Starting phenix.real_space_refine on Wed Feb 4 02:42:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i6b_52652/02_2026/9i6b_52652.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i6b_52652/02_2026/9i6b_52652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i6b_52652/02_2026/9i6b_52652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i6b_52652/02_2026/9i6b_52652.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i6b_52652/02_2026/9i6b_52652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i6b_52652/02_2026/9i6b_52652.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 24 5.16 5 C 5646 2.51 5 N 1339 2.21 5 O 1624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8644 Number of models: 1 Model: "" Number of chains: 18 Chain: "C" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 451 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "E" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 326 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "G" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 298 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "I" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 46} Chain: "A" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2466 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 305} Chain breaks: 1 Chain: "D" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 451 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "F" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 326 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "H" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 298 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "J" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 46} Chain: "B" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2466 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 305} Chain breaks: 1 Chain: "C" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 87 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'DU0': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "A" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 221 Unusual residues: {'DU0': 3, 'PC1': 2, 'PLC': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 40 Chain: "D" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 87 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "H" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'DU0': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 179 Unusual residues: {'DU0': 3, 'PC1': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 40 Time building chain proxies: 2.04, per 1000 atoms: 0.24 Number of scatterers: 8644 At special positions: 0 Unit cell: (135.801, 115.173, 91.107, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 11 15.00 O 1624 8.00 N 1339 7.00 C 5646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 205.8 milliseconds 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1888 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 40.0% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'C' and resid 62 through 117 Proline residue: C 100 - end of helix Processing helix chain 'E' and resid 11 through 50 removed outlier: 3.733A pdb=" N ARG E 16 " --> pdb=" O PRO E 12 " (cutoff:3.500A) Proline residue: E 40 - end of helix Processing helix chain 'G' and resid 17 through 26 removed outlier: 3.993A pdb=" N ALA G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 48 Processing helix chain 'G' and resid 49 through 56 Processing helix chain 'I' and resid 23 through 57 removed outlier: 5.587A pdb=" N LEU I 46 " --> pdb=" O HIS I 42 " (cutoff:3.500A) Proline residue: I 47 - end of helix Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'A' and resid 22 through 34 removed outlier: 3.608A pdb=" N ALA A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 332 through 337 removed outlier: 3.826A pdb=" N LEU A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 117 Proline residue: D 100 - end of helix Processing helix chain 'F' and resid 11 through 50 removed outlier: 3.733A pdb=" N ARG F 16 " --> pdb=" O PRO F 12 " (cutoff:3.500A) Proline residue: F 40 - end of helix Processing helix chain 'H' and resid 17 through 26 removed outlier: 3.993A pdb=" N ALA H 23 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 48 Processing helix chain 'H' and resid 49 through 56 