Starting phenix.real_space_refine on Thu Jul 2 09:33:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ddy_27382/07_2026/8ddy_27382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ddy_27382/07_2026/8ddy_27382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ddy_27382/07_2026/8ddy_27382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ddy_27382/07_2026/8ddy_27382.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ddy_27382/07_2026/8ddy_27382.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ddy_27382/07_2026/8ddy_27382.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ddy_27382/07_2026/8ddy_27382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ddy_27382/07_2026/8ddy_27382.cif" } resolution = 2.89 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 129 atoms to isotropic. 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 S 48 5.16 5 Cl 3 4.86 5 C 4860 2.51 5 N 1284 2.21 5 O 1773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7968 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1226 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 150} Chain: "B" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1233 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {' CL': 1, 'CYC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "F" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Restraints were copied for chains: C, E, D, F Time building chain proxies: 1.55, per 1000 atoms: 0.19 Number of scatterers: 7968 At special positions: 0 Unit cell: (123.968, 127.296, 80.704, 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) Cl 3 17.00 S 48 16.00 O 1773 8.00 N 1284 7.00 C 4860 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 315.0 milliseconds 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1806 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 85.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 29 through 41 removed outlier: 3.654A pdb=" N ALA A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 59 through 73 Processing helix chain 'A' and resid 73 through 89 removed outlier: 3.515A pdb=" N ARG A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 123 removed outlier: 4.002A pdb=" N THR A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 135 through 144 Processing helix chain 'A' and resid 146 through 165 Processing helix chain 'A' and resid 168 through 183 removed outlier: 3.550A pdb=" N LEU A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Proline residue: A 175 - end of helix Processing helix chain 'B' and resid 5 through 16 Proline residue: B 11 - end of helix Processing helix chain 'B' and resid 20 through 32 Processing helix chain 'B' and resid 34 through 47 Processing helix chain 'B' and resid 47 through 60 Processing helix chain 'B' and resid 74 through 98 Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 111 through 120 Processing helix chain 'B' and resid 122 through 141 Processing helix chain 'B' and resid 142 through 160 removed outlier: 3.840A pdb=" N ILE B 156 " --> pdb=" O TYR B 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 41 removed outlier: 3.654A pdb=" N ALA C 41 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 58 Processing helix chain 'C' and resid 59 through 73 Processing helix chain 'C' and resid 73 through 89 removed outlier: 3.515A pdb=" N ARG C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 123 removed outlier: 4.001A pdb=" N THR C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 135 through 144 Processing helix chain 'C' and resid 146 through 165 Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.551A pdb=" N LEU C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'D' and resid 5 through 16 Proline residue: D 11 - end of helix Processing helix chain 'D' and resid 20 through 32 Processing helix chain 'D' and resid 34 through 47 Processing helix chain 'D' and resid 47 through 60 Processing helix chain 'D' and resid 74 through 98 Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 111 through 120 Processing helix chain 'D' and resid 122 through 141 Processing helix chain 'D' and resid 142 through 160 removed outlier: 3.840A pdb=" N ILE D 156 " --> pdb=" O TYR D 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 41 removed outlier: 3.654A pdb=" N ALA E 41 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 58 Processing helix chain 'E' and resid 59 through 73 Processing helix chain 'E' and resid 73 through 89 removed outlier: 3.514A pdb=" N ARG E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 123 removed outlier: 4.001A pdb=" N THR E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'E' and resid 135 through 144 Processing helix chain 'E' and resid 146 through 165 Processing helix chain 'E' and resid 168 through 183 removed outlier: 3.550A pdb=" N LEU E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) Proline residue: E 175 - end of helix Processing helix chain 'F' and resid 5 through 16 Proline residue: F 11 - end of helix