Starting phenix.real_space_refine on Wed Sep 17 13:47:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ddp_46779/09_2025/9ddp_46779.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ddp_46779/09_2025/9ddp_46779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ddp_46779/09_2025/9ddp_46779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ddp_46779/09_2025/9ddp_46779.map" model { file = "/net/cci-nas-00/data/ceres_data/9ddp_46779/09_2025/9ddp_46779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ddp_46779/09_2025/9ddp_46779.cif" } resolution = 3.16 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= 0.019 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 37 5.16 5 C 5791 2.51 5 N 1574 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9072 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1705 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "B" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1702 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1695 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "D" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1702 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "E" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1695 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "F" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 120 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "Y" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 229 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "Z" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 224 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 2, 'TRANS': 26} Time building chain proxies: 2.33, per 1000 atoms: 0.26 Number of scatterers: 9072 At special positions: 0 Unit cell: (83.83, 83.83, 117.86, 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 37 16.00 O 1670 8.00 N 1574 7.00 C 5791 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: 0.97 Conformation dependent library (CDL) restraints added in 283.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 90.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 removed outlier: 3.671A pdb=" N HIS A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 63 removed outlier: 3.963A pdb=" N PHE A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 46 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 76 Processing helix chain 'A' and resid 82 through 98 removed outlier: 4.148A pdb=" N GLU A 90 " --> pdb=" O HIS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 127 Processing helix chain 'A' and resid 129 through 163 removed outlier: 3.765A pdb=" N LEU A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 166 through 233 removed outlier: 3.756A pdb=" N VAL A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Proline residue: A 172 - end of helix removed outlier: 3.727A pdb=" N THR A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Proline residue: A 190 - end of helix Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 20 through 63 removed outlier: 3.659A pdb=" N VAL B 46 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 76 Processing helix chain 'B' and resid 84 through 97 removed outlier: 4.091A pdb=" N GLU B 90 " --> pdb=" O HIS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 127 Processing helix chain 'B' and resid 129 through 163 removed outlier: 3.736A pdb=" N LEU B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 166 through 233 removed outlier: 3.665A pdb=" N VAL B 170 " --> pdb=" O ASN B 166 " (cutoff:3.500A) Proline residue: B 172 - end of helix Proline residue: B 190 - end of helix Processing helix chain 'C' and resid 11 through 19 Processing helix chain 'C' and resid 20 through 63 removed outlier: 3.807A pdb=" N VAL C 46 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 Processing helix chain 'C' and resid 82 through 98 Processing helix chain 'C' and resid 103 through 127 Processing helix chain 'C' and resid 129 through 163 removed outlier: 3.610A pdb=" N LEU C 133 " --> pdb=" O GLY C 129 " (cutoff:3.500A) Proline residue: C 141 - end of helix Processing helix chain 'C' and resid 166 through 231 removed outlier: 4.028A pdb=" N VAL C 170 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Proline residue: C 172 - end of helix removed outlier: 4.116A pdb=" N ALA C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Proline residue: C 190 - end of helix Processing helix chain 'D' and resid 13 through 18 Processing helix chain 'D' and resid 20 through 63 removed outlier: 4.063A pdb=" N GLU D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN D 50 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG D 57 " --> pdb=" O ARG D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 76 Processing helix chain 'D' and resid 82 through 98 removed outlier: 3.888A pdb=" N GLU D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 127 Processing helix chain 'D' and resid 129 through 163 Proline residue: D 141 - end of helix Processing helix chain 'D' and resid 166 through 232 removed outlier: 3.593A pdb=" N VAL D 170 " --> pdb=" O ASN D 166 " (cutoff:3.500A) Proline residue: D 172 - end of helix removed outlier: 3.593A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Proline residue: D 190 - end of helix Processing helix chain 'E' and resid 11 through 19 Processing helix chain 'E' and resid 20 through 63 removed outlier: 3.858A pdb=" N VAL E 46 " --> pdb=" O PHE E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 76 Processing helix chain 'E' and resid 82 through 98 removed outlier: 3.573A pdb=" N GLU E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 127 removed outlier: 3.887A pdb=" N GLY E 127 " --> pdb=" O GLY E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 163 removed outlier: 3.833A pdb=" N LEU E 133 " --> pdb=" O GLY E 129 " (cutoff:3.500A) Proline residue: E 141 - end of helix Processing helix chain 'E' and resid 166 through 169 Processing helix chain 'E' and resid 170 through 231 removed outlier: 3.586A pdb=" N ALA E 180 " --> pdb=" O GLU E 176 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR E 181 " --> pdb=" O ALA E 177 " (cutoff:3.500A) Proline residue: E 190 - end of helix Processing helix chain 'F' and resid 11 through 24 Processing helix chain 'Y' and resid 20 through 41 Proline residue: Y 39 - end of helix Processing helix chain 'Z' and resid 22 through 38 847 hydrogen bonds defined for protein. 