Starting phenix.real_space_refine on Sun Jul 27 00:34:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ddp_46779/07_2025/9ddp_46779.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ddp_46779/07_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_46779/07_2025/9ddp_46779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ddp_46779/07_2025/9ddp_46779.map" model { file = "/net/cci-nas-00/data/ceres_data/9ddp_46779/07_2025/9ddp_46779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ddp_46779/07_2025/9ddp_46779.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.77, per 1000 atoms: 0.64 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: 2.44 Conformation dependent library (CDL) restraints added in 989.8 milliseconds 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: 0.71 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: 2.98 Time building geometry restraints manager: 2.81 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.550 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.210 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.051 0.011 TRP E 13 HIS 0.008 0.002 HIS B 86 PHE 0.048 0.009 PHE A 146 TYR 0.093 0.018 TYR C 16 ARG 0.008 0.001 ARG D 110 Details of bonding type rmsd hydrogen bonds : bond 0.15733 ( 847) hydrogen bonds : angle 6.44492 ( 2538) covalent geometry : bond 0.01082 ( 9206) covalent geometry : angle 1.61372 (12466) *********************** 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 : 0.931 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: 0.8881 (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: 0.8493 (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 77 ASP cc_start: 0.8637 (t0) cc_final: 0.8369 (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: 0.8512 (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: 0.2463 time to fit residues: 116.6285 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 : 0.936 ------------------------------------------------------------------------------- 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 97 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.079362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.062563 restraints weight = 20298.985| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.35 r_work: 0.2764 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9206 Z= 0.157 Angle : 0.594 6.405 12466 Z= 0.319 Chirality : 0.039 0.241 1478 Planarity : 0.004 0.081 1601 Dihedral : 4.811 57.632 1278 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 3.42 % Allowed : 11.74 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.24), residues: 1183 helix: 2.43 (0.16), residues: 1052 sheet: None (None), residues: 0 loop : -0.53 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 13 HIS 0.006 0.002 HIS D 86 PHE 0.021 0.002 PHE Y 34 TYR 0.015 0.002 TYR E 195 ARG 0.006 0.001 ARG B 118 Details of bonding type rmsd hydrogen bonds : bond 0.04847 ( 847) hydrogen bonds : angle 3.75474 ( 2538) covalent geometry : bond 0.00331 ( 9206) covalent geometry : angle 0.59443 (12466) *********************** 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 334 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 302 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.9136 (ptp) cc_final: 0.8101 (ptt) REVERT: A 25 CYS cc_start: 0.9205 (t) cc_final: 0.8963 (t) REVERT: A 64 GLU cc_start: 0.9369 (tm-30) cc_final: 0.9076 (tm-30) REVERT: A 69 ASN cc_start: 0.8392 (t0) cc_final: 0.7766 (t0) REVERT: A 73 ASP cc_start: 0.9266 (m-30) cc_final: 0.8834 (m-30) REVERT: A 89 ASN cc_start: 0.8720 (p0) cc_final: 0.8383 (p0) REVERT: A 94 GLU cc_start: 0.8935 (tp30) cc_final: 0.8520 (tp30) REVERT: A 105 GLU cc_start: 0.8798 (tp30) cc_final: 0.8343 (tp30) REVERT: A 116 GLU cc_start: 0.9135 (tp30) cc_final: 0.8843 (tp30) REVERT: A 150 TRP cc_start: 0.9009 (t-100) cc_final: 0.8568 (t-100) REVERT: A 154 ASN cc_start: 0.9101 (m-40) cc_final: 0.8756 (m110) REVERT: A 166 ASN cc_start: 0.9022 (t0) cc_final: 0.8439 (t0) REVERT: A 227 GLU cc_start: 0.9316 (tp30) cc_final: 0.9099 (tp30) REVERT: B 69 ASN cc_start: 0.9489 (m-40) cc_final: 0.9262 (m-40) REVERT: B 93 ASN cc_start: 0.9252 (t0) cc_final: 0.8822 (t0) REVERT: C 18 HIS cc_start: 0.8871 (t70) cc_final: 0.8473 (t-170) REVERT: C 86 HIS cc_start: 0.8641 (t-90) cc_final: 0.8430 (t-170) REVERT: C 90 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8629 (mm-30) REVERT: C 118 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8749 (tpm170) REVERT: C 176 GLU cc_start: 0.8890 (pt0) cc_final: 0.8491 (pt0) REVERT: C 227 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8676 (tm-30) REVERT: D 52 LYS cc_start: 0.8996 (ttpp) cc_final: 0.8765 (ttpp) REVERT: D 58 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8924 (mm-30) REVERT: D 64 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8260 (tm-30) REVERT: D 66 ARG cc_start: 0.9021 (tpp-160) cc_final: 0.8714 (mmp80) REVERT: D 94 GLU cc_start: 