Starting phenix.real_space_refine on Sun May 11 14:31:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ddy_27382/05_2025/8ddy_27382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ddy_27382/05_2025/8ddy_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_27382/05_2025/8ddy_27382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ddy_27382/05_2025/8ddy_27382.map" model { file = "/net/cci-nas-00/data/ceres_data/8ddy_27382/05_2025/8ddy_27382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ddy_27382/05_2025/8ddy_27382.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.44, per 1000 atoms: 0.56 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: 2.19 Conformation dependent library (CDL) restraints added in 924.8 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: 0.68 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: 2.04 Time building geometry restraints manager: 2.39 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: 4303 17.05 - 34.10: 428 34.10 - 51.15: 81 51.15 - 68.19: 60 68.19 - 85.24: 21 Dihedral angle restraints: 4893 sinusoidal: 2097 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 4890 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: 0.05 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 19.840 Find NCS groups from input model: 0.160 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:10.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 16.382 85.243 3087 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.002 TRP E 86 HIS 0.002 0.001 HIS D 155 PHE 0.025 0.004 PHE E 85 TYR 0.071 0.005 TYR B 62 ARG 0.030 0.004 ARG E 137 Details of bonding type rmsd hydrogen bonds : bond 0.17972 ( 564) hydrogen bonds : angle 6.53131 ( 1692) covalent geometry : bond 0.01571 ( 7764) covalent geometry : angle 1.75329 (10518) Misc. bond : bond 0.00164 ( 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 : 0.825 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: 1.8784 time to fit residues: 358.2441 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 : 0.817 ------------------------------------------------------------------------------- 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 78 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.130791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.110901 restraints weight = 9298.707| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.13 r_work: 0.3100 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7770 Z= 0.127 Angle : 0.664 10.407 10518 Z= 0.317 Chirality : 0.038 0.125 1176 Planarity : 0.006 0.044 1335 Dihedral : 10.040 81.621 1340 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.29 % Allowed : 11.45 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 933 helix: 0.53 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -3.57 (0.43), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.000 0.000 HIS D 155 PHE 0.011 0.001 PHE E 85 TYR 0.014 0.002 TYR A 140 ARG 0.007 0.000 ARG E 137 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 564) hydrogen bonds : angle 4.35574 ( 1692) covalent geometry : bond 0.00276 ( 7764) covalent geometry : angle 0.66398 (10518) Misc. bond : bond 0.00020 ( 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 : 0.894 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7716 (tttm) cc_final: 0.7342 (ttpt) REVERT: A 79 GLN cc_start: 0.6909 (mm-40) cc_final: 0.6272 (pt0) REVERT: A 158 LYS cc_start: 0.8129 (tttt) cc_final: 0.7810 (ttpt) REVERT: B 14 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7059 (pt0) REVERT: B 54 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8513 (mtmt) REVERT: B 133 MET cc_start: 0.8702 (ttm) cc_final: 0.8387 (ttm) REVERT: C 76 LYS cc_start: 0.8175 (tttm) cc_final: 0.7896 (ttpt) REVERT: C 84 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7417 (mtt180) REVERT: C 159 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6920 (mt-10) REVERT: C 168 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5806 (tp30) REVERT: D 107 ARG cc_start: 0.7798 (mmt90) cc_final: 0.7328 (mmt-90) REVERT: E 28 MET cc_start: 0.7648 (ttm) cc_final: 0.7429 (ttm) REVERT: E 54 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7124 (mm-30) REVERT: F 106 GLU cc_start: 0.7059 (pp20) cc_final: 0.6626 (pp20) REVERT: F 107 ARG cc_start: 0.7929 (mmt90) cc_final: 0.7442 (mpt180) outliers start: 18 outliers final: 1 residues processed: 153 average time/residue: 1.8310 time to fit residues: 291.3746 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 : 0.814 ------------------------------------------------------------------------------- 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 51 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 33 GLN C 68 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.109485 restraints weight = 9462.641| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.13 r_work: 0.3059 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7770 Z= 0.124 Angle : 0.637 10.954 10518 Z= 0.297 Chirality : 0.038 0.124 1176 Planarity : 0.005 0.054 1335 Dihedral : 9.051 77.310 1317 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.91 % Allowed : 12.