2538 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2631 1.33 - 1.45: 1256 1.45 - 1.58: 5251 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 9206 Sorted by residual: bond pdb=" CA SER C 140 " pdb=" CB SER C 140 " ideal model delta sigma weight residual 1.534 1.494 0.041 1.18e-02 7.18e+03 1.18e+01 bond pdb=" N ASP C 225 " pdb=" CA ASP C 225 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.30e-02 5.92e+03 1.10e+01 bond pdb=" C SER C 155 " pdb=" N PHE C 156 " ideal model delta sigma weight residual 1.334 1.290 0.044 1.33e-02 5.65e+03 1.09e+01 bond pdb=" N VAL A 12 " pdb=" CA VAL A 12 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.05e+00 bond pdb=" N VAL A 35 " pdb=" CA VAL A 35 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.91e+00 ... (remaining 9201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 10808 2.44 - 4.88: 1611 4.88 - 7.33: 44 7.33 - 9.77: 2 9.77 - 12.21: 1 Bond angle restraints: 12466 Sorted by residual: angle pdb=" CB ARG E 114 " pdb=" CG ARG E 114 " pdb=" CD ARG E 114 " ideal model delta sigma weight residual 111.30 123.51 -12.21 2.30e+00 1.89e-01 2.82e+01 angle pdb=" OE1 GLN D 161 " pdb=" CD GLN D 161 " pdb=" NE2 GLN D 161 " ideal model delta sigma weight residual 122.60 118.61 3.99 1.00e+00 1.00e+00 1.59e+01 angle pdb=" OE1 GLN B 51 " pdb=" CD GLN B 51 " pdb=" NE2 GLN B 51 " ideal model delta sigma weight residual 122.60 118.61 3.99 1.00e+00 1.00e+00 1.59e+01 angle pdb=" CB HIS C 18 " pdb=" CG HIS C 18 " pdb=" CD2 HIS C 18 " ideal model delta sigma weight residual 131.20 126.02 5.18 1.30e+00 5.92e-01 1.59e+01 angle pdb=" C GLY B 123 " pdb=" N ARG B 124 " pdb=" CA ARG B 124 " ideal model delta sigma weight residual 120.28 125.62 -5.34 1.34e+00 5.57e-01 1.59e+01 ... (remaining 12461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5046 17.64 - 35.27: 353 35.27 - 52.91: 48 52.91 - 70.54: 20 70.54 - 88.18: 5 Dihedral angle restraints: 5472 sinusoidal: 2066 harmonic: 3406 Sorted by residual: dihedral pdb=" CG ARG A 118 " pdb=" CD ARG A 118 " pdb=" NE ARG A 118 " pdb=" CZ ARG A 118 " ideal model delta sinusoidal sigma weight residual -90.00 -1.82 -88.18 2 1.50e+01 4.44e-03 2.13e+01 dihedral pdb=" CA LEU E 10 " pdb=" C LEU E 10 " pdb=" N SER E 11 " pdb=" CA SER E 11 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA THR C 164 " pdb=" C THR C 164 " pdb=" N THR C 165 " pdb=" CA THR C 165 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 5469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 904 0.065 - 0.130: 399 0.130 - 0.195: 149 0.195 - 0.260: 22 0.260 - 0.325: 4 Chirality restraints: 1478 Sorted by residual: chirality pdb=" CA ASN B 89 " pdb=" N ASN B 89 " pdb=" C ASN B 89 " pdb=" CB ASN B 89 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA THR Y 21 " pdb=" N THR Y 21 " pdb=" C THR Y 21 " pdb=" CB THR Y 21 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA SER A 140 " pdb=" N SER A 140 " pdb=" C SER A 140 " pdb=" CB SER A 140 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 1475 not shown) Planarity restraints: 1601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 16 " -0.093 2.00e-02 2.50e+03 4.85e-02 4.71e+01 pdb=" CG TYR C 16 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR C 16 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR C 16 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR C 16 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR C 16 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR C 16 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 16 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 16 " 0.067 2.00e-02 2.50e+03 3.51e-02 2.47e+01 pdb=" CG TYR E 16 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR E 16 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR E 16 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR E 16 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR E 16 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR E 16 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 16 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 16 " -0.063 2.00e-02 2.50e+03 3.48e-02 2.43e+01 pdb=" CG TYR B 16 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR B 16 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR B 16 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR B 16 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR B 16 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR B 16 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 16 " -0.051 2.00e-02 2.50e+03 ... (remaining 1598 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2322 2.85 - 3.36: 10213 3.36 - 3.88: 15392 3.88 - 4.39: 15717 4.39 - 4.90: 28867 Nonbonded interactions: 72511 Sorted by model distance: nonbonded pdb=" OG SER C 140 " pdb=" O GLY C 184 " model vdw 2.339 3.040 nonbonded pdb=" O ALA A 232 " pdb=" C HIS A 233 " model vdw 2.407 3.270 nonbonded pdb=" CG ARG A 118 " pdb=" NH1 ARG A 118 " model vdw 2.422 3.520 nonbonded pdb=" O ILE C 152 " pdb=" OG SER C 155 " model vdw 2.426 3.040 nonbonded pdb=" O PHE C 156 " pdb=" C ILE C 157 " model vdw 2.504 3.270 ... (remaining 72506 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' and ((resid 9 and (name N or name CA or name C or name O or name CB ) \ ) or resid 10 through 232)) selection = (chain 'B' and resid 9 through 232) selection = (chain 'C' and ((resid 9 and (name N or name CA or name C or name O or name CB ) \ ) or resid 10 through 232)) selection = (chain 'D' and ((resid 9 and (name N or name CA or name C or name O or name CB ) \ ) or resid 10 through 232)) selection = (chain 'E' and ((resid 9 and (name N or name CA or name C or name O or name CB ) \ ) or resid 10 through 232)) } ncs_group { reference = (chain 'Y' and resid 12 through 39) selection = (chain 'Z' and resid 12 through 39) } 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: 1.010 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.730 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 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 : 0.011 0.044 9206 Z= 0.684 Angle : 1.614 12.210 12466 Z= 1.122 Chirality : 0.081 0.325 1478 Planarity : 0.013 0.120 1601 Dihedral : 13.130 88.178 3272 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.85 % Allowed : 6.08 % Favored : 93.06 % 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 aren not related in a simple way. whole: 0.40 (0.22), residues: 1183 helix: 0.50 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : -0.65 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 110 TYR 0.093 0.018 TYR C 16 PHE 0.048 0.009 PHE A 146 TRP 0.051 0.011 TRP E 13 HIS 0.008 0.002 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.01082 ( 9206) covalent geometry : angle 1.61372 (12466) hydrogen bonds : bond 0.15733 ( 847) hydrogen bonds : angle 6.44492 ( 2538) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 362 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9292 (t) cc_final: 0.9017 (t) REVERT: A 58 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8909 (mt-10) REVERT: A 64 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8860 (tm-30) REVERT: A 69 ASN cc_start: 0.8922 (t0) cc_final: 0.8591 (t0) REVERT: A 73 ASP cc_start: 0.9357 (m-30) cc_final: 0.9139 (m-30) REVERT: A 89 ASN cc_start: 0.8857 (p0) cc_final: 0.8494 (p0) REVERT: A 94 GLU cc_start: 0.8979 (tp30) cc_final: 0.8685 (tp30) REVERT: A 99 GLU cc_start: 0.8791 (pp20) cc_final: 0.8562 (tm-30) REVERT: A 103 ASP cc_start: 0.9310 (t0) cc_final: 0.9007 (t0) REVERT: A 116 GLU cc_start: 0.9047 (tp30) cc_final: 0.8610 (tp30) REVERT: A 154 ASN cc_start: 0.9286 (m-40) cc_final: 0.8874 (m110) REVERT: A 166 ASN cc_start: 0.9134 (t0) cc_final: 0.8672 (t0) REVERT: A 227 GLU cc_start: 0.9116 (tp30) cc_final: 0.8885 (tp30) REVERT: B 64 GLU cc_start: 0.9066 (tp30) cc_final: 0.8661 (tp30) REVERT: B 73 ASP cc_start: 0.8981 (m-30) cc_final: 0.8772 (m-30) REVERT: B 81 LYS cc_start: 0.9245 (mmtm) cc_final: 0.8932 (ptmm) REVERT: B 93 ASN cc_start: 0.9024 (t0) cc_final: 0.8515 (t0) REVERT: B 96 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8810 (mt-10) REVERT: B 132 TYR cc_start: 0.8236 (t80) cc_final: 0.8015 (t80) REVERT: B 206 LYS cc_start: 0.9255 (ttmt) cc_final: 0.9050 (ttmm) REVERT: C 18 HIS cc_start: 0.8799 (t70) cc_final: 0.8433 (t-170) REVERT: C 27 MET cc_start: 0.9323 (mpp) cc_final: 0.8959 (mtt) REVERT: C 86 HIS cc_start: 0.8860 (t-170) cc_final: 0.8646 (t-170) REVERT: C 90 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8769 (mm-30) REVERT: C 96 GLU cc_start: 0.8712 (pt0) cc_final: 0.8407 (pp20) REVERT: C 166 ASN cc_start: 0.8737 (t0) cc_final: 0.8482 (t0) REVERT: C 176 GLU cc_start: 0.8869 (pt0) cc_final: 0.8513 (pt0) REVERT: C 227 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8552 (tm-30) REVERT: D 52 LYS cc_start: 0.8948 (ttpp) cc_final: 0.8687 (ttpp) REVERT: D 64 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8191 (tm-30) REVERT: D 94 GLU cc_start: 0.9083 (tp30) cc_final: 0.8579 (tp30) REVERT: D 103 ASP cc_start: 0.8868 (t0) cc_final: 0.8575 (t0) REVERT: D 118 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8465 (mmp80) REVERT: D 140 SER cc_start: 0.9433 (m) cc_final: 0.9194 (p) REVERT: D 211 ASP cc_start: 0.9005 (t70) cc_final: 0.8715 (m-30) REVERT: E 18 HIS cc_start: 0.8972 (t70) cc_final: 0.8528 (t70) REVERT: E 44 LYS cc_start: 0.9085 (mttp) cc_final: 0.8874 (mttt) REVERT: E 56 LYS cc_start: 0.9277 (tttp) cc_final: 0.9025 (tttp) REVERT: E 77 ASP cc_start: 0.8637 (t0) cc_final: 0.8370 (t0) REVERT: E 89 ASN cc_start: 0.9076 (m110) cc_final: 0.8869 (m-40) REVERT: E 125 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8511 (tm-30) REVERT: E 166 ASN cc_start: 0.9238 (t0) cc_final: 0.9026 (t0) REVERT: E 176 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8114 (mt-10) REVERT: E 223 ASP cc_start: 0.8816 (t0) cc_final: 0.8561 (t0) REVERT: Z 19 ASN cc_start: 0.9032 (t0) cc_final: 0.8775 (t0) outliers start: 8 outliers final: 2 residues processed: 365 average time/residue: 0.1188 time to fit residues: 56.5306 Evaluate side-chains 286 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 283 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain D residue 118 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 51 GLN ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 ASN B 201 GLN C 86 HIS C 93 ASN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 HIS D 130 ASN E 50 ASN E 89 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.078994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.062114 restraints weight = 20475.754| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.40 r_work: 0.2758 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9206 Z= 0.158 Angle : 0.599 6.380 12466 Z= 0.321 Chirality : 0.039 0.245 1478 Planarity : 0.004 0.081 1601 Dihedral : 4.834 57.550 1278 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 3.31 % Allowed : 12.17 % Favored : 84.53 % 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 aren not related in a simple way. whole: 3.17 (0.24), residues: 1183 helix: 2.41 (0.15), residues: 1052 sheet: None (None), residues: 0 loop : -0.54 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 118 TYR 0.014 0.002 TYR E 195 PHE 0.021 0.002 PHE Y 34 TRP 0.023 0.002 TRP B 13 HIS 0.006 0.002 HIS Z 16 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9206) covalent geometry : angle 0.59855 (12466) hydrogen bonds : bond 0.04947 ( 847) hydrogen bonds : angle 3.77366 ( 2538) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 299 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.9151 (ptp) cc_final: 0.8018 (ptp) REVERT: A 25 CYS cc_start: 0.9229 (t) cc_final: 0.8985 (t) REVERT: A 64 GLU cc_start: 0.9368 (tm-30) cc_final: 0.9073 (tm-30) REVERT: A 69 ASN cc_start: 0.8405 (t0) cc_final: 0.7778 (t0) REVERT: A 73 ASP cc_start: 0.9278 (m-30) cc_final: 0.8856 (m-30) REVERT: A 89 ASN cc_start: 0.8742 (p0) cc_final: 0.8393 (p0) REVERT: A 94 GLU cc_start: 0.8921 (tp30) cc_final: 0.8503 (tp30) REVERT: A 103 ASP cc_start: 0.9143 (t0) cc_final: 0.8903 (t0) REVERT: A 105 GLU cc_start: 0.8811 (tp30) cc_final: 0.8412 (tp30) REVERT: A 116 GLU cc_start: 0.9139 (tp30) cc_final: 0.8848 (tp30) REVERT: A 150 TRP cc_start: 0.9003 (t-100) cc_final: 0.8582 (t-100) REVERT: A 154 ASN cc_start: 0.9109 (m-40) cc_final: 0.8784 (m110) REVERT: A 166 ASN cc_start: 0.9018 (t0) cc_final: 0.8446 (t0) REVERT: A 227 GLU cc_start: 0.9320 (tp30) cc_final: 0.9104 (tp30) REVERT: B 69 ASN cc_start: 0.9494 (m-40) cc_final: 0.9266 (m-40) REVERT: B 93 ASN cc_start: 0.9240 (t0) cc_final: 0.8806 (t0) REVERT: C 18 HIS cc_start: 0.8873 (t70) cc_final: 0.8479 (t-170) REVERT: C 86 HIS cc_start: 0.8669 (t-90) cc_final: 0.8445 (t-170) REVERT: C 90 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8641 (mm-30) REVERT: C 118 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8752 (tpm170) REVERT: C 176 GLU cc_start: 0.8868 (pt0) cc_final: 0.8487 (pt0) REVERT: C 227 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8698 (tm-30) REVERT: D 52 LYS cc_start: 0.9004 (ttpp) cc_final: 0.8776 (ttpp) REVERT: D 58 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8923 (mm-30) REVERT: D 64 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8228 (tm-30) REVERT: D 66 ARG cc_start: 0.9010 (tpp-160) cc_final: 0.8702 (mmp80) REVERT: D 94 GLU cc_start: 0.9064 (tp30) cc_final: 0.8801 (tp30) REVERT: D 140 SER cc_start: 0.9331 (m) cc_final: 0.9126 (m) REVERT: D 211 ASP cc_start: 0.9054 (t70) cc_final: 0.8836 (t70) REVERT: E 13 TRP cc_start: 0.8232 (t60) cc_final: 0.7988 (t60) REVERT: E 18 HIS cc_start: 0.9163 (t70) cc_final: 0.8624 (t-170) REVERT: E 20 ASP cc_start: 0.8454 (t0) cc_final: 0.8126 (t0) REVERT: E 44 LYS cc_start: 0.8924 (mttp) cc_final: 0.8684 (mttt) REVERT: E 77 ASP