Processing helix chain 'J' and resid 23 through 57 removed outlier: 5.587A pdb=" N LEU J 46 " --> pdb=" O HIS J 42 " (cutoff:3.500A) Proline residue: J 47 - end of helix Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'B' and resid 22 through 34 removed outlier: 3.608A pdb=" N ALA B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 332 through 337 removed outlier: 3.826A pdb=" N LEU B 336 " --> pdb=" O GLY B 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 73 removed outlier: 6.401A pdb=" N PHE A 78 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA A 146 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR A 174 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 73 removed outlier: 6.401A pdb=" N PHE B 78 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA B 146 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR B 174 " --> pdb=" O PRO B 166 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1698 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1342 1.32 - 1.44: 2320 1.44 - 1.56: 5103 1.56 - 1.68: 28 1.68 - 1.80: 46 Bond restraints: 8839 Sorted by residual: bond pdb=" CB PRO F 8 " pdb=" CG PRO F 8 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.31e+00 bond pdb=" CB PRO E 8 " pdb=" CG PRO E 8 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.31e+00 bond pdb=" CG1 ILE B 327 " pdb=" CD1 ILE B 327 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.41e+00 bond pdb=" CG1 ILE A 327 " pdb=" CD1 ILE A 327 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.41e+00 bond pdb=" CG LEU B 193 " pdb=" CD1 LEU B 193 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.31e+00 ... (remaining 8834 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 11296 1.71 - 3.42: 557 3.42 - 5.12: 92 5.12 - 6.83: 36 6.83 - 8.54: 10 Bond angle restraints: 11991 Sorted by residual: angle pdb=" CA PRO E 12 " pdb=" N PRO E 12 " pdb=" CD PRO E 12 " ideal model delta sigma weight residual 112.00 105.51 6.49 1.40e+00 5.10e-01 2.15e+01 angle pdb=" CA PRO F 12 " pdb=" N PRO F 12 " pdb=" CD PRO F 12 " ideal model delta sigma weight residual 112.00 105.51 6.49 1.40e+00 5.10e-01 2.15e+01 angle pdb=" N GLY A 332 " pdb=" CA GLY A 332 " pdb=" C GLY A 332 " ideal model delta sigma weight residual 112.73 118.18 -5.45 1.20e+00 6.94e-01 2.06e+01 angle pdb=" N GLY B 332 " pdb=" CA GLY B 332 " pdb=" C GLY B 332 " ideal model delta sigma weight residual 112.73 118.18 -5.45 1.20e+00 6.94e-01 2.06e+01 angle pdb=" CA PRO F 40 " pdb=" N PRO F 40 " pdb=" CD PRO F 40 " ideal model delta sigma weight residual 112.00 106.13 5.87 1.40e+00 5.10e-01 1.76e+01 ... (remaining 11986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.58: 5418 27.58 - 55.15: 347 55.15 - 82.73: 96 82.73 - 110.30: 34 110.30 - 137.87: 18 Dihedral angle restraints: 5913 sinusoidal: 2975 harmonic: 2938 Sorted by residual: dihedral pdb=" CD ARG E 16 " pdb=" NE ARG E 16 " pdb=" CZ ARG E 16 " pdb=" NH1 ARG E 16 " ideal model delta sinusoidal sigma weight residual 0.00 68.09 -68.09 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CD ARG F 16 " pdb=" NE ARG F 16 " pdb=" CZ ARG F 16 " pdb=" NH1 ARG F 16 " ideal model delta sinusoidal sigma weight residual 0.00 68.09 -68.09 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" C26 DU0 A 403 " pdb=" C24 DU0 A 403 " pdb=" C25 DU0 A 403 " pdb=" O23 DU0 A 403 " ideal model delta sinusoidal sigma weight residual 189.32 51.45 137.87 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 5910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 975 0.055 - 0.111: 278 0.111 - 0.166: 62 0.166 - 0.221: 8 0.221 - 0.277: 6 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CB VAL A 249 " pdb=" CA VAL A 249 " pdb=" CG1 VAL A 249 " pdb=" CG2 VAL A 249 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB VAL B 249 " pdb=" CA VAL B 249 " pdb=" CG1 VAL B 249 " pdb=" CG2 VAL B 249 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA PRO F 40 " pdb=" N PRO F 40 " pdb=" C PRO F 40 " pdb=" CB PRO F 40 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1326 not shown) Planarity restraints: 1428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 16 " -0.843 9.50e-02 1.11e+02 3.79e-01 1.01e+02 pdb=" NE ARG E 16 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG E 16 " -0.054 2.00e-02 2.50e+03 pdb=" NH1 ARG E 16 