0.9064 (tp30) cc_final: 0.8798 (tp30) REVERT: D 211 ASP cc_start: 0.9050 (t70) cc_final: 0.8833 (t70) REVERT: E 13 TRP cc_start: 0.8213 (t60) cc_final: 0.7968 (t60) REVERT: E 18 HIS cc_start: 0.9160 (t70) cc_final: 0.8619 (t-170) REVERT: E 20 ASP cc_start: 0.8451 (t0) cc_final: 0.8129 (t0) REVERT: E 44 LYS cc_start: 0.8922 (mttp) cc_final: 0.8670 (mttt) REVERT: E 77 ASP cc_start: 0.8754 (t0) cc_final: 0.8494 (t0) REVERT: E 89 ASN cc_start: 0.9033 (m-40) cc_final: 0.8816 (m-40) REVERT: E 93 ASN cc_start: 0.9248 (t0) cc_final: 0.8922 (t0) REVERT: E 125 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8458 (tm-30) REVERT: E 223 ASP cc_start: 0.8924 (t0) cc_final: 0.8718 (t0) REVERT: E 227 GLU cc_start: 0.9314 (tt0) cc_final: 0.9076 (tm-30) REVERT: Z 19 ASN cc_start: 0.9192 (t0) cc_final: 0.8810 (t0) outliers start: 32 outliers final: 10 residues processed: 319 average time/residue: 0.1953 time to fit residues: 86.5767 Evaluate side-chains 278 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 267 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 126 MET Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 202 ILE 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 110 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3280 r_free = 0.3280 target = 0.080226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.063204 restraints weight = 21445.041| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.33 r_work: 0.2759 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9206 Z= 0.150 Angle : 0.568 6.423 12466 Z= 0.299 Chirality : 0.037 0.215 1478 Planarity : 0.003 0.044 1601 Dihedral : 3.934 30.368 1270 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 3.31 % Allowed : 15.58 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.58 (0.24), residues: 1183 helix: 2.67 (0.15), residues: 1054 sheet: None (None), residues: 0 loop : -0.46 (0.59), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 13 HIS 0.008 0.001 HIS D 86 PHE 0.018 0.001 PHE A 49 TYR 0.017 0.002 TYR B 195 ARG 0.007 0.001 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 847) hydrogen bonds : angle 3.63089 ( 2538) covalent geometry : bond 0.00331 ( 9206) covalent geometry : angle 0.56830 (12466) *********************** 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 312 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 281 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9247 (t) cc_final: 0.9009 (t) REVERT: A 64 GLU cc_start: 0.9310 (tm-30) cc_final: 0.9108 (tm-30) REVERT: A 69 ASN cc_start: 0.8425 (t0) cc_final: 0.7802 (t0) REVERT: A 73 ASP cc_start: 0.9239 (m-30) cc_final: 0.8829 (m-30) REVERT: A 88 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9207 (mm) REVERT: A 89 ASN cc_start: 0.8556 (p0) cc_final: 0.8281 (p0) REVERT: A 94 GLU cc_start: 0.9003 (tp30) cc_final: 0.8595 (tp30) REVERT: A 150 TRP cc_start: 0.9086 (t-100) cc_final: 0.8631 (t-100) REVERT: A 154 ASN cc_start: 0.9068 (m-40) cc_final: 0.8700 (m110) REVERT: A 166 ASN cc_start: 0.8914 (t0) cc_final: 0.8415 (t0) REVERT: A 227 GLU cc_start: 0.9335 (tp30) cc_final: 0.9124 (tp30) REVERT: B 64 GLU cc_start: 0.8883 (tp30) cc_final: 0.8612 (tp30) REVERT: B 70 GLN cc_start: 0.8937 (tt0) cc_final: 0.8720 (tt0) REVERT: B 81 LYS cc_start: 0.9315 (mmtm) cc_final: 0.9030 (ptmm) REVERT: B 93 ASN cc_start: 0.9309 (t0) cc_final: 0.8898 (t0) REVERT: C 18 HIS cc_start: 0.8724 (t70) cc_final: 0.8374 (t-170) REVERT: C 96 GLU cc_start: 0.8550 (pt0) cc_final: 0.8317 (pt0) REVERT: C 176 GLU cc_start: 0.8842 (pt0) cc_final: 0.8576 (pt0) REVERT: C 227 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8682 (tm-30) REVERT: D 52 LYS cc_start: 0.8977 (ttpp) cc_final: 0.8733 (ttpp) REVERT: D 58 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8943 (mm-30) REVERT: D 64 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8246 (tm-30) REVERT: D 66 ARG cc_start: 0.9050 (tpp-160) cc_final: 0.8589 (mmp80) REVERT: D 94 GLU cc_start: 0.9012 (tp30) cc_final: 0.8460 (tp30) REVERT: D 99 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8522 (mm-30) REVERT: D 128 ARG cc_start: 0.8844 (tpp80) cc_final: 0.8594 (tpp80) REVERT: D 132 TYR cc_start: 0.7835 (m-80) cc_final: 0.7591 (m-80) REVERT: E 13 TRP cc_start: 0.8230 (t60) cc_final: 0.7942 (t60) REVERT: E 18 HIS cc_start: 0.9100 (t70) cc_final: 0.8603 (t-170) REVERT: E 58 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8660 (mm-30) REVERT: E 77 ASP cc_start: 0.8754 (t0) cc_final: 0.8543 (t0) REVERT: E 89 ASN cc_start: 0.9048 (m-40) cc_final: 0.8809 (m-40) REVERT: E 93 ASN cc_start: 0.9286 (t0) cc_final: 0.8864 (t0) REVERT: E 125 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8584 (tm-30) REVERT: E 223 ASP cc_start: 0.8962 (t0) cc_final: 0.8708 (t0) outliers start: 31 outliers final: 14 residues processed: 296 average time/residue: 0.1933 time to fit residues: 79.5239 Evaluate side-chains 280 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 