Processing helix chain 'F' and resid 20 through 32 Processing helix chain 'F' and resid 34 through 47 Processing helix chain 'F' and resid 47 through 60 Processing helix chain 'F' and resid 74 through 98 Processing helix chain 'F' and resid 102 through 107 Processing helix chain 'F' and resid 111 through 120 Processing helix chain 'F' and resid 122 through 141 Processing helix chain 'F' and resid 142 through 160 removed outlier: 3.839A pdb=" N ILE F 156 " --> pdb=" O TYR F 152 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1281 1.29 - 1.42: 1827 1.42 - 1.55: 4548 1.55 - 1.68: 27 1.68 - 1.81: 81 Bond restraints: 7764 Sorted by residual: bond pdb=" NB CYC F 201 " pdb=" C4B CYC F 201 " ideal model delta sigma weight residual 1.369 1.524 -0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" NB CYC B 201 " pdb=" C4B CYC B 201 " ideal model delta sigma weight residual 1.369 1.524 -0.155 2.00e-02 2.50e+03 6.00e+01 bond pdb=" NB CYC D 201 " pdb=" C4B CYC D 201 " ideal model delta sigma weight residual 1.369 1.524 -0.155 2.00e-02 2.50e+03 5.99e+01 bond pdb=" NB CYC B 201 " pdb=" C1B CYC B 201 " ideal model delta sigma weight residual 1.377 1.528 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NB CYC D 201 " pdb=" C1B CYC D 201 " ideal model delta sigma weight residual 1.377 1.528 -0.151 2.00e-02 2.50e+03 5.66e+01 ... (remaining 7759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 10149 4.08 - 8.16: 303 8.16 - 12.23: 45 12.23 - 16.31: 3 16.31 - 20.39: 18 Bond angle restraints: 10518 Sorted by residual: angle pdb=" CA ARG A 151 " pdb=" CB ARG A 151 " pdb=" CG ARG A 151 " ideal model delta sigma weight residual 114.10 134.13 -20.03 2.00e+00 2.50e-01 1.00e+02 angle pdb=" CA ARG E 151 " pdb=" CB ARG E 151 " pdb=" CG ARG E 151 " ideal model delta sigma weight residual 114.10 134.09 -19.99 2.00e+00 2.50e-01 9.99e+01 angle pdb=" CA ARG C 151 " pdb=" CB ARG C 151 " pdb=" CG ARG C 151 " ideal model delta sigma weight residual 114.10 134.06 -19.96 2.00e+00 2.50e-01 9.96e+01 angle pdb=" CB ARG E 151 " pdb=" CG ARG E 151 " pdb=" CD ARG E 151 " ideal model delta sigma weight residual 111.30 131.69 -20.39 2.30e+00 1.89e-01 7.86e+01 angle pdb=" CB ARG C 151 " pdb=" CG ARG C 151 " pdb=" CD ARG C 151 " ideal model delta sigma weight residual 111.30 131.67 -20.37 2.30e+00 1.89e-01 7.84e+01 ... (remaining 10513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 4162 17.05 - 34.10: 398 34.10 - 51.15: 78 51.15 - 68.19: 54 68.19 - 85.24: 21 Dihedral angle restraints: 4713 sinusoidal: 1917 harmonic: 2796 Sorted by residual: dihedral pdb=" CA GLN B 32 " pdb=" C GLN B 32 " pdb=" N SER B 33 " pdb=" CA SER B 33 " ideal model delta harmonic sigma weight residual 180.00 150.51 29.49 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA GLN F 32 " pdb=" C GLN F 32 " pdb=" N SER F 33 " pdb=" CA SER F 33 " ideal model delta harmonic sigma weight residual 180.00 150.52 29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA GLN D 32 " pdb=" C GLN D 32 " pdb=" N SER D 33 " pdb=" CA SER D 33 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 4710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 782 0.059 - 0.117: 305 0.117 - 0.176: 68 0.176 - 0.234: 13 0.234 - 0.293: 8 Chirality restraints: 1176 Sorted by residual: chirality pdb=" CG LEU E 45 " pdb=" CB LEU E 45 " pdb=" CD1 LEU E 45 " pdb=" CD2 LEU E 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CG LEU A 45 " pdb=" CB LEU A 45 " pdb=" CD1 LEU A 45 " pdb=" CD2 LEU A 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU C 45 " pdb=" CB LEU C 45 " pdb=" CD1 LEU C 45 " pdb=" CD2 LEU C 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1173 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 62 " -0.017 2.00e-02 2.50e+03 2.97e-02 1.77e+01 pdb=" CG TYR B 62 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR B 62 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR B 62 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR B 62 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 62 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 62 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 62 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 62 " 0.017 2.00e-02 2.50e+03 2.97e-02 1.76e+01 pdb=" CG TYR F 62 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR F 62 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR F 62 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR F 62 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 62 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR F 62 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 62 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 62 " -0.017 2.00e-02 2.50e+03 2.96e-02 1.76e+01 pdb=" CG TYR D 62 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR D 62 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR D 62 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR D 62 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 62 