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG E 16 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 16 " 0.843 9.50e-02 1.11e+02 3.79e-01 1.01e+02 pdb=" NE ARG F 16 " -0.074 2.00e-02 2.50e+03 pdb=" CZ ARG F 16 " 0.054 2.00e-02 2.50e+03 pdb=" NH1 ARG F 16 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG F 16 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 11 " -0.083 5.00e-02 4.00e+02 1.22e-01 2.37e+01 pdb=" N PRO E 12 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO E 12 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO E 12 " -0.066 5.00e-02 4.00e+02 ... (remaining 1425 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2093 2.81 - 3.33: 7421 3.33 - 3.86: 13932 3.86 - 4.38: 16811 4.38 - 4.90: 29427 Nonbonded interactions: 69684 Sorted by model distance: nonbonded pdb=" OH TYR A 237 " pdb=" OE1 GLN A 239 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR B 237 " pdb=" OE1 GLN B 239 " model vdw 2.288 3.040 nonbonded pdb=" OE2 GLU A 88 " pdb=" NH1 ARG A 89 " model vdw 2.293 3.120 nonbonded pdb=" OE2 GLU B 88 " pdb=" NH1 ARG B 89 " model vdw 2.293 3.120 nonbonded pdb=" OG SER A 73 " pdb=" O PRO A 76 " model vdw 2.296 3.040 ... (remaining 69679 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 21 through 347 or resid 403 or resid 405)) selection = (chain 'B' and (resid 21 through 347 or resid 403 or resid 405)) } ncs_group { reference = (chain 'C' and (resid 62 through 118 or (resid 201 through 202 and (name N or na \ me C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C2A or name C2B or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or n \ ame C39 or name C3A or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) selection = (chain 'D' and (resid 62 through 201 or (resid 202 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C2A or name C2B or name C3 or name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ ame C3A or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )))) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 13.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 7.970 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.007 0.091 8839 Z= 0.302 Angle : 0.904 8.540 11991 Z= 0.464 Chirality : 0.056 0.277 1329 Planarity : 0.017 0.379 1428 Dihedral : 21.113 137.875 4025 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.25), residues: 996 helix: 0.28 (0.23), residues: 368 sheet: 1.43 (0.25), residues: 396 loop : -0.11 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.064 0.004 ARG E 16 TYR 0.014 0.002 TYR J 43 PHE 0.018 0.002 PHE G 45 TRP 0.032 0.004 TRP B 197 HIS 0.004 0.002 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00735 ( 8839) covalent geometry : angle 0.90362 (11991) hydrogen bonds : bond 0.17739 ( 590) hydrogen bonds : angle 7.19866 ( 1698) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.284 Fit side-chains REVERT: C 109 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7838 (mm-40) REVERT: E 49 MET cc_start: 0.5807 (mmm) cc_final: 0.5485 (mtm) REVERT: A 48 LYS cc_start: 0.7919 (tttt) cc_final: 0.7643 (ttpp) REVERT: A 145 MET cc_start: 0.7625 (mtm) cc_final: 0.7390 (mmm) REVERT: A 151 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7490 (tt0) REVERT: A 217 LYS cc_start: 0.8700 (tttp) cc_final: 0.8322 (tttp) REVERT: A 308 MET cc_start: 0.8375 (mmm) cc_final: 0.7553 (tmt) REVERT: D 109 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7834 (mm-40) REVERT: F 49 MET cc_start: 0.5806 (mmm) cc_final: 0.5485 (mtm) REVERT: B 48 LYS cc_start: 0.7922 (tttt) cc_final: 0.7644 (ttpp) REVERT: B 145 MET cc_start: 0.7627 (mtm) cc_final: 0.7392 (mmm) REVERT: B 151 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7491 (tt0) REVERT: B 217 LYS cc_start: 0.8700 (tttp) cc_final: 0.8322 (tttp) REVERT: B 308 MET cc_start: 0.8378 (mmm) cc_final: 0.7552 (tmt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.6853 time to fit residues: 94.8552 Evaluate side-chains 80 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 83 GLN A 135 GLN B 29 GLN B 83 GLN B 135 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.181070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131569 restraints weight = 7995.568| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.75 r_work: 0.3247 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8839 Z= 0.163 Angle : 