265 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 C residue 32 LEU Chi-restraints excluded: chain C residue 118 ARG 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 53 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 HIS 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 = 0.3269 r_free = 0.3269 target = 0.079128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.062335 restraints weight = 20341.315| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.40 r_work: 0.2718 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9206 Z= 0.161 Angle : 0.574 7.761 12466 Z= 0.295 Chirality : 0.037 0.236 1478 Planarity : 0.003 0.027 1601 Dihedral : 3.747 27.359 1270 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.63 % Allowed : 16.76 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.24), residues: 1183 helix: 2.86 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -0.58 (0.57), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 13 HIS 0.008 0.001 HIS D 86 PHE 0.014 0.001 PHE Y 34 TYR 0.021 0.002 TYR B 16 ARG 0.006 0.000 ARG C 118 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 847) hydrogen bonds : angle 3.58606 ( 2538) covalent geometry : bond 0.00369 ( 9206) covalent geometry : angle 0.57394 (12466) *********************** 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 306 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 272 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 CYS cc_start: 0.9186 (t) cc_final: 0.8984 (t) REVERT: A 64 GLU cc_start: 0.9362 (tm-30) cc_final: 0.9125 (tm-30) REVERT: A 69 ASN cc_start: 0.8326 (t0) cc_final: 0.7733 (t0) REVERT: A 73 ASP cc_start: 0.9264 (m-30) cc_final: 0.8830 (m-30) REVERT: A 86 HIS cc_start: 0.8756 (t70) cc_final: 0.8497 (t70) REVERT: A 88 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9135 (mm) REVERT: A 89 ASN cc_start: 0.8543 (p0) cc_final: 0.8298 (p0) REVERT: A 150 TRP cc_start: 0.9027 (t-100) cc_final: 0.8576 (t-100) REVERT: A 154 ASN cc_start: 0.9047 (m-40) cc_final: 0.8700 (m110) REVERT: A 166 ASN cc_start: 0.8922 (t0) cc_final: 0.8392 (t0) REVERT: A 227 GLU cc_start: 0.9339 (tp30) cc_final: 0.9114 (tp30) REVERT: B 56 LYS cc_start: 0.9076 (tptm) cc_final: 0.8752 (tppp) REVERT: B 58 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8537 (mm-30) REVERT: B 64 GLU cc_start: 0.8960 (tp30) cc_final: 0.8755 (tp30) REVERT: B 81 LYS cc_start: 0.9364 (mmtm) cc_final: 0.9033 (ptmm) REVERT: B 93 ASN cc_start: 0.9336 (t0) cc_final: 0.8986 (t0) REVERT: B 94 GLU cc_start: 0.9059 (tp30) cc_final: 0.8857 (tp30) REVERT: B 179 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8637 (mm) REVERT: C 18 HIS cc_start: 0.8722 (t70) cc_final: 0.8358 (t-170) REVERT: C 86 HIS cc_start: 0.8663 (t-90) cc_final: 0.8156 (t-170) REVERT: C 90 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8573 (mm-30) REVERT: C 118 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8795 (tpm170) REVERT: C 176 GLU cc_start: 0.8814 (pt0) cc_final: 0.8469 (pt0) REVERT: C 227 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8652 (tm-30) REVERT: D 52 LYS cc_start: 0.8927 (ttpp) cc_final: 0.8688 (ttpp) REVERT: E 13 TRP cc_start: 0.8259 (t60) cc_final: 0.7935 (t60) REVERT: E 18 HIS cc_start: 0.9186 (t70) cc_final: 0.8650 (t-170) REVERT: E 47 GLU cc_start: 0.9099 (tp30) cc_final: 0.8888 (tp30) REVERT: E 58 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8608 (mm-30) REVERT: E 89 ASN cc_start: 0.9033 (m-40) cc_final: 0.8805 (m-40) REVERT: E 93 ASN cc_start: 0.9165 (t0) cc_final: 0.8886 (t0) REVERT: E 125 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8651 (tm-30) REVERT: E 166 ASN cc_start: 0.9231 (t0) cc_final: 0.8945 (t0) REVERT: E 223 ASP cc_start: 0.8992 (t0) cc_final: 0.8774 (t0) REVERT: E 227 GLU cc_start: 0.9339 (tt0) cc_final: 0.9077 (tm-30) REVERT: Z 14 GLU cc_start: 0.8841 (pt0) cc_final: 0.8609 (pt0) outliers start: 34 outliers final: 18 residues processed: 287 average time/residue: 0.1883 time to fit residues: 75.6796 Evaluate side-chains 295 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 274 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 186 VAL Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 181 THR 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 153 MET 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 D residue 36 VAL 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 Z residue 32 ILE Chi-restraints excluded: chain Z residue 33 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 113 optimal weight: 0.0980 chunk 110 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.079352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.062688 restraints weight = 20350.868| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.33 r_work: 0.2771 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9206 Z= 0.132 Angle : 0.554 7.838 12466 Z= 0.286 Chirality : 0.037 0.210 1478 Planarity : 0.003 0.026 1601 Dihedral : 