cc_start: 0.8734 (t0) cc_final: 0.8465 (t0) REVERT: E 89 ASN cc_start: 0.9043 (m-40) cc_final: 0.8770 (m110) REVERT: E 93 ASN cc_start: 0.9242 (t0) cc_final: 0.8910 (t0) REVERT: E 125 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8347 (tm-30) REVERT: E 126 MET cc_start: 0.9394 (mmp) cc_final: 0.8996 (mmp) REVERT: E 223 ASP cc_start: 0.8927 (t0) cc_final: 0.8709 (t0) REVERT: E 227 GLU cc_start: 0.9313 (tt0) cc_final: 0.9076 (tm-30) REVERT: Z 19 ASN cc_start: 0.9187 (t0) cc_final: 0.8830 (t0) outliers start: 31 outliers final: 9 residues processed: 315 average time/residue: 0.0858 time to fit residues: 37.9375 Evaluate side-chains 276 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 266 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 126 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 165 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS D 86 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.079834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.062656 restraints weight = 21275.321| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.34 r_work: 0.2750 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9206 Z= 0.165 Angle : 0.577 7.221 12466 Z= 0.303 Chirality : 0.037 0.153 1478 Planarity : 0.003 0.045 1601 Dihedral : 3.944 30.723 1270 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 3.52 % Allowed : 14.83 % Favored : 81.64 % 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 aren not related in a simple way. whole: 3.55 (0.24), residues: 1183 helix: 2.66 (0.15), residues: 1054 sheet: None (None), residues: 0 loop : -0.55 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 118 TYR 0.017 0.002 TYR B 195 PHE 0.018 0.002 PHE A 49 TRP 0.019 0.001 TRP B 13 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 9206) covalent geometry : angle 0.57674 (12466) hydrogen bonds : bond 0.04444 ( 847) hydrogen bonds : angle 3.64530 ( 2538) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9250 (t) cc_final: 0.9020 (t) REVERT: A 64 GLU cc_start: 0.9321 (tm-30) cc_final: 0.9037 (tm-30) REVERT: A 69 ASN cc_start: 0.8429 (t0) cc_final: 0.7789 (t0) REVERT: A 73 ASP cc_start: 0.9240 (m-30) cc_final: 0.8830 (m-30) REVERT: A 88 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9208 (mm) REVERT: A 89 ASN cc_start: 0.8573 (p0) cc_final: 0.8292 (p0) REVERT: A 94 GLU cc_start: 0.9028 (tp30) cc_final: 0.8621 (tp30) REVERT: A 154 ASN cc_start: 0.9083 (m-40) cc_final: 0.8808 (m110) REVERT: A 166 ASN cc_start: 0.8915 (t0) cc_final: 0.8409 (t0) REVERT: A 227 GLU cc_start: 0.9332 (tp30) cc_final: 0.9119 (tp30) REVERT: B 58 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8588 (mm-30) REVERT: B 64 GLU cc_start: 0.8890 (tp30) cc_final: 0.8591 (tp30) REVERT: B 70 GLN cc_start: 0.8943 (tt0) cc_final: 0.8726 (tt0) REVERT: B 81 LYS cc_start: 0.9323 (mmtm) cc_final: 0.9016 (ptmm) REVERT: B 93 ASN cc_start: 0.9312 (t0) cc_final: 0.8890 (t0) REVERT: C 18 HIS cc_start: 0.8722 (t70) cc_final: 0.8371 (t-170) REVERT: C 96 GLU cc_start: 0.8553 (pt0) cc_final: 0.8323 (pt0) REVERT: C 176 GLU cc_start: 0.8851 (pt0) cc_final: 0.8590 (pt0) REVERT: C 227 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8688 (tm-30) REVERT: D 52 LYS cc_start: 0.8988 (ttpp) cc_final: 0.8750 (ttpp) REVERT: D 58 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8945 (mm-30) REVERT: D 64 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8221 (tm-30) REVERT: D 66 ARG cc_start: 0.9055 (tpp-160) cc_final: 0.8586 (mmp80) REVERT: D 94 GLU cc_start: 0.9024 (tp30) cc_final: 0.8476 (tp30) REVERT: D 99 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8471 (mm-30) REVERT: D 128 ARG cc_start: 0.8864 (tpp80) cc_final: 0.8606 (tpp80) REVERT: D 132 TYR cc_start: 0.7833 (m-80) cc_final: 0.7577 (m-80) REVERT: D 140 SER cc_start: 0.9327 (m) cc_final: 0.9057 (p) REVERT: D 211 ASP cc_start: 0.9034 (t70) cc_final: 0.8833 (t70) REVERT: E 13 TRP cc_start: 0.8254 (t60) cc_final: 0.7959 (t60) REVERT: E 18 HIS cc_start: 0.9121 (t70) cc_final: 0.8620 (t-170) REVERT: E 58 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8654 (mm-30) REVERT: E 77 ASP cc_start: 0.8761 (t0) cc_final: 0.8553 (t0) REVERT: E 89 ASN cc_start: 0.9058 (m-40) cc_final: 0.8821 (m-40) REVERT: E 93 ASN cc_start: 0.9296 (t0) cc_final: 0.8879 (t0) REVERT: E 125 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8568 (tm-30) REVERT: E 223 ASP cc_start: 0.8961 (t0) cc_final: 0.8702 (t0) outliers start: 33 outliers final: 17 residues processed: 296 average time/residue: 0.0799 time to fit residues: 33.6125 Evaluate side-chains 284 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 266 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 186 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 7 optimal weight: 0.0970 chunk 96 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 44 optimal weight: 0.0020 chunk 17 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN D 86 HIS E 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.080066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.063109 restraints weight = 21028.173| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.25 r_work: 0.2785 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9206 Z= 0.141 Angle : 0.567 8.049 12466 Z= 0.291 Chirality : 0.037 0.254 1478 Planarity : 0.003 0.027 1601 Dihedral : 3.783 25.272 1270 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.42 % Allowed : 16.76 % Favored : 79.83 % 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 aren not related in a simple way. whole: 3.76 (0.24), residues: 1183 helix: 2.80 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -0.58 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 118 TYR 0.022 0.002 TYR B 132 PHE 0.015 0.001 PHE Y 34 TRP 0.023 0.001 TRP B 13 HIS 0.009 0.002 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9206) covalent geometry : angle 0.56713 (12466) hydrogen bonds : bond 0.04085 ( 847) hydrogen bonds : angle 3.58740 ( 2538) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 281 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.9306 (tm-30) cc_final: 0.9098 (tm-30) REVERT: A 69 ASN cc_start: 0.8361 (t0) cc_final: 0.8125 (t0) REVERT: A 86 HIS cc_start: 0.8791 (t70) cc_final: 0.8529 (t70) REVERT: A 88 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9180 (mm) REVERT: A 89 ASN cc_start: 0.8532 (p0) cc_final: 0.8265 (p0) REVERT: A 150 TRP cc_start: 0.9107 (t-100) cc_final: 0.8664 (t-100) REVERT: A 154 ASN cc_start: 0.9018 (m-40) cc_final: 0.8663 (m110) REVERT: A 166 ASN cc_start: 0.8935 (t0) cc_final: 0.8421 (t0) REVERT: A 227 GLU cc_start: 0.9320 (tp30) cc_final: 0.9115 (tp30) REVERT: B 56 LYS cc_start: 0.9124 (tptm) cc_final: 0.8806 (tppp) REVERT: B 64 GLU