0.652 6.737 11991 Z= 0.331 Chirality : 0.043 0.168 1329 Planarity : 0.005 0.052 1428 Dihedral : 17.875 139.656 2227 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.97 % Allowed : 8.25 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.27), residues: 996 helix: 2.03 (0.26), residues: 370 sheet: 1.41 (0.25), residues: 394 loop : 0.27 (0.46), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 215 TYR 0.009 0.001 TYR I 43 PHE 0.011 0.001 PHE A 72 TRP 0.014 0.002 TRP B 197 HIS 0.002 0.001 HIS B 150 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8839) covalent geometry : angle 0.65172 (11991) hydrogen bonds : bond 0.04383 ( 590) hydrogen bonds : angle 5.07158 ( 1698) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.222 Fit side-chains REVERT: C 109 GLN cc_start: 0.7613 (mm-40) cc_final: 0.7340 (mm-40) REVERT: E 49 MET cc_start: 0.5716 (mmm) cc_final: 0.5321 (mtp) REVERT: A 48 LYS cc_start: 0.7963 (tttt) cc_final: 0.7524 (ttpp) REVERT: A 145 MET cc_start: 0.8010 (mtm) cc_final: 0.7761 (mmm) REVERT: A 301 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7088 (tpt170) REVERT: A 308 MET cc_start: 0.8772 (mmm) cc_final: 0.7724 (tmt) REVERT: D 109 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7339 (mm-40) REVERT: F 49 MET cc_start: 0.5713 (mmm) cc_final: 0.5318 (mtp) REVERT: B 48 LYS cc_start: 0.7962 (tttt) cc_final: 0.7524 (ttpp) REVERT: B 145 MET cc_start: 0.8024 (mtm) cc_final: 0.7771 (mmm) REVERT: B 301 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7114 (tpt170) REVERT: B 308 MET cc_start: 0.8762 (mmm) cc_final: 0.7688 (tmt) outliers start: 8 outliers final: 2 residues processed: 100 average time/residue: 0.6224 time to fit residues: 65.6711 Evaluate side-chains 88 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 301 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 21 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.182571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133876 restraints weight = 7995.308| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.72 r_work: 0.3263 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8839 Z= 0.126 Angle : 0.550 5.549 11991 Z= 0.285 Chirality : 0.040 0.151 1329 Planarity : 0.004 0.044 1428 Dihedral : 16.049 132.566 2227 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.21 % Allowed : 11.17 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.27), residues: 996 helix: 2.51 (0.26), residues: 372 sheet: 1.12 (0.25), residues: 404 loop : -0.07 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 133 TYR 0.008 0.001 TYR J 45 PHE 0.009 0.001 PHE H 45 TRP 0.014 0.001 TRP B 197 HIS 0.001 0.001 HIS D 67 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8839) covalent geometry : angle 0.54996 (11991) hydrogen bonds : bond 0.03477 ( 590) hydrogen bonds : angle 4.64145 ( 1698) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.320 Fit side-chains REVERT: C 109 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7341 (mm-40) REVERT: E 49 MET cc_start: 0.5752 (mmm) cc_final: 0.5351 (mtp) REVERT: A 48 LYS cc_start: 0.7903 (tttt) cc_final: 0.7471 (ttpp) REVERT: A 151 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7510 (tt0) REVERT: A 215 ARG cc_start: 0.8704 (ttp-170) cc_final: 0.8342 (ttm-80) REVERT: A 308 MET cc_start: 0.8752 (mmm) cc_final: 0.7685 (tmt) REVERT: D 109 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7389 (mm-40) REVERT: F 49 MET cc_start: 0.5748 (mmm) cc_final: 0.5349 (mtp) REVERT: B 48 LYS cc_start: 0.7895 (tttt) cc_final: 0.7463 (ttpp) REVERT: B 151 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7514 (tt0) REVERT: B 215 ARG cc_start: 0.8708 (ttp-170) cc_final: 0.8347 (ttm-80) REVERT: B 308 MET cc_start: 0.8720 (mmm) cc_final: 0.7670 (tmt) outliers start: 10 outliers final: 2 residues processed: 100 average time/residue: 0.5863 time to fit residues: 61.9351 Evaluate side-chains 92 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 129 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 27 GLN J 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.179817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.130540 restraints weight = 8192.964| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.76 r_work: 0.3224 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8839 Z= 0.165 Angle : 0.571 5.528 