3.658 29.305 1270 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.74 % Allowed : 16.97 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.98 (0.24), residues: 1183 helix: 2.99 (0.15), residues: 1040 sheet: None (None), residues: 0 loop : -0.40 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 13 HIS 0.010 0.001 HIS D 86 PHE 0.014 0.001 PHE B 142 TYR 0.023 0.002 TYR B 132 ARG 0.007 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 847) hydrogen bonds : angle 3.48798 ( 2538) covalent geometry : bond 0.00280 ( 9206) covalent geometry : angle 0.55431 (12466) *********************** 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 315 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8678 (p0) cc_final: 0.8325 (p0) REVERT: A 24 LYS cc_start: 0.8950 (tppp) cc_final: 0.8708 (mmmm) REVERT: A 64 GLU cc_start: 0.9333 (tm-30) cc_final: 0.9097 (tm-30) REVERT: A 69 ASN cc_start: 0.8333 (t0) cc_final: 0.8086 (t0) REVERT: A 85 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8844 (tm) REVERT: A 88 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9166 (mm) REVERT: A 89 ASN cc_start: 0.8520 (p0) cc_final: 0.8263 (p0) REVERT: A 90 GLU cc_start: 0.8467 (tt0) cc_final: 0.8229 (tt0) REVERT: A 150 TRP cc_start: 0.9047 (t-100) cc_final: 0.8680 (t-100) REVERT: A 154 ASN cc_start: 0.9029 (m-40) cc_final: 0.8770 (m110) REVERT: A 166 ASN cc_start: 0.8913 (t0) cc_final: 0.8385 (t0) REVERT: B 56 LYS cc_start: 0.9094 (tptm) cc_final: 0.8782 (tppp) REVERT: B 64 GLU cc_start: 0.9005 (tp30) cc_final: 0.8613 (tp30) REVERT: B 70 GLN cc_start: 0.8935 (tt0) cc_final: 0.8711 (tt0) REVERT: B 81 LYS cc_start: 0.9338 (mmtm) cc_final: 0.9036 (ptmm) REVERT: B 93 ASN cc_start: 0.9349 (t0) cc_final: 0.9017 (t0) REVERT: B 179 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8722 (mm) REVERT: C 18 HIS cc_start: 0.8652 (t70) cc_final: 0.8266 (t-170) REVERT: C 86 HIS cc_start: 0.8612 (t-90) cc_final: 0.8303 (t70) REVERT: C 176 GLU cc_start: 0.8741 (pt0) cc_final: 0.8393 (pt0) REVERT: C 227 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8669 (tm-30) REVERT: D 52 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8683 (ttpp) REVERT: D 64 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8464 (tm-30) REVERT: D 94 GLU cc_start: 0.8985 (tp30) cc_final: 0.8677 (tp30) REVERT: D 132 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7281 (t80) REVERT: D 140 SER cc_start: 0.9275 (m) cc_final: 0.9072 (p) REVERT: E 13 TRP cc_start: 0.8261 (t60) cc_final: 0.7905 (t60) REVERT: E 18 HIS cc_start: 0.9159 (t70) cc_final: 0.8648 (t-170) REVERT: E 58 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8584 (mm-30) REVERT: E 89 ASN cc_start: 0.9048 (m-40) cc_final: 0.8786 (m110) REVERT: E 93 ASN cc_start: 0.9204 (t0) cc_final: 0.8943 (t0) REVERT: E 125 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8691 (tm-30) REVERT: E 223 ASP cc_start: 0.8943 (t0) cc_final: 0.8625 (t0) REVERT: Z 15 MET cc_start: 0.8810 (ptm) cc_final: 0.8566 (ptp) outliers start: 35 outliers final: 16 residues processed: 302 average time/residue: 0.1934 time to fit residues: 81.4003 Evaluate side-chains 279 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 259 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS 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 32 LEU Chi-restraints excluded: chain C residue 118 ARG 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 25 CYS 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 D residue 148 THR Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain Z residue 32 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 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 = 0.3283 r_free = 0.3283 target = 0.079329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.062723 restraints weight = 20211.738| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.27 r_work: 0.2777 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9206 Z= 0.144 Angle : 0.600 9.912 12466 Z= 0.306 Chirality : 0.037 0.224 1478 Planarity : 0.003 0.027 1601 Dihedral : 3.609 29.728 1270 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.31 % Allowed : 19.42 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.99 (0.24), residues: 1183 helix: 3.00 (0.15), residues: 1040 sheet: None (None), residues: 0 loop : -0.47 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 13 HIS 0.009 0.001 HIS D 86 PHE 0.017 0.001 PHE Y 34 TYR 0.022 0.002 TYR B 16 ARG 0.007 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 847) hydrogen bonds : angle 3.49185 ( 2538) covalent geometry : bond 0.00325 ( 9206) covalent geometry : angle 0.60040 (12466) *********************** 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 295 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 264 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8677 (p0) cc_final: 0.8414 (p0) REVERT: A 85 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8868 (tm) REVERT: A 88 