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 62 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 62 " 0.004 2.00e-02 2.50e+03 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1542 2.78 - 3.31: 7693 3.31 - 3.84: 14694 3.84 - 4.37: 18355 4.37 - 4.90: 28679 Nonbonded interactions: 70963 Sorted by model distance: nonbonded pdb=" OE1 GLN B 128 " pdb=" O HOH B 301 " model vdw 2.247 3.040 nonbonded pdb=" OE1 GLN D 128 " pdb=" O HOH D 301 " model vdw 2.252 3.040 nonbonded pdb=" OE1 GLN F 128 " pdb=" O HOH F 301 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR E 118 " pdb=" O SER F 17 " model vdw 2.264 3.040 nonbonded pdb=" NH2 ARG E 151 " pdb=" O ILE E 181 " model vdw 2.277 3.120 ... (remaining 70958 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.360 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 : 0.016 0.155 7770 Z= 0.736 Angle : 1.753 20.388 10518 Z= 0.863 Chirality : 0.067 0.293 1176 Planarity : 0.009 0.071 1335 Dihedral : 16.391 85.243 2907 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.82 % Allowed : 4.58 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.48 (0.24), residues: 933 helix: -1.18 (0.16), residues: 804 sheet: None (None), residues: 0 loop : -3.44 (0.43), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.004 ARG E 137 TYR 0.071 0.005 TYR B 62 PHE 0.025 0.004 PHE E 85 TRP 0.009 0.002 TRP E 86 HIS 0.002 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.01571 / 0.74 ( 7764) covalent geometry : angle 1.75329 / 0.86 (10518) hydrogen bonds : bond 0.17972 / 12.01 ( 564) hydrogen bonds : angle 6.53131 / 4.61 ( 1692) Misc. bond : bond 0.00164 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 55 ASP cc_start: 0.6874 (m-30) cc_final: 0.6554 (t70) REVERT: A 79 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.6150 (pp30) REVERT: B 14 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6837 (pt0) REVERT: B 54 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8271 (mtmm) REVERT: C 151 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.5969 (mmm160) REVERT: D 107 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7202 (mmm160) REVERT: F 3 ASP cc_start: 0.8458 (p0) cc_final: 0.8208 (p0) REVERT: F 107 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.7034 (mmp80) REVERT: F 128 GLN cc_start: 0.7376 (tm-30) cc_final: 0.7164 (tm-30) outliers start: 30 outliers final: 2 residues processed: 184 average time/residue: 0.7670 time to fit residues: 146.3984 Evaluate side-chains 133 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain F residue 107 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN A 109 GLN ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN D 35 ASN D 131 ASN E 61 GLN E 75 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN F 28 ASN F 131 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.130992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.111001 restraints weight = 9438.874| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.15 r_work: 0.3100 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7770 Z= 0.130 Angle : 0.662 10.544 10518 Z= 0.316 Chirality : 0.038 0.124 1176 Planarity : 0.005 0.043 1335 Dihedral : 10.326 81.822 1160 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.29 % Allowed : 11.20 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.09 (0.26), residues: 933 helix: 0.57 (0.18), residues: 798 sheet: None (None), residues: 0 loop : -3.62 (0.42), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 137 TYR 0.015 0.002 TYR A 140 PHE 0.013 0.001 PHE E 85 TRP 0.006 0.001 TRP A 86 HIS 0.001 0.000 HIS F 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 7764) covalent geometry : angle 0.66228 / 0.32 (10518) hydrogen bonds : bond 0.03818 / 2.49 ( 564) hydrogen bonds : angle 4.33071 / 3.09 ( 1692) Misc. bond : bond 0.00019 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7739 (tttm) cc_final: 0.7341 (ttpt) REVERT: A 79 GLN cc_start: 0.6950 (mm-40) cc_final: 0.6154 (pt0) REVERT: A 158 LYS cc_start: 0.8138 (tttt) cc_final: 0.7821 (ttpt) REVERT: A 179 ARG cc_start: 0.8107 (tpt90) cc_final: 0.7887 (tmt170) REVERT: B 14 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7058 (pt0) REVERT: B 54 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8531 (mtmt) REVERT: B 133 MET cc_start: 0.8702 (ttm) cc_final: 0.8380 (ttm) REVERT: C 76 LYS cc_start: 0.8187 (tttm) cc_final: 0.7917 (ttpt) REVERT: C 84 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7460 (mmm-85) REVERT: C 159 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6940 (mt-10) REVERT: C 168 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5770 (tp30) REVERT: D 107 ARG cc_start: 0.7803 (mmt90) cc_final: 0.7113 (mmt90) REVERT: E 28 MET cc_start: 0.7628 (ttm) cc_final: 0.7407 (ttm) REVERT: E 54 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7114 (mm-30) REVERT: F 106 GLU cc_start: 0.7056 (pp20) cc_final: 0.6649 (pp20) REVERT: F 107 ARG cc_start: 0.7923 (mmt90) cc_final: 