11991 Z= 0.295 Chirality : 0.041 0.142 1329 Planarity : 0.004 0.044 1428 Dihedral : 15.756 128.413 2227 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.21 % Allowed : 12.86 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.27), residues: 996 helix: 2.64 (0.26), residues: 372 sheet: 1.09 (0.25), residues: 404 loop : -0.13 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 133 TYR 0.008 0.001 TYR I 45 PHE 0.011 0.002 PHE D 101 TRP 0.013 0.002 TRP B 197 HIS 0.002 0.001 HIS D 67 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8839) covalent geometry : angle 0.57122 (11991) hydrogen bonds : bond 0.03534 ( 590) hydrogen bonds : angle 4.67829 ( 1698) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.200 Fit side-chains REVERT: C 109 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7304 (mm-40) REVERT: E 49 MET cc_start: 0.5744 (mmm) cc_final: 0.5313 (mtp) REVERT: A 48 LYS cc_start: 0.7916 (tttt) cc_final: 0.7476 (ttpp) REVERT: A 144 ASP cc_start: 0.7787 (m-30) cc_final: 0.7525 (m-30) REVERT: A 151 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7502 (tt0) REVERT: A 308 MET cc_start: 0.8727 (mmm) cc_final: 0.7616 (tmt) REVERT: D 109 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7316 (mm-40) REVERT: F 49 MET cc_start: 0.5741 (mmm) cc_final: 0.5315 (mtp) REVERT: B 48 LYS cc_start: 0.7914 (tttt) cc_final: 0.7475 (ttpp) REVERT: B 144 ASP cc_start: 0.7794 (m-30) cc_final: 0.7528 (m-30) REVERT: B 151 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7508 (tt0) REVERT: B 308 MET cc_start: 0.8684 (mmm) cc_final: 0.7604 (tmt) outliers start: 10 outliers final: 2 residues processed: 98 average time/residue: 0.5460 time to fit residues: 56.7701 Evaluate side-chains 88 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 129 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.181401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.132814 restraints weight = 8169.726| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.73 r_work: 0.3232 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8839 Z= 0.147 Angle : 0.545 5.640 11991 Z= 0.281 Chirality : 0.040 0.135 1329 Planarity : 0.004 0.047 1428 Dihedral : 15.134 120.829 2227 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.18 % Allowed : 11.65 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.27), residues: 996 helix: 2.88 (0.26), residues: 372 sheet: 1.01 (0.26), residues: 404 loop : -0.09 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 56 TYR 0.008 0.001 TYR J 45 PHE 0.009 0.001 PHE G 45 TRP 0.013 0.001 TRP A 197 HIS 0.002 0.001 HIS D 67 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8839) covalent geometry : angle 0.54486 (11991) hydrogen bonds : bond 0.03255 ( 590) hydrogen bonds : angle 4.54099 ( 1698) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.309 Fit side-chains REVERT: C 109 GLN cc_start: 0.7580 (mm-40) cc_final: 0.7274 (mm-40) REVERT: E 49 MET cc_start: 0.5685 (mmm) cc_final: 0.5283 (mtp) REVERT: A 48 LYS cc_start: 0.7865 (tttt) cc_final: 0.7410 (ttpp) REVERT: A 151 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7498 (tt0) REVERT: A 161 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7817 (tp) REVERT: A 215 ARG cc_start: 0.8705 (ttp-170) cc_final: 0.8363 (ttm-80) REVERT: A 308 MET cc_start: 0.8664 (mmm) cc_final: 0.7657 (tmt) REVERT: D 109 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7310 (mm-40) REVERT: F 49 MET cc_start: 0.5680 (mmm) cc_final: 0.5281 (mtp) REVERT: B 48 LYS cc_start: 0.7859 (tttt) cc_final: 0.7405 (ttpp) REVERT: B 151 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7498 (tt0) REVERT: B 161 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7819 (tp) REVERT: B 215 ARG cc_start: 0.8707 (ttp-170) cc_final: 0.8369 (ttm-80) REVERT: B 301 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7326 (tpt170) REVERT: B 308 MET cc_start: 0.8626 (mmm) cc_final: 0.7628 (tmt) outliers start: 18 outliers final: 10 residues processed: 98 average time/residue: 0.5175 time to fit residues: 53.8755 Evaluate side-chains 102 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 301 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 39 optimal weight: 0.6980 chunk 42 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 76 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.182990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.134106 