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9183 (mm) REVERT: A 89 ASN cc_start: 0.8534 (p0) cc_final: 0.8240 (p0) REVERT: A 150 TRP cc_start: 0.9040 (t-100) cc_final: 0.8686 (t-100) REVERT: A 154 ASN cc_start: 0.9016 (m-40) cc_final: 0.8752 (m110) REVERT: A 166 ASN cc_start: 0.8882 (t0) cc_final: 0.8345 (t0) REVERT: B 56 LYS cc_start: 0.9121 (tptm) cc_final: 0.8783 (tppp) REVERT: B 81 LYS cc_start: 0.9312 (mmtm) cc_final: 0.9043 (ptmm) REVERT: B 93 ASN cc_start: 0.9359 (t0) cc_final: 0.9059 (t0) REVERT: B 115 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9260 (mm) REVERT: B 179 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8725 (mm) REVERT: C 18 HIS cc_start: 0.8761 (t70) cc_final: 0.8516 (t-170) REVERT: C 86 HIS cc_start: 0.8645 (t-90) cc_final: 0.8071 (t-170) REVERT: C 90 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8478 (mm-30) REVERT: C 105 GLU cc_start: 0.8550 (pm20) cc_final: 0.8346 (pp20) REVERT: C 176 GLU cc_start: 0.8751 (pt0) cc_final: 0.8525 (pt0) REVERT: C 227 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8647 (tm-30) REVERT: D 64 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8502 (tm-30) REVERT: D 132 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.7331 (t80) REVERT: D 140 SER cc_start: 0.9294 (m) cc_final: 0.9071 (p) REVERT: E 13 TRP cc_start: 0.8353 (t60) cc_final: 0.7932 (t60) REVERT: E 18 HIS cc_start: 0.9133 (t70) cc_final: 0.8632 (t-170) REVERT: E 58 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8575 (mm-30) REVERT: E 89 ASN cc_start: 0.9058 (m-40) cc_final: 0.8797 (m110) REVERT: E 93 ASN cc_start: 0.9249 (t0) cc_final: 0.9010 (t0) REVERT: E 94 GLU cc_start: 0.9293 (tp30) cc_final: 0.9053 (tp30) REVERT: E 125 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8706 (tm-30) REVERT: E 223 ASP cc_start: 0.8935 (t0) cc_final: 0.8627 (t0) REVERT: Z 15 MET cc_start: 0.8772 (ptm) cc_final: 0.8561 (ptp) outliers start: 31 outliers final: 17 residues processed: 282 average time/residue: 0.1923 time to fit residues: 75.7710 Evaluate side-chains 274 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 252 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 81 LYS 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 118 ARG 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 36 VAL 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 176 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 33 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3288 r_free = 0.3288 target = 0.079616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.063257 restraints weight = 20404.900| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.30 r_work: 0.2790 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3796 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= 0.138 Angle : 0.607 10.523 12466 Z= 0.307 Chirality : 0.038 0.193 1478 Planarity : 0.004 0.127 1601 Dihedral : 3.616 29.475 1270 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.52 % Allowed : 19.96 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.24), residues: 1183 helix: 2.95 (0.15), residues: 1040 sheet: None (None), residues: 0 loop : -0.54 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 13 HIS 0.019 0.002 HIS D 86 PHE 0.033 0.001 PHE Y 34 TYR 0.024 0.002 TYR B 132 ARG 0.007 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 847) hydrogen bonds : angle 3.54394 ( 2538) covalent geometry : bond 0.00302 ( 9206) covalent geometry : angle 0.60654 (12466) *********************** 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 294 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 261 time to evaluate : 0.946 Fit side-chains REVERT: A 20 ASP cc_start: 0.8576 (p0) cc_final: 0.8192 (p0) REVERT: A 24 LYS cc_start: 0.8870 (mmtp) cc_final: 0.8636 (mmmt) REVERT: A 85 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8815 (tm) REVERT: A 88 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9138 (mm) REVERT: A 89 ASN cc_start: 0.8534 (p0) cc_final: 0.8295 (p0) REVERT: A 118 ARG cc_start: 0.8558 (tpp80) cc_final: 0.8265 (tpp80) REVERT: A 150 TRP cc_start: 0.9031 (t-100) cc_final: 0.8681 (t-100) REVERT: A 154 ASN cc_start: 0.8996 (m-40) cc_final: 0.8729 (m110) REVERT: A 166 ASN cc_start: 0.8888 (t0) cc_final: 0.8344 (t0) REVERT: B 56 LYS cc_start: 0.9090 (tptm) cc_final: 0.8744 (tppp) REVERT: B 81 LYS cc_start: 0.9340 (mmtm) cc_final: 0.9040 (ptmm) REVERT: B 93 ASN cc_start: 0.9323 (t0) cc_final: 0.9030 (t0) REVERT: B 115 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9258 (mm) REVERT: B 179 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8747 (mm) REVERT: C 18 HIS cc_start: 0.8731 (t70) cc_final: 0.8494 (t-170) REVERT: C 86 HIS cc_start: 0.8629 (t-90) cc_final: 0.8042 (t-170) REVERT: C 90 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8447 (mm-30) REVERT: C 105 GLU cc_start: 0.8542 (pm20) cc_final: 0.8315 (pp20) REVERT: C 176 GLU cc_start: 0.8744 (pt0) cc_final: 0.8491 (pt0) REVERT: C 227 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8626 (tm-30) REVERT: D 64 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8554 (tm-30) REVERT: D 94 GLU cc_start: 0.9154 (tp30) cc_final: 0.8924 (tp30) REVERT: D 99 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8190 (mm-30) REVERT: D 132 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.7378 (t80) REVERT: D 140 SER cc_start: 0.9287 (m) cc_final: 0.9064 (p) REVERT: E 13 TRP cc_start: 0.8364 (t60) cc_final: 0.7928 (t60) REVERT: E 18 HIS cc_start: 0.9157 (t70) cc_final: 0.8652 (t-170) REVERT: E 58 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8558 (mm-30) REVERT: E 89 ASN cc_start: 0.9047 (m-40) cc_final: 0.8781 (m110) REVERT: E 93 ASN cc_start: 0.9243 (t0) cc_final: 0.9001 (t0) REVERT: E 94 GLU cc_start: 0.9248 (tp30) cc_final: 0.8918 (tp30) REVERT: E 125 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8711 (tm-30) REVERT: E 166 ASN cc_start: 0.9135 (t0) cc_final: 0.8922 (t0) REVERT: E 223 ASP cc_start: 0.8929 (t0) cc_final: 0.8623 (t0) REVERT: Z 15 MET cc_start: 0.8729 (ptm) cc_final: 0.8511 (ptp) outliers start: 33 outliers final: 20 residues processed: 281 average time/residue: 0.1852 time to fit residues: 73.1007 Evaluate side-chains 287 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 262 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 81 LYS 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 32 LEU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 118 ARG 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 36 VAL 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 176 GLU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 33 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 66 optimal weight: 0.0170 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 HIS D 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.081738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.065514 restraints weight = 20880.888| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.26 r_work: 0.2845 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3921 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= 0.139 Angle : 0.630 12.263 12466 Z= 0.315 Chirality : 0.038 0.219 1478 Planarity : 0.004 0.104 1601 Dihedral : 3.584 29.424 1270 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.09 % Allowed : 21.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.24), residues: 1183 helix: 2.98 (0.15), residues: 1038 sheet: None (None), residues: 0 loop : -0.75 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 13 HIS 0.024 0.002 HIS D 86 PHE 0.018 0.001 PHE C 156 TYR 0.025 0.002 TYR B 132 ARG 0.007 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 847) hydrogen bonds : angle 3.53632 ( 2538) covalent geometry : bond 0.00307 ( 9206) covalent geometry : angle 0.63040 (12466) *********************** 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 298 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 269 time to evaluate : 0.961 Fit side-chains REVERT: A 20 ASP cc_start: 0.8588 (p0) cc_final: 0.8198 (p0) REVERT: A 24 LYS cc_start: 0.8874 (mmtp) cc_final: 0.8646 (mmmt) REVERT: A 85 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8801 (tm) REVERT: A 88 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9236 (mm) REVERT: A 89 ASN cc_start: 0.8513 (p0) cc_final: 0.8312 (p0) REVERT: A 118 ARG cc_start: 0.8542 (tpp80) cc_final: 0.8152 (tpp80) REVERT: A 150 TRP cc_start: 0.8989 (t-100) cc_final: 0.8670 (t-100) REVERT: A 154 ASN cc_start: 0.8987 (m-40) cc_final: 0.8717 (m110) REVERT: A 166 ASN cc_start: 0.8887 (t0) cc_final: 0.8597 (t0) REVERT: A 174 ILE cc_start: 0.9040 (pt) cc_final: 0.8808 (pt) REVERT: B 20 ASP cc_start: 0.8792 (t0) cc_final: 0.8564 (t0) REVERT: B 56 LYS cc_start: 0.9087 (tptm) cc_final: 0.8754 (tppp) REVERT: B 81 LYS cc_start: 0.9335 (mmtm) cc_final: 0.9038 (ptmm) REVERT: B 115 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9252 (mm) REVERT: B 118 ARG cc_start: 0.8904 (tpp80) cc_final: 0.8583 (tpp80) REVERT: B 179 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8705 (mm) REVERT: C 86 HIS cc_start: 0.8601 (t-90) cc_final: 0.7988 (t-170) REVERT: C 90 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8426 (mm-30) REVERT: C 105 GLU cc_start: 0.8569 (pm20) cc_final: 0.8328 (pp20) REVERT: C 176 GLU cc_start: 0.8682 (pt0) cc_final: 0.8444 (pt0) REVERT: C 227 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8663 (tm-30) REVERT: D 64 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8571 (tm-30) REVERT: D 94 GLU cc_start: 0.9112 (tp30) cc_final: 0.8521 (tp30) REVERT: D 99 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8215 (mm-30) REVERT: D 132 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.7378 (t80) REVERT: D 140 SER cc_start: 0.9303 (m) cc_final: 0.9074 (p) REVERT: E 13 TRP cc_start: 0.8376 (t60) cc_final: 0.7935 (t60) REVERT: E 18 HIS cc_start: 0.9149 (t70) cc_final: 0.8636 (t-170) REVERT: E 58 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8582 (mm-30) REVERT: E 89 ASN cc_start: 0.9058 (m-40) cc_final: 0.8762 (m110) REVERT: E 93 ASN cc_start: 0.9265 (t0) cc_final: 0.9011 (t0) REVERT: E 94 GLU cc_start: 0.9263 (tp30) cc_final: 0.8958 (tp30) REVERT: E 125 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8762 (tm-30) REVERT: E 166 ASN cc_start: 0.9107 (t0) cc_final: 0.8846 (t0) REVERT: E 223 ASP cc_start: 0.8948 (t0) cc_final: 0.8649 (t0) REVERT: Z 15 MET cc_start: 0.8684 (ptm) cc_final: 0.8461 (ptp) outliers start: 29 outliers final: 16 residues processed: 284 average time/residue: 0.2046 time to fit residues: 80.5011 Evaluate side-chains 279 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 258 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 81 LYS 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 118 ARG 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 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 E residue 206 LYS Chi-restraints excluded: chain Z residue 32 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 3 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.079486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.063022 restraints weight = 20396.460| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.29 r_work: 0.2788 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3956 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= 0.152 Angle : 0.654 11.840 12466 Z= 0.326 Chirality : 0.039 0.254 1478 Planarity : 0.004 0.096 1601 Dihedral : 3.571 30.316 1270 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.88 % Allowed : 21.56 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.99 (0.24), residues: 1183 helix: 3.04 (0.15), residues: 1037 sheet: None (None), residues: 0 loop : -0.73 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 13 HIS 0.015 0.002 HIS C 18 PHE 0.037 0.001 PHE Y 34 TYR 0.022 0.001 TYR B 132 ARG 0.007 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 847) hydrogen bonds : angle 3.54287 ( 2538) covalent geometry : bond 0.00345 ( 9206) covalent geometry : angle 0.65355 (12466) *********************** 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 284 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 257 time to evaluate : 1.057 Fit side-chains REVERT: A 15 MET cc_start: 0.8947 (pmm) cc_final: 0.8742 (pmm) REVERT: A 20 ASP cc_start: 0.8620 (p0) cc_final: 0.8208 (p0) REVERT: A 24 LYS cc_start: 0.8870 (mmtp) cc_final: 0.8631 (mmmt) REVERT: A 85 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8785 (tm) REVERT: A 88 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9193 (mm) REVERT: A 118 ARG cc_start: 0.8627 (tpp80) cc_final: 0.8245 (tpp80) REVERT: A 150 TRP cc_start: 0.8992 (t-100) cc_final: 0.8690 (t-100) REVERT: A 154 ASN cc_start: 0.8999 (m-40) cc_final: 0.8742 (m110) REVERT: A 166 ASN cc_start: 0.8863 (t0) cc_final: 0.8576 (t0) REVERT: B 81 LYS cc_start: 0.9317 (mmtm) cc_final: 0.9014 (ptmm) REVERT: B 118 ARG cc_start: 0.8918 (tpp80) cc_final: 0.8227 (tpp80) REVERT: C 86 HIS cc_start: 0.8651 (t-90) cc_final: 0.8037 (t-170) REVERT: C 90 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8439 (mm-30) REVERT: C 105 GLU cc_start: 0.8556 (pm20) cc_final: 0.8350 (pp20) REVERT: C 176 GLU cc_start: 0.8742 (pt0) cc_final: 0.8499 (pt0) REVERT: C 227 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8643 (tm-30) REVERT: D 32 LEU cc_start: 0.9060 (mm) cc_final: 0.8858 (mm) REVERT: D 64 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8565 (tm-30) REVERT: D 94 GLU cc_start: 0.9092 (tp30) cc_final: 0.8528 (tp30) REVERT: D 96 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8459 (mp0) REVERT: D 132 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.7412 (t80) REVERT: E 13 TRP cc_start: 0.8417 (t60) cc_final: 0.7986 (t60) REVERT: E 18 HIS cc_start: 0.9175 (t70) cc_final: 0.8647 (t-170) REVERT: E 58 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8572 (mm-30) REVERT: E 89 ASN cc_start: 0.9050 (m-40) cc_final: 0.8772 (m110) REVERT: E 93 ASN cc_start: 0.9244 (t0) cc_final: 0.9014 (t0) REVERT: E 94 GLU cc_start: 0.9255 (tp30) cc_final: 0.8928 (tp30) REVERT: E 125 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8707 (tm-30) REVERT: E 166 ASN cc_start: 0.9079 (t0) cc_final: 0.8796 (t0) REVERT: E 223 ASP cc_start: 0.8957 (t0) cc_final: 0.8662 (t0) REVERT: Z 15 MET cc_start: 0.8707 (ptm) cc_final: 0.8481 (ptp) outliers start: 27 outliers final: 17 residues processed: 276 average time/residue: 0.1957 time to fit residues: 75.6218 Evaluate side-chains 278 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 258 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 81 LYS 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 C residue 101 SER Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 VAL 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 E residue 206 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 