processed: 290 average time/residue: 0.6662 time to fit residues: 202.0631 Evaluate side-chains 280 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 269 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain G residue 157 SER Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain I residue 157 SER Chi-restraints excluded: chain K residue 157 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 0.0050 chunk 6 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 1 optimal weight: 0.0770 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN C 185 GLN D 117 GLN E 147 GLN F 117 GLN H 179 GLN H 185 GLN I 147 GLN J 147 GLN L 147 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.059839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.050826 restraints weight = 17737.882| |-----------------------------------------------------------------------------| r_work (start): 0.2475 rms_B_bonded: 2.51 r_work: 0.2325 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8448 Z= 0.124 Angle : 0.642 7.956 11472 Z= 0.308 Chirality : 0.036 0.155 1272 Planarity : 0.006 0.071 1452 Dihedral : 3.090 11.665 1092 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.69 % Allowed : 19.71 % Favored : 78.60 % 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: 3.04 (0.29), residues: 972 helix: 2.66 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.45 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 194 TYR 0.009 0.001 TYR A 146 PHE 0.009 0.001 PHE I 114 TRP 0.002 0.000 TRP A 169 HIS 0.001 0.000 HIS I 113 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8448) covalent geometry : angle 0.64181 (11472) hydrogen bonds : bond 0.02514 ( 537) hydrogen bonds : angle 3.22557 ( 1548) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 271 time to evaluate : 0.216 Fit side-chains REVERT: B 143 ASP cc_start: 0.8682 (t70) cc_final: 0.8402 (t70) REVERT: B 147 GLN cc_start: 0.9100 (mt0) cc_final: 0.8851 (mt0) REVERT: B 179 GLN cc_start: 0.8692 (tp40) cc_final: 0.8344 (tp40) REVERT: C 147 GLN cc_start: 0.9124 (mt0) cc_final: 0.8738 (mt0) REVERT: D 130 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6246 (tt0) REVERT: D 143 ASP cc_start: 0.8453 (t70) cc_final: 0.8038 (t70) REVERT: D 147 GLN cc_start: 0.9016 (mt0) cc_final: 0.8698 (mt0) REVERT: F 182 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8485 (ttp-170) REVERT: I 130 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6231 (tt0) REVERT: I 139 LYS cc_start: 0.9551 (mtmm) cc_final: 0.9176 (mttp) REVERT: K 179 GLN cc_start: 0.8977 (tp40) cc_final: 0.8205 (tp-100) outliers start: 15 outliers final: 6 residues processed: 280 average time/residue: 0.6357 time to fit residues: 186.0591 Evaluate side-chains 275 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 266 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain F residue 182 ARG Chi-restraints excluded: chain G residue 157 SER Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 157 SER Chi-restraints excluded: chain K residue 157 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 92 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 20 optimal weight: 0.0020 chunk 83 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN C 185 GLN D 117 GLN D 179 GLN E 147 GLN F 179 GLN H 179 GLN H 185 GLN I 147 GLN J 147 GLN J 179 GLN L 147 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.058864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.049852 restraints weight = 17924.884| |-----------------------------------------------------------------------------| r_work (start): 0.2512 rms_B_bonded: 2.55 r_work: 0.2359 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8448 Z= 0.124 Angle : 0.627 8.221 11472 Z= 0.303 Chirality : 0.035 0.123 1272 Planarity : 0.005 0.076 1452 Dihedral : 3.093 12.169 1092 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.35 % Allowed : 20.83 % Favored : 77.82 % 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: 3.02 (0.28), residues: 972 helix: 2.65 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.44 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 194 TYR 0.009 0.001 TYR A 146 PHE 0.009 0.001 PHE L 114 TRP 0.002 0.000 TRP G 171 HIS 0.001 0.000 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8448) covalent geometry : angle 0.62695 (11472) hydrogen bonds : bond 0.02586 ( 537) hydrogen bonds : angle 3.24434 ( 1548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3491.36 seconds wall clock time: 59 minutes 53.75 seconds (3593.75 seconds total)