restraints weight = 8119.994| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.75 r_work: 0.3272 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8839 Z= 0.105 Angle : 0.493 5.590 11991 Z= 0.255 Chirality : 0.038 0.136 1329 Planarity : 0.004 0.047 1428 Dihedral : 14.337 108.427 2227 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.21 % Allowed : 12.62 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.28), residues: 996 helix: 3.11 (0.26), residues: 372 sheet: 0.95 (0.26), residues: 404 loop : 0.07 (0.47), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 133 TYR 0.009 0.001 TYR I 45 PHE 0.007 0.001 PHE H 45 TRP 0.012 0.001 TRP B 197 HIS 0.001 0.000 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8839) covalent geometry : angle 0.49274 (11991) hydrogen bonds : bond 0.02779 ( 590) hydrogen bonds : angle 4.30585 ( 1698) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.370 Fit side-chains REVERT: C 109 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7312 (mm-40) REVERT: E 49 MET cc_start: 0.5647 (mmm) cc_final: 0.5231 (mtp) REVERT: A 48 LYS cc_start: 0.7847 (tttt) cc_final: 0.7424 (ttpp) REVERT: A 130 THR cc_start: 0.8692 (m) cc_final: 0.8458 (t) REVERT: A 144 ASP cc_start: 0.7742 (m-30) cc_final: 0.7485 (m-30) REVERT: A 151 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7477 (tt0) REVERT: A 215 ARG cc_start: 0.8681 (ttp-170) cc_final: 0.8371 (ttm-80) REVERT: A 308 MET cc_start: 0.8678 (mmm) cc_final: 0.7595 (tmt) REVERT: D 109 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7337 (mm-40) REVERT: F 49 MET cc_start: 0.5644 (mmm) cc_final: 0.5230 (mtp) REVERT: B 48 LYS cc_start: 0.7841 (tttt) cc_final: 0.7420 (ttpp) REVERT: B 130 THR cc_start: 0.8698 (m) cc_final: 0.8464 (t) REVERT: B 144 ASP cc_start: 0.7730 (m-30) cc_final: 0.7480 (m-30) REVERT: B 151 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7476 (tt0) REVERT: B 215 ARG cc_start: 0.8684 (ttp-170) cc_final: 0.8376 (ttm-80) REVERT: B 308 MET cc_start: 0.8612 (mmm) cc_final: 0.7545 (tmt) outliers start: 10 outliers final: 6 residues processed: 104 average time/residue: 0.5552 time to fit residues: 61.1724 Evaluate side-chains 96 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 249 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 234 ASN B 226 GLN B 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.183156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.134475 restraints weight = 8192.492| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.73 r_work: 0.3245 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8839 Z= 0.132 Angle : 0.520 5.618 11991 Z= 0.268 Chirality : 0.039 0.136 1329 Planarity : 0.004 0.046 1428 Dihedral : 14.187 102.047 2227 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.70 % Allowed : 12.26 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.28), residues: 996 helix: 3.10 (0.26), residues: 372 sheet: 0.98 (0.26), residues: 404 loop : 0.02 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 56 TYR 0.008 0.001 TYR I 45 PHE 0.010 0.001 PHE D 101 TRP 0.012 0.001 TRP B 197 HIS 0.001 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8839) covalent geometry : angle 0.52028 (11991) hydrogen bonds : bond 0.02994 ( 590) hydrogen bonds : angle 4.37948 ( 1698) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.313 Fit side-chains REVERT: C 109 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7274 (mm-40) REVERT: E 49 MET cc_start: 0.5670 (mmm) cc_final: 0.5244 (mtp) REVERT: A 48 LYS cc_start: 0.7858 (tttt) cc_final: 0.7406 (ttpp) REVERT: A 144 ASP cc_start: 0.7703 (m-30) cc_final: 0.7370 (m-30) REVERT: A 151 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7469 (tt0) REVERT: A 215 ARG cc_start: 0.8710 (ttp-170) cc_final: 0.8388 (ttm-80) REVERT: A 250 ASP cc_start: 0.8883 (t70) cc_final: 0.8682 (t70) REVERT: A 308 MET cc_start: 0.8662 (mmm) cc_final: 0.7673 (tmt) REVERT: D 109 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7311 (mm-40) REVERT: F 49 MET cc_start: 0.5668 (mmm) cc_final: 0.5243 (mtp) REVERT: B 48 LYS cc_start: 0.7863 (tttt) cc_final: 0.7412 (ttpp) REVERT: B 144 ASP cc_start: 0.7699 (m-30) cc_final: 0.7367 (m-30) REVERT: B 151 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7472 (tt0) REVERT: B 215 ARG