38 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.081733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.065454 restraints weight = 20738.056| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.23 r_work: 0.2840 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9206 Z= 0.154 Angle : 0.664 12.322 12466 Z= 0.332 Chirality : 0.039 0.230 1478 Planarity : 0.003 0.085 1601 Dihedral : 3.560 30.276 1270 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.45 % Allowed : 22.73 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.97 (0.24), residues: 1183 helix: 3.02 (0.15), residues: 1037 sheet: None (None), residues: 0 loop : -0.72 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 13 HIS 0.008 0.001 HIS D 86 PHE 0.015 0.001 PHE C 156 TYR 0.021 0.002 TYR B 132 ARG 0.006 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 847) hydrogen bonds : angle 3.55260 ( 2538) covalent geometry : bond 0.00349 ( 9206) covalent geometry : angle 0.66439 (12466) ********************** 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 285 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 262 time to evaluate : 1.124 Fit side-chains REVERT: A 20 ASP cc_start: 0.8646 (p0) cc_final: 0.8205 (p0) REVERT: A 24 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8657 (mmmt) REVERT: A 88 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9117 (mm) REVERT: A 118 ARG cc_start: 0.8653 (tpp80) cc_final: 0.8208 (tpp80) REVERT: A 150 TRP cc_start: 0.8980 (t-100) cc_final: 0.8673 (t-100) REVERT: A 154 ASN cc_start: 0.8997 (m-40) cc_final: 0.8627 (m110) REVERT: A 166 ASN cc_start: 0.8855 (t0) cc_final: 0.8563 (t0) REVERT: B 56 LYS cc_start: 0.9162 (tppp) cc_final: 0.8811 (tppp) REVERT: B 81 LYS cc_start: 0.9313 (mmtm) cc_final: 0.9030 (ptmm) REVERT: B 118 ARG cc_start: 0.8922 (tpp80) cc_final: 0.8238 (tpp80) REVERT: B 179 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8748 (mm) REVERT: C 86 HIS cc_start: 0.8644 (t-90) cc_final: 0.8020 (t-170) REVERT: C 90 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8417 (mm-30) REVERT: C 105 GLU cc_start: 0.8564 (pm20) cc_final: 0.8364 (pp20) REVERT: C 176 GLU cc_start: 0.8632 (pt0) cc_final: 0.8401 (pt0) REVERT: C 227 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8661 (tm-30) REVERT: D 15 MET cc_start: 0.9150 (ptp) cc_final: 0.8610 (pmm) REVERT: D 32 LEU cc_start: 0.9090 (mm) cc_final: 0.8880 (mm) REVERT: D 64 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8593 (tm-30) REVERT: D 94 GLU cc_start: 0.9098 (tp30) cc_final: 0.8466 (tp30) REVERT: D 128 ARG cc_start: 0.8757 (tpp80) cc_final: 0.8045 (tpp80) REVERT: D 132 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7423 (t80) REVERT: E 13 TRP cc_start: 0.8403 (t60) cc_final: 0.7972 (t60) REVERT: E 18 HIS cc_start: 0.9147 (t70) cc_final: 0.8649 (t-170) REVERT: E 58 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8560 (mm-30) REVERT: E 89 ASN cc_start: 0.9074 (m-40) cc_final: 0.8775 (m110) REVERT: E 93 ASN cc_start: 0.9274 (t0) cc_final: 0.9043 (t0) REVERT: E 125 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8747 (tm-30) REVERT: E 166 ASN cc_start: 0.9054 (t0) cc_final: 0.8770 (t0) REVERT: E 223 ASP cc_start: 0.8966 (t0) cc_final: 0.8695 (t0) REVERT: Z 15 MET cc_start: 0.8708 (ptm) cc_final: 0.8470 (ptp) outliers start: 23 outliers final: 15 residues processed: 278 average time/residue: 0.2302 time to fit residues: 90.1091 Evaluate side-chains 273 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 81 LYS 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 179 LEU Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 VAL 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 E residue 206 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 0.0970 chunk 86 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS C 18 HIS ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.078561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.062169 restraints weight = 20681.057| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.26 r_work: 0.2772 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9206 Z= 0.173 Angle : 0.681 11.724 12466 Z= 0.340 Chirality : 0.040 0.268 1478 Planarity : 0.003 0.074 1601 Dihedral : 3.580 31.121 1270 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.56 % Allowed : 22.09 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.24), residues: 1183 helix: 2.99 (0.15), residues: 1039 sheet: None (None), residues: 0 loop : -0.71 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 13 HIS 0.009 0.002 HIS A 18 PHE 0.023 0.001 PHE Y 34 TYR 0.018 0.002 TYR B 132 ARG 0.008 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 847) hydrogen bonds : angle 3.60261 ( 2538) covalent geometry : bond 0.00399 ( 9206) covalent geometry : angle 0.68070 (12466) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3905.08 seconds wall clock time: 68 minutes 24.49 seconds (4104.49 seconds total)