0.7380 (mpt180) outliers start: 18 outliers final: 1 residues processed: 153 average time/residue: 0.8016 time to fit residues: 127.4856 Evaluate side-chains 136 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 117 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 77 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** 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 = 0.3435 r_free = 0.3435 target = 0.130064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.110149 restraints weight = 9373.562| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.12 r_work: 0.3078 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7770 Z= 0.119 Angle : 0.631 10.848 10518 Z= 0.293 Chirality : 0.038 0.123 1176 Planarity : 0.005 0.053 1335 Dihedral : 9.470 77.030 1137 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.16 % Allowed : 12.60 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.27), residues: 933 helix: 1.31 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -3.20 (0.45), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 83 TYR 0.014 0.002 TYR D 87 PHE 0.011 0.001 PHE C 85 TRP 0.004 0.001 TRP A 111 HIS 0.001 0.000 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 7764) covalent geometry : angle 0.63087 / 0.29 (10518) hydrogen bonds : bond 0.03492 / 2.28 ( 564) hydrogen bonds : angle 3.97174 / 2.84 ( 1692) Misc. bond : bond 0.00013 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7709 (tttm) cc_final: 0.7208 (ttpt) REVERT: A 79 GLN cc_start: 0.6813 (mm-40) cc_final: 0.6033 (pt0) REVERT: B 14 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7113 (pt0) REVERT: B 54 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8503 (mtmt) REVERT: B 133 MET cc_start: 0.8710 (ttm) cc_final: 0.8391 (ttm) REVERT: B 144 GLU cc_start: 0.7444 (pt0) cc_final: 0.7237 (pt0) REVERT: C 55 ASP cc_start: 0.7088 (m-30) cc_final: 0.6847 (t70) REVERT: C 76 LYS cc_start: 0.8219 (tttm) cc_final: 0.7832 (ttpt) REVERT: C 84 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7542 (mmm-85) REVERT: C 159 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6851 (mt-10) REVERT: C 168 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5904 (tp30) REVERT: E 28 MET cc_start: 0.7753 (ttm) cc_final: 0.7541 (ttm) REVERT: E 54 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7188 (mm-30) REVERT: E 73 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7678 (p0) REVERT: E 84 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7469 (mtt180) REVERT: F 106 GLU cc_start: 0.7056 (pp20) cc_final: 0.6636 (pp20) REVERT: F 107 ARG cc_start: 0.7949 (mmt90) cc_final: 0.7393 (mpt180) outliers start: 17 outliers final: 1 residues processed: 158 average time/residue: 0.7297 time to fit residues: 120.4272 Evaluate side-chains 144 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 84 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 72 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN A 109 GLN ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 75 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.127401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.107153 restraints weight = 9546.804| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.15 r_work: 0.3036 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7770 Z= 0.147 Angle : 0.660 10.924 10518 Z= 0.308 Chirality : 0.039 0.149 1176 Planarity : 0.004 0.035 1335 Dihedral : 9.376 77.025 1137 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.42 % Allowed : 14.76 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.27), residues: 933 helix: 1.50 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.92 (0.47), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 151 TYR 0.018 0.002 TYR D 152 PHE 0.010 0.001 PHE E 85 TRP 0.003 0.001 TRP A 111 HIS 0.001 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 7764) covalent geometry : angle 0.66016 / 0.31 (10518) hydrogen bonds : bond 0.03710 / 2.42 ( 564) hydrogen bonds : angle 3.97789 / 2.84 ( 1692) Misc. bond : bond 0.00026 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.305 Fit side-chains REVERT: A 76 LYS cc_start: 0.7700 (tttm) cc_final: 0.7267 (ttpt) REVERT: A 79 GLN cc_start: 0.6801 (mm-40) cc_final: 0.6009 (pt0) REVERT: B 54 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8534 (mtmt) REVERT: B 133 MET cc_start: 0.8697 (ttm) cc_final: 0.8472 (ttm) REVERT: C 43 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.6566 (ptt180) REVERT: C 76 LYS cc_start: 0.8223 (tttm) cc_final: 0.7805 (ttpt) REVERT: C 159 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6987 (mt-10) REVERT: C 168 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5955 (tp30) REVERT: D 42 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7898 (ttpt) REVERT: E 28 MET cc_start: 0.7718 (ttm) cc_final: 0.7463 (ttm) REVERT: E 54 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7202 (mm-30) REVERT: E 59 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7453 (ptpt) REVERT: E 73 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7673 (p0) REVERT: E 79 GLN cc_start: 0.7444 (mm-40) cc_final: 0.7169 (mm-40) REVERT: E 80 GLU cc_start: 0.8244 (tp30) cc_final: 0.8013 (tp30) REVERT: E 84 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.6711 (mtm-85) REVERT: F 106 GLU cc_start: 0.6982 (pp20) cc_final: 0.6666 (pp20) REVERT: F 107 ARG cc_start: 0.7946 (mmt90) cc_final: 0.7423 (mpt180) REVERT: F 128 GLN cc_start: 0.7919 (tt0) cc_final: 0.7354 (tt0) REVERT: F 154 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7412 (m-30) outliers start: 19 outliers final: 4 residues processed: 156 average time/residue: 0.7005 time to fit residues: 114.0061 Evaluate side-chains 153 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 154 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 75 GLN E 98 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.127442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.107499 restraints weight = 9399.628| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.12 r_work: 0.3032 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7770 Z= 0.150 Angle : 0.663 10.829 10518 Z= 0.308 Chirality : 0.039 0.137 1176 Planarity : 0.004 0.029 1335 Dihedral : 9.050 68.108 1134 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.54 % Allowed : 16.79 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.27), residues: 933 helix: 1.62 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.87 (0.48), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 107 TYR 0.015 0.002 TYR D 87 PHE 0.012 0.001 PHE C 85 TRP 0.002 0.001 TRP A 111 HIS 0.001 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 7764) covalent geometry : angle 0.66254 / 0.31 (10518) hydrogen bonds : bond 0.03686 / 2.41 ( 564) hydrogen bonds : angle 3.98421 / 2.84 ( 1692) Misc. bond : bond 0.00033 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.267 Fit side-chains REVERT: A 43 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.6521 (ptt180) REVERT: A 76 LYS cc_start: 0.7734 (tttm) cc_final: 0.7255 (ttpt) REVERT: A 79 GLN cc_start: 0.6760 (mm-40) cc_final: 0.5976 (pt0) REVERT: A 164 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6716 (mt) REVERT: B 54 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8553 (mtmt) REVERT: B 133 MET cc_start: 0.8715 (ttm) cc_final: 0.8496 (ttm) REVERT: C 43 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.6596 (ptt180) REVERT: C 76 LYS cc_start: 0.8248 (tttm) cc_final: 0.7827 (ttpt) REVERT: C 84 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7434 (mtt180) REVERT: C 159 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6917 (mt-10) REVERT: C 168 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.6027 (tp30) REVERT: D 107 ARG cc_start: 0.7877 (mmt-90) cc_final: 0.7030 (mmt180) REVERT: D 114 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: E 28 MET cc_start: 0.7732 (ttm) cc_final: 0.7440 (ttm) REVERT: E 54 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7159 (mm-30) REVERT: E 73 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7663 (p0) REVERT: E 79 GLN cc_start: 0.7446 (mm-40) cc_final: 0.7198 (mm-40) REVERT: E 84 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.6561 (mtm-85) REVERT: F 106 GLU cc_start: 0.6935 (pp20) cc_final: 0.6556 (pp20) REVERT: F 107 ARG cc_start: 0.7957 (mmt90) cc_final: 0.7420 (mpt180) REVERT: F 128 GLN cc_start: 0.7921 (tt0) cc_final: 0.7362 (tt0) outliers start: 20 outliers final: 3 residues processed: 155 average time/residue: 0.7340 time to fit residues: 118.7329 Evaluate side-chains 150 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain F residue 36 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 68 optimal weight: 0.0970 chunk 69 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 98 ASN E 109 GLN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.109761 restraints weight = 9410.657| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.13 r_work: 0.3063 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7770 Z= 0.111 Angle : 0.610 10.697 10518 Z= 0.284 Chirality : 0.037 0.125 1176 Planarity : 0.004 0.028 1335 Dihedral : 9.013 70.981 1134 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.80 % Allowed : 16.79 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.27), residues: 933 helix: 1.93 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -2.86 (0.48), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 107 TYR 0.018 0.001 TYR F 87 PHE 0.012 0.001 PHE C 85 TRP 0.002 0.000 TRP A 111 HIS 0.001 0.000 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 7764) covalent geometry : angle 0.61046 / 0.28 (10518) hydrogen bonds : bond 0.03215 / 2.09 ( 564) hydrogen bonds : angle 3.83220 / 2.72 ( 1692) Misc. bond : bond 0.00011 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.317 Fit side-chains REVERT: A 52 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7489 (ttmt) REVERT: A 74 GLU cc_start: 0.7941 (tt0) cc_final: 