cc_start: 0.8710 (ttp-170) cc_final: 0.8390 (ttm-80) REVERT: B 308 MET cc_start: 0.8590 (mmm) cc_final: 0.7645 (tmt) outliers start: 14 outliers final: 6 residues processed: 102 average time/residue: 0.5046 time to fit residues: 54.8056 Evaluate side-chains 107 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 249 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 58 optimal weight: 0.0060 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.182966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.133846 restraints weight = 8126.066| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.75 r_work: 0.3263 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8839 Z= 0.111 Angle : 0.498 5.611 11991 Z= 0.258 Chirality : 0.038 0.136 1329 Planarity : 0.004 0.048 1428 Dihedral : 13.754 92.410 2227 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.97 % Allowed : 12.99 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.28), residues: 996 helix: 3.22 (0.26), residues: 370 sheet: 0.95 (0.26), residues: 404 loop : 0.05 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 56 TYR 0.008 0.001 TYR J 45 PHE 0.007 0.001 PHE G 45 TRP 0.012 0.001 TRP B 197 HIS 0.001 0.000 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8839) covalent geometry : angle 0.49811 (11991) hydrogen bonds : bond 0.02777 ( 590) hydrogen bonds : angle 4.27375 ( 1698) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 109 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7272 (mm-40) REVERT: E 49 MET cc_start: 0.5646 (mmm) cc_final: 0.5216 (mtp) REVERT: A 48 LYS cc_start: 0.7822 (tttt) cc_final: 0.7383 (ttpp) REVERT: A 144 ASP cc_start: 0.7734 (m-30) cc_final: 0.7420 (m-30) REVERT: A 151 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7494 (tt0) REVERT: A 215 ARG cc_start: 0.8697 (ttp-170) cc_final: 0.8391 (ttm-80) REVERT: A 308 MET cc_start: 0.8667 (mmm) cc_final: 0.7611 (tmt) REVERT: D 109 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7343 (mm-40) REVERT: F 49 MET cc_start: 0.5641 (mmm) cc_final: 0.5215 (mtp) REVERT: B 48 LYS cc_start: 0.7806 (tttt) cc_final: 0.7367 (ttpp) REVERT: B 144 ASP cc_start: 0.7737 (m-30) cc_final: 0.7413 (m-30) REVERT: B 151 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7497 (tt0) REVERT: B 215 ARG cc_start: 0.8697 (ttp-170) cc_final: 0.8394 (ttm-80) REVERT: B 308 MET cc_start: 0.8605 (mmm) cc_final: 0.7580 (tmt) outliers start: 8 outliers final: 6 residues processed: 103 average time/residue: 0.4904 time to fit residues: 53.8478 Evaluate side-chains 98 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 249 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 1 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 0.0370 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 66 optimal weight: 0.0570 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.184658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.135689 restraints weight = 8100.608| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.74 r_work: 0.3289 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8839 Z= 0.097 Angle : 0.480 5.593 11991 Z= 0.248 Chirality : 0.038 0.137 1329 Planarity : 0.004 0.048 1428 Dihedral : 13.116 88.830 2227 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.97 % Allowed : 12.74 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.28), residues: 996 helix: 3.32 (0.26), residues: 370 sheet: 0.92 (0.26), residues: 404 loop : 0.10 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 56 TYR 0.008 0.001 TYR I 45 PHE 0.007 0.001 PHE G 45 TRP 0.012 0.001 TRP A 197 HIS 0.001 0.000 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8839) covalent geometry : angle 0.47952 (11991) hydrogen bonds : bond 0.02569 ( 590) hydrogen bonds : angle 4.14379 ( 1698) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 109 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7433 (mm-40) REVERT: E 49 MET cc_start: 0.5608 (mmm) cc_final: 0.5139 (mtp) REVERT: A 48 LYS cc_start: 0.7826 (tttt) cc_final: 0.7395 (ttpp) REVERT: A 144 ASP cc_start: 0.7639 (m-30) cc_final: 0.7309 (m-30) REVERT: A 151 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7482 (tt0) REVERT: A 215 ARG cc_start: 0.8671 (ttp-170) cc_final: 0.8376 (ttm-80) REVERT: A 308 MET cc_start: 0.8605 (mmm) cc_final: 0.7595 (tmt) REVERT: D 109 