cc_start: 0.8940 (tp30) cc_final: 0.8623 (tp30) REVERT: B 70 GLN cc_start: 0.8948 (tt0) cc_final: 0.8741 (tt0) REVERT: B 81 LYS cc_start: 0.9318 (mmtm) cc_final: 0.9045 (ptmm) REVERT: B 93 ASN cc_start: 0.9389 (t0) cc_final: 0.9032 (t0) REVERT: B 94 GLU cc_start: 0.9093 (tp30) cc_final: 0.8774 (tp30) REVERT: B 179 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8748 (mm) REVERT: C 18 HIS cc_start: 0.8652 (t70) cc_final: 0.8338 (t-170) REVERT: C 176 GLU cc_start: 0.8807 (pt0) cc_final: 0.8469 (pt0) REVERT: C 227 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8657 (tm-30) REVERT: D 20 ASP cc_start: 0.8250 (t0) cc_final: 0.8025 (t70) REVERT: D 52 LYS cc_start: 0.8989 (ttpp) cc_final: 0.8746 (ttpp) REVERT: D 64 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8434 (tm-30) REVERT: D 128 ARG cc_start: 0.8785 (tpp80) cc_final: 0.8405 (tpp80) REVERT: D 140 SER cc_start: 0.9374 (m) cc_final: 0.9107 (p) REVERT: D 211 ASP cc_start: 0.9015 (t70) cc_final: 0.8808 (t70) REVERT: E 13 TRP cc_start: 0.8257 (t60) cc_final: 0.7932 (t60) REVERT: E 18 HIS cc_start: 0.9143 (t70) cc_final: 0.8868 (t-170) REVERT: E 58 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8629 (mm-30) REVERT: E 89 ASN cc_start: 0.9076 (m-40) cc_final: 0.8816 (m110) REVERT: E 93 ASN cc_start: 0.9260 (t0) cc_final: 0.8990 (t0) REVERT: E 125 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8741 (tm-30) REVERT: E 166 ASN cc_start: 0.9276 (t0) cc_final: 0.8955 (t0) REVERT: E 176 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8234 (mm-30) REVERT: E 223 ASP cc_start: 0.8944 (t0) cc_final: 0.8655 (t0) REVERT: E 227 GLU cc_start: 0.9290 (tt0) cc_final: 0.9081 (tm-30) REVERT: Y 17 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8597 (m-30) REVERT: Z 15 MET cc_start: 0.8838 (ptm) cc_final: 0.8563 (ptp) outliers start: 32 outliers final: 14 residues processed: 299 average time/residue: 0.0878 time to fit residues: 37.3594 Evaluate side-chains 281 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 263 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain Y residue 17 ASP Chi-restraints excluded: chain Z residue 32 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.081319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.064055 restraints weight = 20923.592| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.38 r_work: 0.2767 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9206 Z= 0.137 Angle : 0.571 8.017 12466 Z= 0.292 Chirality : 0.037 0.213 1478 Planarity : 0.003 0.028 1601 Dihedral : 3.528 14.119 1266 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.63 % Allowed : 18.14 % Favored : 78.23 % 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 aren not related in a simple way. whole: 3.95 (0.24), residues: 1183 helix: 2.98 (0.15), residues: 1040 sheet: None (None), residues: 0 loop : -0.51 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 118 TYR 0.023 0.002 TYR B 132 PHE 0.028 0.001 PHE Y 34 TRP 0.024 0.001 TRP B 13 HIS 0.008 0.001 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9206) covalent geometry : angle 0.57054 (12466) hydrogen bonds : bond 0.03928 ( 847) hydrogen bonds : angle 3.48519 ( 2538) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.9325 (tm-30) cc_final: 0.9098 (tm-30) REVERT: A 85 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8859 (tm) REVERT: A 88 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9181 (mm) REVERT: A 89 ASN cc_start: 0.8520 (p0) cc_final: 0.8229 (p0) REVERT: A 90 GLU cc_start: 0.8553 (tt0) cc_final: 0.8343 (tt0) REVERT: A 150 TRP cc_start: 0.9050 (t-100) cc_final: 0.8689 (t-100) REVERT: A 154 ASN cc_start: 0.9023 (m-40) cc_final: 0.8758 (m110) REVERT: A 166 ASN cc_start: 0.8892 (t0) cc_final: 0.8356 (t0) REVERT: B 56 LYS cc_start: 0.9102 (tptm) cc_final: 0.8788 (tppp) REVERT: B 58 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8550 (mm-30) REVERT: B 64 GLU cc_start: 0.8992 (tp30) cc_final: 0.8730 (tp30) REVERT: B 70 GLN cc_start: 0.8905 (tt0) cc_final: 0.8698 (tt0) REVERT: B 81 LYS cc_start: 0.9328 (mmtm) cc_final: 0.9045 (ptmm) REVERT: B 93 ASN cc_start: 0.9360 (t0) cc_final: 0.9024 (t0) REVERT: B 115 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9241 (mm) REVERT: B 179 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8747 (mm) REVERT: C 18 HIS cc_start: 0.8640 (t70) cc_final: 0.8255 (t-170) REVERT: C 86 HIS cc_start: 0.8684 (t70) cc_final: 0.8399 (t-170) REVERT: C 176 GLU cc_start: 0.8757 (pt0) cc_final: 0.8405 (pt0) REVERT: C 227 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8665 (tm-30) REVERT: D 30 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9102 (mm) REVERT: D 52 LYS cc_start: 0.8940 (ttpp) cc_final: 0.8693 (ttpp) REVERT: D 56 LYS cc_start: 0.8927 (tppp) cc_final: 0.8493 (tptp) REVERT: D 64 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8503 (tm-30) REVERT: D 94 GLU cc_start: 0.9203 (tp30) cc_final: 0.8932 (tp30) REVERT: D 128 ARG cc_start: 0.8777 (tpp80) cc_final: 0.8394 (tpp80) REVERT: D 132 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.7306 (t80) REVERT: D 140 SER cc_start: 0.9368 (m) cc_final: 0.9070 (p) REVERT: D 211 ASP cc_start: 0.9001 (t70) cc_final: 0.8785 (t70) REVERT: E 13 TRP cc_start: 0.8269 (t60) cc_final: 0.7893 (t60) REVERT: E 18 HIS cc_start: 0.9152 (t70) cc_final: 0.8873 (t-170) REVERT: E 89 ASN cc_start: 0.9049 (m-40) cc_final: 0.8813 (m-40) REVERT: E 93 ASN cc_start: 0.9252 (t0) cc_final: 0.9009 (t0) REVERT: E 125 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8693 (tm-30) REVERT: E 166 ASN cc_start: 0.9250 (t0) cc_final: 0.8846 (t0) REVERT: E 176 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8261 (mm-30) REVERT: E 223 ASP cc_start: 0.8937 (t0) cc_final: 0.8654 (t0) REVERT: E 227 GLU cc_start: 0.9314 (tt0) cc_final: 0.9096 (tm-30) REVERT: Y 17 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8631 (m-30) REVERT: Z 15 MET cc_start: 0.8795 (ptm) cc_final: 0.8575 (ptp) outliers start: 34 outliers final: 12 residues processed: 297 average time/residue: 0.0827 time to fit residues: 35.0470 Evaluate side-chains 287 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 267 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain Y residue 17 ASP Chi-restraints excluded: chain Z residue 31 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.062666 restraints weight = 20519.045| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.32 r_work: 0.2778 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9206 Z= 0.144 Angle : 0.596 10.098 12466 Z= 0.304 Chirality : 0.037 0.225 1478 Planarity : 0.003 0.026 1601 Dihedral : 3.474 13.424 1266 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.20 % Allowed : 19.85 % Favored : 76.95 % 