0.7665 (tt0) REVERT: A 76 LYS cc_start: 0.7675 (tttm) cc_final: 0.7315 (ttpt) REVERT: A 164 ILE cc_start: 0.6939 (OUTLIER) cc_final: 0.6643 (mt) REVERT: B 54 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8555 (mtmt) REVERT: B 107 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7726 (tpp80) REVERT: B 133 MET cc_start: 0.8716 (ttm) cc_final: 0.8485 (ttm) REVERT: C 73 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7458 (p0) REVERT: C 76 LYS cc_start: 0.8190 (tttm) cc_final: 0.7866 (ttpt) REVERT: C 84 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7405 (mtt180) REVERT: C 159 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6855 (mt-10) REVERT: C 168 GLU cc_start: 0.6305 (OUTLIER) cc_final: 0.6020 (tp30) REVERT: D 14 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: D 107 ARG cc_start: 0.7823 (mmt-90) cc_final: 0.6995 (mmt180) REVERT: E 54 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7144 (mm-30) REVERT: E 80 GLU cc_start: 0.8370 (tp30) cc_final: 0.7967 (tp30) REVERT: E 84 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7502 (mtt180) REVERT: F 32 GLN cc_start: 0.6820 (pt0) cc_final: 0.6589 (mt0) REVERT: F 106 GLU cc_start: 0.6942 (pp20) cc_final: 0.6546 (pp20) REVERT: F 107 ARG cc_start: 0.7949 (mmt90) cc_final: 0.7399 (mpt180) REVERT: F 128 GLN cc_start: 0.7954 (tt0) cc_final: 0.7396 (tt0) REVERT: F 154 ASP cc_start: 0.7784 (m-30) cc_final: 0.7524 (m-30) outliers start: 22 outliers final: 3 residues processed: 158 average time/residue: 0.7427 time to fit residues: 122.2801 Evaluate side-chains 155 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain F residue 36 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 98 ASN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 98 ASN E 109 GLN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.130724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.110817 restraints weight = 9437.113| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.13 r_work: 0.3080 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7770 Z= 0.110 Angle : 0.605 10.696 10518 Z= 0.283 Chirality : 0.037 0.123 1176 Planarity : 0.004 0.027 1335 Dihedral : 8.949 71.785 1134 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.42 % Allowed : 17.56 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.10 (0.28), residues: 933 helix: 2.00 (0.18), residues: 807 sheet: None (None), residues: 0 loop : -2.79 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 137 TYR 0.016 0.001 TYR D 87 PHE 0.012 0.001 PHE C 85 TRP 0.002 0.000 TRP A 111 HIS 0.000 0.000 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 7764) covalent geometry : angle 0.60453 / 0.28 (10518) hydrogen bonds : bond 0.03080 / 2.00 ( 564) hydrogen bonds : angle 3.76662 / 2.67 ( 1692) Misc. bond : bond 0.00007 / 0.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.215 Fit side-chains REVERT: A 43 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.6423 (ptt180) REVERT: A 74 GLU cc_start: 0.7964 (tt0) cc_final: 0.7688 (tt0) REVERT: A 76 LYS cc_start: 0.7651 (tttm) cc_final: 0.7361 (ttpt) REVERT: B 14 GLU cc_start: 0.7675 (mm-30) cc_final: 0.6968 (tp30) REVERT: B 54 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8545 (mtmt) REVERT: B 107 ARG cc_start: 0.7944 (ttm-80) cc_final: 0.7733 (tpp80) REVERT: C 68 GLN cc_start: 0.7296 (tp-100) cc_final: 0.6983 (mm110) REVERT: C 73 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7443 (p0) REVERT: C 76 LYS cc_start: 0.8181 (tttm) cc_final: 0.7894 (ttpt) REVERT: C 159 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6953 (mt-10) REVERT: C 168 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5935 (tp30) REVERT: D 14 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: D 107 ARG cc_start: 0.7870 (mmt-90) cc_final: 0.7041 (mmt180) REVERT: E 54 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7233 (mm-30) REVERT: E 73 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7564 (p0) REVERT: E 80 GLU cc_start: 0.8344 (tp30) cc_final: 0.7931 (tp30) REVERT: E 84 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7496 (mtt180) REVERT: F 106 GLU cc_start: 0.6942 (pp20) cc_final: 0.6535 (pp20) REVERT: F 107 ARG cc_start: 0.7933 (mmt90) cc_final: 0.7387 (mpt180) REVERT: F 128 GLN cc_start: 0.7946 (tt0) cc_final: 0.7460 (tt0) REVERT: F 154 ASP cc_start: 0.7716 (m-30) cc_final: 0.7471 (m-30) outliers start: 19 outliers final: 5 residues processed: 156 average time/residue: 0.6659 time to fit residues: 108.5100 Evaluate side-chains 153 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain F residue 36 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 66 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 98 ASN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 75 GLN E 98 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.130475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.109751 restraints weight = 9437.238| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.23 