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7321 (mm-40) REVERT: F 49 MET cc_start: 0.5602 (mmm) cc_final: 0.5143 (mtp) REVERT: B 48 LYS cc_start: 0.7807 (tttt) cc_final: 0.7375 (ttpp) REVERT: B 144 ASP cc_start: 0.7648 (m-30) cc_final: 0.7305 (m-30) REVERT: B 151 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7489 (tt0) REVERT: B 215 ARG cc_start: 0.8673 (ttp-170) cc_final: 0.8108 (ttm-80) REVERT: B 308 MET cc_start: 0.8562 (mmm) cc_final: 0.7560 (tmt) outliers start: 8 outliers final: 4 residues processed: 102 average time/residue: 0.4775 time to fit residues: 52.0299 Evaluate side-chains 102 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 249 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 1 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.181803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.132669 restraints weight = 8134.327| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.75 r_work: 0.3245 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8839 Z= 0.133 Angle : 0.522 5.591 11991 Z= 0.269 Chirality : 0.039 0.136 1329 Planarity : 0.004 0.045 1428 Dihedral : 12.912 85.777 2227 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.97 % Allowed : 13.47 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.28), residues: 996 helix: 3.37 (0.25), residues: 358 sheet: 0.96 (0.26), residues: 410 loop : 0.05 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 56 TYR 0.008 0.001 TYR I 45 PHE 0.010 0.001 PHE D 101 TRP 0.008 0.001 TRP A 197 HIS 0.002 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8839) covalent geometry : angle 0.52152 (11991) hydrogen bonds : bond 0.02949 ( 590) hydrogen bonds : angle 4.30302 ( 1698) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.315 Fit side-chains REVERT: C 109 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7325 (mm-40) REVERT: E 49 MET cc_start: 0.5631 (mmm) cc_final: 0.5206 (mtp) REVERT: G 54 ILE cc_start: 0.7528 (mt) cc_final: 0.7285 (OUTLIER) REVERT: A 48 LYS cc_start: 0.7893 (tttt) cc_final: 0.7454 (ttpp) REVERT: A 144 ASP cc_start: 0.7745 (m-30) cc_final: 0.7458 (m-30) REVERT: A 151 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7523 (tt0) REVERT: A 215 ARG cc_start: 0.8717 (ttp-170) cc_final: 0.8142 (ttm-80) REVERT: A 301 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7492 (tpm170) REVERT: A 308 MET cc_start: 0.8682 (mmm) cc_final: 0.7616 (tmt) REVERT: F 49 MET cc_start: 0.5630 (mmm) cc_final: 0.5208 (mtp) REVERT: H 54 ILE cc_start: 0.7522 (mt) cc_final: 0.7278 (OUTLIER) REVERT: B 48 LYS cc_start: 0.7863 (tttt) cc_final: 0.7419 (ttpp) REVERT: B 144 ASP cc_start: 0.7743 (m-30) cc_final: 0.7447 (m-30) REVERT: B 151 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7523 (tt0) REVERT: B 215 ARG cc_start: 0.8717 (ttp-170) cc_final: 0.8141 (ttm-80) REVERT: B 301 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7526 (tpm170) REVERT: B 308 MET cc_start: 0.8620 (mmm) cc_final: 0.7602 (tmt) outliers start: 8 outliers final: 8 residues processed: 93 average time/residue: 0.6285 time to fit residues: 61.9741 Evaluate side-chains 93 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 301 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 5 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.182622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.133669 restraints weight = 8079.710| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.75 r_work: 0.3258 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8839 Z= 0.115 Angle : 0.508 5.591 11991 Z= 0.264 Chirality : 0.039 0.137 1329 Planarity : 0.004 0.047 1428 Dihedral : 12.669 83.128 2227 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.73 % Allowed : 13.47 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.28), residues: 996 helix: 3.29 (0.25), residues: 370 sheet: 0.98 (0.26), residues: 404 loop : 0.00 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 56 TYR 0.007 0.001 TYR I 45 PHE 0.008 0.001 PHE C 101 TRP 0.010 0.001 TRP A 197 HIS 0.001 0.001 HIS A 150 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8839) covalent geometry : angle 0.50756 (11991) hydrogen bonds : bond 0.02812 ( 590) hydrogen bonds : angle 4.26189 ( 1698) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3458.79 seconds wall clock time: 59 minutes 31.82 seconds (3571.82 seconds total)