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 aren not related in a simple way. whole: 3.98 (0.24), residues: 1183 helix: 3.00 (0.15), residues: 1040 sheet: None (None), residues: 0 loop : -0.56 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 124 TYR 0.024 0.002 TYR B 132 PHE 0.017 0.001 PHE Y 34 TRP 0.028 0.001 TRP B 13 HIS 0.010 0.001 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9206) covalent geometry : angle 0.59570 (12466) hydrogen bonds : bond 0.03903 ( 847) hydrogen bonds : angle 3.50544 ( 2538) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 274 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8849 (tm) REVERT: A 88 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9171 (mm) REVERT: A 89 ASN cc_start: 0.8555 (p0) cc_final: 0.8246 (p0) REVERT: A 150 TRP cc_start: 0.9024 (t-100) cc_final: 0.8678 (t-100) REVERT: A 154 ASN cc_start: 0.9009 (m-40) cc_final: 0.8744 (m110) REVERT: A 166 ASN cc_start: 0.8905 (t0) cc_final: 0.8362 (t0) REVERT: B 56 LYS cc_start: 0.9115 (tptm) cc_final: 0.8777 (tppp) REVERT: B 64 GLU cc_start: 0.9016 (tp30) cc_final: 0.8741 (tp30) REVERT: B 81 LYS cc_start: 0.9337 (mmtm) cc_final: 0.9058 (ptmm) REVERT: B 93 ASN cc_start: 0.9342 (t0) cc_final: 0.9035 (t0) REVERT: B 179 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8709 (mm) REVERT: C 18 HIS cc_start: 0.8763 (t70) cc_final: 0.8522 (t-170) REVERT: C 86 HIS cc_start: 0.8686 (t70) cc_final: 0.8363 (t-170) REVERT: C 176 GLU cc_start: 0.8773 (pt0) cc_final: 0.8545 (pt0) REVERT: C 227 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8666 (tm-30) REVERT: D 30 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9110 (mm) REVERT: D 64 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8528 (tm-30) REVERT: D 94 GLU cc_start: 0.9125 (tp30) cc_final: 0.8523 (tp30) REVERT: D 99 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8287 (mm-30) REVERT: D 132 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.7345 (t80) REVERT: D 140 SER cc_start: 0.9374 (m) cc_final: 0.9074 (p) REVERT: D 211 ASP cc_start: 0.8967 (t70) cc_final: 0.8745 (t70) REVERT: E 13 TRP cc_start: 0.8310 (t60) cc_final: 0.7891 (t60) REVERT: E 18 HIS cc_start: 0.9153 (t70) cc_final: 0.8656 (t-170) REVERT: E 58 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8587 (mm-30) REVERT: E 89 ASN cc_start: 0.9063 (m-40) cc_final: 0.8784 (m110) REVERT: E 93 ASN cc_start: 0.9274 (t0) cc_final: 0.9026 (t0) REVERT: E 94 GLU cc_start: 0.9316 (tp30) cc_final: 0.9059 (tp30) REVERT: E 125 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8703 (tm-30) REVERT: E 166 ASN cc_start: 0.9225 (t0) cc_final: 0.8773 (t0) REVERT: E 223 ASP cc_start: 0.8923 (t0) cc_final: 0.8613 (t0) REVERT: Y 17 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8615 (m-30) REVERT: Z 15 MET cc_start: 0.8761 (ptm) cc_final: 0.8538 (ptp) outliers start: 30 outliers final: 16 residues processed: 293 average time/residue: 0.0839 time to fit residues: 34.8358 Evaluate side-chains 271 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain Y residue 17 ASP Chi-restraints excluded: chain Z residue 32 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 ASN D 86 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.078760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.062235 restraints weight = 20724.806| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.32 r_work: 0.2770 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9206 Z= 0.153 Angle : 0.610 10.353 12466 Z= 0.309 Chirality : 0.038 0.194 1478 Planarity : 0.004 0.127 1601 Dihedral : 3.478 16.377 1266 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.42 % Allowed : 20.70 % Favored : 75.88 % 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 aren not related in a simple way. whole: 3.96 (0.24), residues: 1183 helix: 3.00 (0.15), residues: 1039 sheet: None (None), residues: 0 loop : -0.61 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 128 TYR 0.024 0.002 TYR B 132 PHE 0.014 0.001 PHE B 142 TRP 0.029 0.001 TRP B 13 HIS 0.018 0.002 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9206) covalent geometry : angle 0.61027 (12466) hydrogen bonds : bond 0.03892 ( 847) hydrogen bonds : angle 3.54381 ( 2538) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 261 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8848 (tm) REVERT: A 88 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9152 (mm) REVERT: A 89 ASN cc_start: 0.8575 (p0) cc_final: 0.8321 (p0) REVERT: A 118 ARG cc_start: 0.8585 (tpp80) cc_final: 0.8303 (tpp80) REVERT: A 150 TRP cc_start: 0.9035 (t-100) cc_final: 0.8700 (t-100) REVERT: A 154 ASN cc_start: 0.9013 (m-40) cc_final: 0.8751 (m110) REVERT: A 166 ASN cc_start: 0.8893 (t0) cc_final: 0.8344 (t0) REVERT: B 56 LYS cc_start: 0.9116 (tptm) cc_final: 0.8770 (tppp) REVERT: B 81 LYS cc_start: 0.9303 (mmtm) cc_final: 0.9022 (ptmm) REVERT: B 93 ASN cc_start: 0.9343 (t0) cc_final: 0.9054 (t0) REVERT: B 179 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8763 (mm) REVERT: C 18 HIS cc_start: 0.8728 (t70) cc_final: 0.8500 (t-170) REVERT: C 86 HIS cc_start: 0.8712 (t70) cc_final: 0.8353 (t-170) REVERT: C 176 GLU cc_start: 0.8741 (pt0) cc_final: 0.8503 (pt0) REVERT: C 227 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8646 (tm-30) REVERT: D 30 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9117 (mm) REVERT: D 64 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8562 (tm-30) REVERT: D 94 GLU cc_start: 0.9161 (tp30) cc_final: 0.8542 (tp30) REVERT: D 96 GLU cc_start: 0.8471 (pt0) cc_final: 0.8231 (mt-10) REVERT: D 128 ARG cc_start: 0.8710 (tpp80) cc_final: 0.7961 (tpp80) REVERT: D 132 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.7393 (t80) REVERT: D 140 SER cc_start: 0.9374 (m) cc_final: 0.9075 (p) REVERT: D 211 ASP cc_start: 0.8963 (t70) cc_final: 0.8732 (t70) REVERT: E 13 TRP cc_start: 0.8403 (t60) cc_final: 0.7964 (t60) REVERT: E 18 HIS cc_start: 0.9168 (t70) cc_final: 0.8671 (t-170) REVERT: E 58 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8579 (mm-30) REVERT: E 89 ASN cc_start: 0.9071 (m-40) cc_final: 0.8792 (m110) REVERT: E 93 ASN cc_start: 0.9269 (t0) cc_final: 0.9030 (t0) REVERT: E 125 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8704 (tm-30) REVERT: E 166 ASN cc_start: 0.9207 (t0) cc_final: 0.8857 (t0) REVERT: E 223 ASP cc_start: 0.8947 (t0) cc_final: 0.8639 (t0) REVERT: Y 17 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8617 (m-30) REVERT: Z 15 MET cc_start: 0.8750 (ptm) cc_final: 0.8530 (ptp) REVERT: Z 35 MET cc_start: 0.8974 (tpp) cc_final: 0.8768 (mmp) outliers start: 32 outliers final: 14 residues processed: 283 average time/residue: 0.0880 time to fit residues: 35.3554 Evaluate side-chains 