r_work: 0.3040 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7770 Z= 0.121 Angle : 0.622 10.746 10518 Z= 0.291 Chirality : 0.038 0.122 1176 Planarity : 0.004 0.027 1335 Dihedral : 8.843 71.093 1134 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.54 % Allowed : 17.18 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.12 (0.28), residues: 933 helix: 2.04 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -2.79 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 137 TYR 0.020 0.002 TYR D 87 PHE 0.012 0.001 PHE C 85 TRP 0.001 0.000 TRP E 111 HIS 0.001 0.000 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 7764) covalent geometry : angle 0.62228 / 0.29 (10518) hydrogen bonds : bond 0.03218 / 2.09 ( 564) hydrogen bonds : angle 3.78541 / 2.68 ( 1692) Misc. bond : bond 0.00012 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.183 Fit side-chains REVERT: A 43 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.6449 (ptt180) REVERT: A 50 ILE cc_start: 0.7940 (mm) cc_final: 0.7721 (mp) REVERT: A 52 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7425 (ttmt) REVERT: A 74 GLU cc_start: 0.7931 (tt0) cc_final: 0.7640 (tt0) REVERT: A 76 LYS cc_start: 0.7619 (tttm) cc_final: 0.7311 (ttpt) REVERT: B 14 GLU cc_start: 0.7669 (mm-30) cc_final: 0.6912 (tp30) REVERT: B 54 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8539 (mtmt) REVERT: B 107 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7690 (tpp80) REVERT: C 68 GLN cc_start: 0.7308 (tp-100) cc_final: 0.6993 (mm110) REVERT: C 73 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7298 (p0) REVERT: C 76 LYS cc_start: 0.8142 (tttm) cc_final: 0.7737 (ttpt) REVERT: C 159 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6928 (mt-10) REVERT: C 168 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.6079 (tp30) REVERT: D 14 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: D 107 ARG cc_start: 0.7873 (mmt-90) cc_final: 0.7086 (mmt180) REVERT: E 43 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.6996 (ptt90) REVERT: E 54 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7222 (mm-30) REVERT: E 73 ASN cc_start: 0.7842 (OUTLIER) cc_final: 0.7515 (p0) REVERT: E 80 GLU cc_start: 0.8431 (tp30) cc_final: 0.8041 (tp30) REVERT: E 84 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7433 (mtt180) REVERT: F 106 GLU cc_start: 0.6902 (pp20) cc_final: 0.6533 (pp20) REVERT: F 107 ARG cc_start: 0.7942 (mmt90) cc_final: 0.7387 (mpt180) REVERT: F 128 GLN cc_start: 0.7845 (tt0) cc_final: 0.7326 (tt0) REVERT: F 154 ASP cc_start: 0.7781 (m-30) cc_final: 0.7496 (m-30) outliers start: 20 outliers final: 7 residues processed: 157 average time/residue: 0.6643 time to fit residues: 108.9241 Evaluate side-chains 158 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain F residue 36 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 47 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 98 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.110307 restraints weight = 9404.611| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.23 r_work: 0.3052 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7770 Z= 0.117 Angle : 0.618 10.703 10518 Z= 0.290 Chirality : 0.037 0.123 1176 Planarity : 0.004 0.027 1335 Dihedral : 8.827 71.503 1134 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.54 % Allowed : 17.94 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.16 (0.28), residues: 933 helix: 2.06 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.81 (0.51), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 137 TYR 0.022 0.001 TYR D 87 PHE 0.012 0.001 PHE C 85 TRP 0.001 0.000 TRP A 111 HIS 0.001 0.000 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 7764) covalent geometry : angle 0.61800 / 0.29 (10518) hydrogen bonds : bond 0.03108 / 2.02 ( 564) hydrogen bonds : angle 3.75815 / 2.66 ( 1692) Misc. bond : bond 0.00010 / 0.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.339 Fit side-chains REVERT: A 43 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.6447 (ptt180) REVERT: A 52 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7399 (ttmt) REVERT: A 76 LYS cc_start: 0.7578 (tttm) cc_final: 0.7228 (ttpt) REVERT: B 14 GLU cc_start: 0.7607 (mm-30) cc_final: 0.6866 (tp30) REVERT: B 54 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8531 (mtmt) REVERT: B 107 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7721 (tpp80) REVERT: C 68 GLN cc_start: 0.7294 (tp-100) cc_final: 0.6961 (mm110) REVERT: C 73 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7272 (p0) REVERT: C 76 LYS cc_start: 0.8101 (tttm) cc_final: 0.7773 (ttpt) REVERT: C 159 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6876 (mt-10) REVERT: C 168 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.6113 (tp30) REVERT: D 14 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: D 107 ARG cc_start: 0.7864 (mmt-90) cc_final: 0.7102 (mmt180) REVERT: E 43 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.6952 (ptt90) REVERT: E 54 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7175 (mm-30) REVERT: E 75 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7031 (pm20) REVERT: E 80 GLU cc_start: 0.8426 (tp30) cc_final: 0.7931 (tp30) REVERT: E 84 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7394 (mtt180) REVERT: F 106 GLU cc_start: 0.6873 (pp20) cc_final: 0.6441 (pp20) REVERT: F 107 ARG cc_start: 0.7923 (mmt90) cc_final: 0.7347 (mpt180) REVERT: F 128 GLN cc_start: 0.7856 (tt0) cc_final: 0.7337 (tt0) REVERT: F 154 ASP cc_start: 0.7756 (m-30) cc_final: 0.7470 (m-30) outliers start: 20 outliers final: 8 residues processed: 155 average time/residue: 0.7235 time to fit residues: 117.0252 Evaluate side-chains 152 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain F residue 36 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 0.0020 chunk 5 optimal weight: 0.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN C 75 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 98 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.130383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.108896 restraints weight = 9437.926| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.31 r_work: 0.3054 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7770 Z= 0.117 Angle : 0.620 10.692 10518 Z= 0.292 Chirality : 0.038 0.123 1176 Planarity : 0.004 0.027 1335 Dihedral : 8.780 71.650 1134 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.04 % Allowed : 18.96 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.21 (0.28), residues: 933 helix: 2.10 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.81 (0.51), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 107 TYR 0.025 0.002 TYR D 87 PHE 0.013 0.001 PHE C 85 TRP 0.001 0.000 TRP E 111 HIS 0.001 0.000 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 7764) covalent geometry : angle 0.62031 / 0.29 (10518) hydrogen bonds : bond 0.03122 / 2.03 ( 564) hydrogen bonds : angle 3.75544 / 2.66 ( 1692) Misc. bond : bond 0.00013 / 0.01 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.303 Fit side-chains REVERT: A 43 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.6469 (ptt180) REVERT: A 52 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7383 (ttmt) REVERT: A 74 GLU cc_start: 0.7898 (tt0) cc_final: 0.7659 (tt0) REVERT: A 76 LYS cc_start: 0.7560 (tttm) cc_final: 0.7190 (ttmt) REVERT: B 14 GLU cc_start: 0.7617 (mm-30) cc_final: 0.6862 (tp30) REVERT: B 54 LYS cc_start: 0.8775 (mtmt) cc_final: 0.8528 (mtmt) REVERT: B 107 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7712 (tpp80) REVERT: C 68 GLN cc_start: 0.7285 (tp-100) cc_final: 0.6941 (mm110) REVERT: C 73 ASN cc_start: 0.7719 (OUTLIER) cc_final: 0.7200 (p0) REVERT: C 76 LYS cc_start: 0.8027 (tttm) cc_final: 0.7699 (ttpt) REVERT: C 159 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6941 (mt-10) REVERT: C 168 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6171 (tp30) REVERT: D 14 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: E 43 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.6938 (ptt90) REVERT: E 75 GLN cc_start: 0.7963 (mm-40) cc_final: 0.6805 (pm20) REVERT: E 80 GLU cc_start: 0.8437 (tp30) cc_final: 0.7973 (tp30) REVERT: E 84 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7382 (mtt180) REVERT: F 106 GLU cc_start: 0.6876 (pp20) cc_final: 0.6513 (pp20) REVERT: F 107 ARG cc_start: 0.7929 (mmt90) cc_final: 0.7362 (mpt180) REVERT: F 128 GLN cc_start: 0.7876 (tt0) cc_final: 0.7351 (tt0) REVERT: F 154 ASP cc_start: 0.7765 (m-30) cc_final: 0.7473 (m-30) outliers start: 16 outliers final: 7 residues processed: 147 average time/residue: 0.6988 time to fit residues: 107.3948 Evaluate side-chains 149 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain F residue 36 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 11 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.108751 restraints weight = 9402.604| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.28 r_work: 0.3045 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7770 Z= 0.126 Angle : 0.635 10.721 10518 Z= 0.300 Chirality : 0.038 0.122 1176 Planarity : 0.004 0.032 1335 Dihedral : 8.750 71.167 1134 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.29 % Allowed : 18.96 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.20 (0.28), residues: 933 helix: 2.10 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -2.75 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 107 TYR 0.027 0.002 TYR D 87 PHE 0.014 0.001 PHE C 85 TRP 0.001 0.000 TRP A 111 HIS 0.001 0.000 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 7764) covalent geometry : angle 0.63499 / 0.30 (10518) hydrogen bonds : bond 0.03205 / 2.09 ( 564) hydrogen bonds : angle 3.78082 / 2.67 ( 1692) Misc. bond : bond 0.00018 / 0.01 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3179.12 seconds wall clock time: 54 minutes 43.87 seconds (3283.87 seconds total)