277 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 257 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain Y residue 17 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 89 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 7 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.080836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.064597 restraints weight = 20693.339| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.23 r_work: 0.2833 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9206 Z= 0.148 Angle : 0.637 11.357 12466 Z= 0.320 Chirality : 0.039 0.343 1478 Planarity : 0.004 0.099 1601 Dihedral : 3.445 13.902 1266 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.88 % Allowed : 21.45 % Favored : 75.67 % 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 aren not related in a simple way. whole: 3.97 (0.24), residues: 1183 helix: 3.02 (0.15), residues: 1038 sheet: None (None), residues: 0 loop : -0.69 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 128 TYR 0.025 0.002 TYR B 132 PHE 0.016 0.001 PHE B 142 TRP 0.034 0.001 TRP B 13 HIS 0.007 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9206) covalent geometry : angle 0.63732 (12466) hydrogen bonds : bond 0.03860 ( 847) hydrogen bonds : angle 3.55922 ( 2538) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 266 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.9098 (t80) cc_final: 0.8838 (t80) REVERT: A 20 ASP cc_start: 0.8435 (p0) cc_final: 0.8067 (p0) REVERT: A 85 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8782 (tm) REVERT: A 88 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9143 (mm) REVERT: A 89 ASN cc_start: 0.8535 (p0) cc_final: 0.8325 (p0) REVERT: A 118 ARG cc_start: 0.8558 (tpp80) cc_final: 0.8235 (tpp80) REVERT: A 150 TRP cc_start: 0.9005 (t-100) cc_final: 0.8681 (t-100) REVERT: A 154 ASN cc_start: 0.9010 (m-40) cc_final: 0.8747 (m110) REVERT: A 166 ASN cc_start: 0.8871 (t0) cc_final: 0.8587 (t0) REVERT: B 58 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8718 (mm-30) REVERT: B 81 LYS cc_start: 0.9303 (mmtm) cc_final: 0.9019 (ptmm) REVERT: B 115 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9218 (mm) REVERT: B 179 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8673 (mm) REVERT: C 86 HIS cc_start: 0.8671 (t70) cc_final: 0.8306 (t-170) REVERT: C 176 GLU cc_start: 0.8689 (pt0) cc_final: 0.8447 (pt0) REVERT: C 227 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8644 (tm-30) REVERT: D 30 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9122 (mm) REVERT: D 64 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8589 (tm-30) REVERT: D 94 GLU cc_start: 0.9104 (tp30) cc_final: 0.8496 (tp30) REVERT: D 99 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8328 (mm-30) REVERT: D 128 ARG cc_start: 0.8686 (tpp80) cc_final: 0.7941 (tpp80) REVERT: D 132 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7380 (t80) REVERT: D 140 SER cc_start: 0.9388 (m) cc_final: 0.9081 (p) REVERT: D 211 ASP cc_start: 0.8883 (t70) cc_final: 0.8649 (t70) REVERT: E 13 TRP cc_start: 0.8376 (t60) cc_final: 0.7939 (t60) REVERT: E 18 HIS cc_start: 0.9163 (t70) cc_final: 0.8669 (t-170) REVERT: E 58 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8575 (mm-30) REVERT: E 89 ASN cc_start: 0.9082 (m-40) cc_final: 0.8775 (m110) REVERT: E 93 ASN cc_start: 0.9283 (t0) cc_final: 0.9044 (t0) REVERT: E 94 GLU cc_start: 0.9302 (tp30) cc_final: 0.9102 (tp30) REVERT: E 125 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8727 (tm-30) REVERT: E 166 ASN cc_start: 0.9185 (t0) cc_final: 0.8815 (t0) REVERT: E 223 ASP cc_start: 0.8943 (t0) cc_final: 0.8638 (t0) REVERT: Y 17 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8586 (m-30) REVERT: Z 15 MET cc_start: 0.8695 (ptm) cc_final: 0.8456 (ptp) REVERT: Z 35 MET cc_start: 0.8961 (tpp) cc_final: 0.8755 (mmp) outliers start: 27 outliers final: 15 residues processed: 284 average time/residue: 0.0874 time to fit residues: 35.3037 Evaluate side-chains 283 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 261 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain Y residue 17 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 43 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS D 86 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.078086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.061443 restraints weight = 20569.753| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.31 r_work: 0.2761 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9206 Z= 0.178 Angle : 0.655 11.588 12466 Z= 0.332 Chirality : 0.039 0.252 1478 Planarity : 0.004 0.094 1601 Dihedral : 3.442 15.423 1266 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.74 % Allowed : 21.56 % Favored : 74.71 % 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 aren not related in a simple way. whole: 3.97 (0.24), residues: 1183 helix: 3.00 (0.15), residues: 1040 sheet: None (None), residues: 0 loop : -0.62 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 128 TYR 0.023 0.002 TYR B 132 PHE 0.015 0.001 PHE B 142 TRP 0.037 0.001 TRP B 13 HIS 0.019 0.002 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 9206) covalent geometry : angle 0.65538 (12466) hydrogen bonds : bond 0.03924 ( 847) hydrogen bonds : angle 3.58609 ( 2538) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 265 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 16 TYR cc_start: 0.9088 (t80) cc_final: 0.8884 (t80) REVERT: A 85 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8817 (tm) REVERT: A 88 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9128 (mm) REVERT: A 89 ASN cc_start: 0.8556 (p0) cc_final: 0.8351 (p0) REVERT: A 118 ARG cc_start: 0.8613 (tpp80) cc_final: 0.8203 (tpp80) REVERT: A 150 TRP cc_start: 0.9001 (t-100) cc_final: 0.8674 (t-100) REVERT: A 154 ASN cc_start: 0.9020 (m-40) cc_final: 0.8735 (m110) REVERT: A 166 ASN cc_start: 0.8883 (t0) cc_final: 0.8598 (t0) REVERT: B 56 LYS cc_start: 0.9131 (tppp) cc_final: 0.8810 (tppp) REVERT: B 58 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8762 (mm-30) REVERT: B 81 LYS cc_start: 0.9316 (mmtm) cc_final: 0.9012 (ptmm) REVERT: B 115 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9210 (mm) REVERT: C 86 HIS cc_start: 0.8721 (t70) cc_final: 0.8352 (t-170) REVERT: C 176 GLU cc_start: 0.8768 (pt0) cc_final: 0.8384 (pt0) REVERT: C 227 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8638 (tm-30) REVERT: D 30 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9144 (mm) REVERT: D 64 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8576 (tm-30) REVERT: D 94 GLU cc_start: 0.9129 (tp30) cc_final: 0.8545 (tp30) REVERT: D 96 GLU cc_start: 0.8492 (pt0) cc_final: 0.8242 (mt-10) REVERT: D 99 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8275 (mm-30) REVERT: D 128 ARG cc_start: 0.8727 (tpp80) cc_final: 0.7961 (tpp80) REVERT: D 132 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7388 (t80) REVERT: D 140 SER cc_start: 0.9388 (m) cc_final: 0.9078 (p) REVERT: D 211 ASP cc_start: 0.8977 (t70) cc_final: 0.8739 (t70) REVERT: E 13 TRP cc_start: 0.8371 (t60) cc_final: 0.7934 (t60) REVERT: E 18 HIS cc_start: 0.9165 (t70) cc_final: 0.8651 (t-170) REVERT: E 58 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8560 (mm-30) REVERT: E 89 ASN cc_start: 0.9077 (m-40) cc_final: 0.8795 (m110) REVERT: E 93 ASN cc_start: 0.9269 (t0) cc_final: 0.9055 (t0) REVERT: E 94 GLU cc_start: 0.9294 (tp30) cc_final: 0.9054 (tp30) REVERT: E 125 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8669 (tm-30) REVERT: E 166 ASN cc_start: 0.9170 (t0) cc_final: 0.8813 (t0) REVERT: E 223 ASP cc_start: 0.8957 (t0) cc_final: 0.8721 (t0) REVERT: Y 17 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8620 (m-30) REVERT: Z 15 MET cc_start: 0.8731 (ptm) cc_final: 0.8515 (ptp) outliers start: 35 outliers final: 22 residues processed: 287 average time/residue: 0.0894 time to fit residues: 36.4479 Evaluate side-chains 292 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 25 CYS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain E residue 15 MET Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain Y residue 17 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 110 optimal weight: 0.1980 chunk 55 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.081401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.065055 restraints weight = 20625.523| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.25 r_work: 0.2831 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9206 Z= 0.147 Angle : 0.669 12.331 12466 Z= 0.336 Chirality : 0.039 0.223 1478 Planarity : 0.004 0.085 1601 Dihedral : 3.500 16.091 1266 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.20 % Allowed : 22.31 % Favored : 74.49 % 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 aren not related in a simple way. whole: 3.89 (0.24), residues: 1183 helix: 2.96 (0.15), residues: 1039 sheet: None (None), residues: 0 loop : -0.73 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 128 TYR 0.023 0.002 TYR B 132 PHE 0.018 0.001 PHE Y 34 TRP 0.038 0.001 TRP B 13 HIS 0.025 0.002 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9206) covalent geometry : angle 0.66889 (12466) hydrogen bonds : bond 0.03858 ( 847) hydrogen bonds : angle 3.59773 ( 2538) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 273 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.8976 (t80) cc_final: 0.8704 (t80) REVERT: A 85 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8829 (tm) REVERT: A 88 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9164 (mm) REVERT: A 150 TRP cc_start: 0.9013 (t-100) cc_final: 0.8705 (t-100) REVERT: A 154 ASN cc_start: 0.8965 (m-40) cc_final: 0.8740 (m110) REVERT: A 166 ASN cc_start: 0.8880 (t0) cc_final: 0.8596 (t0) REVERT: B 56 LYS cc_start: 0.9124 (tppp) cc_final: 0.8799 (tppp) REVERT: B 58 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8688 (mm-30) REVERT: B 81 LYS cc_start: 0.9294 (mmtm) cc_final: 0.9028 (ptmm) REVERT: B 115 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9254 (mm) REVERT: B 118 ARG cc_start: 0.8945 (tpp80) cc_final: 0.8632 (tpp80) REVERT: B 132 TYR cc_start: 0.7858 (t80) cc_final: 0.7566 (t80) REVERT: C 52 LYS cc_start: 0.8833 (mtpp) cc_final: 0.8597 (tptp) REVERT: C 86 HIS cc_start: 0.8661 (t70) cc_final: 0.8281 (t-170) REVERT: C 176 GLU cc_start: 0.8660 (pt0) cc_final: 0.8447 (pt0) REVERT: C 227 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8654 (tm-30) REVERT: D 15 MET cc_start: 0.9144 (ptp) cc_final: 0.8543 (pmm) REVERT: D 30 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9158 (mm) REVERT: D 64 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8573 (tm-30) REVERT: D 94 GLU cc_start: 0.9090 (tp30) cc_final: 0.8821 (tp30) REVERT: D 99 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8291 (mm-30) REVERT: D 132 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.7427 (t80) REVERT: D 140 SER cc_start: 0.9404 (m) cc_final: 0.9108 (p) REVERT: D 211 ASP cc_start: 0.8869 (t70) cc_final: 0.8638 (t70) REVERT: E 13 TRP cc_start: 0.8363 (t60) cc_final: 0.7935 (t60) REVERT: E 18 HIS cc_start: 0.9123 (t70) cc_final: 0.8645 (t-170) REVERT: E 58 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8577 (mm-30) REVERT: E 89 ASN cc_start: 0.9102 (m-40) cc_final: 0.8806 (m110) REVERT: E 93 ASN cc_start: 0.9307 (t0) cc_final: 0.9082 (t0) REVERT: E 94 GLU cc_start: 0.9296 (tp30) cc_final: 0.9087 (tp30) REVERT: E 125 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8754 (tm-30) REVERT: E 166 ASN cc_start: 0.9203 (t0) cc_final: 0.8872 (t0) REVERT: E 223 ASP cc_start: 0.8939 (t0) cc_final: 0.8650 (t0) REVERT: Z 15 MET cc_start: 0.8709 (ptm) cc_final: 0.8467 (ptp) outliers start: 30 outliers final: 17 residues processed: 292 average time/residue: 0.0925 time to fit residues: 38.1882 Evaluate side-chains 287 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 265 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain D residue 132 TYR Chi-restraints excluded: chain E residue 15 MET Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 0.0870 chunk 111 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 overall best weight: 1.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS D 86 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.078569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.061938 restraints weight = 20496.740| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.31 r_work: 0.2760 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9206 Z= 0.180 Angle : 0.685 11.756 12466 Z= 0.347 Chirality : 0.040 0.206 1478 Planarity : 0.003 0.028 1601 Dihedral : 3.485 19.749 1266 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.99 % Allowed : 22.73 % Favored : 74.28 % 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 aren not related in a simple way. whole: 3.90 (0.24), residues: 1183 helix: 2.97 (0.15), residues: 1039 sheet: None (None), residues: 0 loop : -0.73 (0.50), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 128 TYR 0.021 0.002 TYR B 132 PHE 0.020 0.001 PHE C 156 TRP 0.039 0.002 TRP B 13 HIS 0.022 0.002 HIS D 86 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9206) covalent geometry : angle 0.68484 (12466) hydrogen bonds : bond 0.03939 ( 847) hydrogen bonds : angle 3.61999 ( 2538) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1964.07 seconds wall clock time: 34 minutes 27.83 seconds (2067.83 seconds total)