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.27), residues: 933 helix: 1.28 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -3.12 (0.46), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 111 HIS 0.001 0.000 HIS D 155 PHE 0.010 0.001 PHE C 85 TYR 0.013 0.002 TYR D 87 ARG 0.005 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 564) hydrogen bonds : angle 3.98718 ( 1692) covalent geometry : bond 0.00276 ( 7764) covalent geometry : angle 0.63710 (10518) Misc. bond : bond 0.00022 ( 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 167 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7670 (tttm) cc_final: 0.7279 (ttpt) REVERT: A 79 GLN cc_start: 0.6835 (mm-40) cc_final: 0.6055 (pt0) REVERT: A 179 ARG cc_start: 0.8205 (tpt-90) cc_final: 0.7607 (tpt170) REVERT: B 14 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7405 (mm-30) REVERT: B 54 LYS cc_start: 0.8775 (mtmt) cc_final: 0.8522 (mtmt) REVERT: B 133 MET cc_start: 0.8722 (ttm) cc_final: 0.8476 (ttm) REVERT: C 55 ASP cc_start: 0.7086 (m-30) cc_final: 0.6853 (t70) REVERT: C 76 LYS cc_start: 0.8228 (tttm) cc_final: 0.7829 (ttpt) REVERT: C 84 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7545 (mmm-85) REVERT: C 159 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6863 (mt-10) REVERT: C 168 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5929 (tp30) REVERT: E 28 MET cc_start: 0.7767 (ttm) cc_final: 0.7536 (ttm) REVERT: E 54 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7203 (mm-30) REVERT: F 106 GLU cc_start: 0.7045 (pp20) cc_final: 0.6619 (pp20) REVERT: F 107 ARG cc_start: 0.7966 (mmt90) cc_final: 0.7414 (mpt180) outliers start: 15 outliers final: 1 residues processed: 158 average time/residue: 1.6373 time to fit residues: 269.8294 Evaluate side-chains 140 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 69 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.108712 restraints weight = 9333.066| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.11 r_work: 0.3046 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7770 Z= 0.134 Angle : 0.639 10.794 10518 Z= 0.298 Chirality : 0.038 0.122 1176 Planarity : 0.004 0.037 1335 Dihedral : 8.967 76.095 1317 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.80 % Allowed : 14.50 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.27), residues: 933 helix: 1.59 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -2.94 (0.47), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 111 HIS 0.001 0.000 HIS D 155 PHE 0.010 0.001 PHE C 85 TYR 0.015 0.002 TYR D 152 ARG 0.007 0.000 ARG E 151 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 564) hydrogen bonds : angle 3.92435 ( 1692) covalent geometry : bond 0.00303 ( 7764) covalent geometry : angle 0.63860 (10518) Misc. bond : bond 0.00037 ( 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 168 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.906 Fit side-chains REVERT: A 76 LYS cc_start: 0.7752 (tttm) cc_final: 0.7298 (ttpt) REVERT: A 79 GLN cc_start: 0.6827 (mm-40) cc_final: 0.6051 (pt0) REVERT: B 54 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8530 (mtmt) REVERT: B 133 MET cc_start: 0.8723 (ttm) cc_final: 0.8490 (ttm) REVERT: C 43 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.6533 (ptt180) REVERT: C 76 LYS cc_start: 0.8249 (tttm) cc_final: 0.7841 (ttpt) REVERT: C 159 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6903 (mt-10) REVERT: C 168 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.5965 (tp30) REVERT: D 42 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7920 (ttpt) REVERT: D 110 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: D 114 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: E 28 MET cc_start: 0.7737 (ttm) cc_final: 0.7489 (ttm) REVERT: E 54 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7251 (mm-30) REVERT: E 73 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7720 (p0) REVERT: E 74 GLU cc_start: 0.7790 (tt0) cc_final: 0.7454 (tt0) REVERT: F 106 GLU cc_start: 0.6979 (pp20) cc_final: 0.6668 (pp20) REVERT: F 107 ARG cc_start: 0.7948 (mmt90) cc_final: 0.7423 (mpt180) REVERT: F 128 GLN cc_start: 0.7940 (tt0) cc_final: 0.7395 (tt0) REVERT: F 154 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7465 (m-30) outliers start: 22 outliers final: 2 residues processed: 156 average time/residue: 1.6647 time to fit residues: 270.7614 Evaluate side-chains 148 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 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 110 GLN 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 F residue 154 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 15 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3420 r_free = 0.3420 target = 0.128670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.108778 restraints weight = 9261.519| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.11 r_work: 0.3051 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2575 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= 0.127 Angle : 0.631 10.771 10518 Z= 0.293 Chirality : 0.038 0.128 1176 Planarity : 0.004 0.030 1335 Dihedral : 8.603 68.827 1314 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.54 % Allowed : 16.54 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.27), residues: 933 helix: 1.82 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -2.88 (0.47), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 111 HIS 0.001 0.000 HIS D 155 PHE 0.011 0.001 PHE C 85 TYR 0.015 0.002 TYR D 87 ARG 0.006 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 564) hydrogen bonds : angle 3.87949 ( 1692) covalent geometry : bond 0.00285 ( 7764) covalent geometry : angle 0.63117 (10518) Misc. bond : bond 0.00028 ( 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 175 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.871 Fit side-chains REVERT: A 76 LYS cc_start: 0.7714 (tttm) cc_final: 0.7218 (ttpt) REVERT: A 79 GLN cc_start: 0.6781 (mm-40) cc_final: 0.5973 (pt0) REVERT: A 164 ILE cc_start: 0.7026 (OUTLIER) cc_final: 0.6720 (mt) REVERT: B 54 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8555 (mtmt) REVERT: B 133 MET cc_start: 0.8735 (ttm) cc_final: 0.8492 (ttm) REVERT: B 149 MET cc_start: 0.8061 (mmm) cc_final: 0.7835 (mmm) REVERT: C 43 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.6509 (ptt180) REVERT: C 76 LYS cc_start: 0.8243 (tttm) cc_final: 0.7834 (ttpt) REVERT: C 84 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7458 (mtt180) REVERT: C 159 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6908 (mt-10) REVERT: C 168 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.6071 (tp30) REVERT: D 83 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8183 (ppt90) REVERT: D 107 ARG cc_start: 0.7849 (mmt-90) cc_final: 0.6975 (mmt180) REVERT: E 28 MET cc_start: 0.7728 (ttm) cc_final: 0.7433 (ttm) REVERT: E 54 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7198 (mm-30) REVERT: E 73 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7697 (p0) REVERT: E 74 GLU cc_start: 0.7770 (tt0) cc_final: 0.7396 (tt0) REVERT: F 32 GLN cc_start: 0.6865 (pt0) cc_final: 0.6629 (mt0) REVERT: F 128 GLN cc_start: 0.7962 (tt0) cc_final: 0.7411 (tt0) REVERT: F 154 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7479 (m-30) outliers start: 20 outliers final: 5 residues processed: 162 average time/residue: 1.5970 time to fit residues: 270.1449 Evaluate side-chains 160 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 84 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 154 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 4 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 74 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 83 optimal weight: 0.0470 chunk 73 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 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 73 ASN E 75 GLN E 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.111906 restraints weight = 9363.784| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.12 r_work: 0.3107 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7770 Z= 0.099 Angle : 0.584 10.561 10518 Z= 0.273 Chirality : 0.036 0.125 1176 Planarity : 0.004 0.030 1335 Dihedral : 8.490 73.248 1314 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.28), residues: 933 helix: 2.01 (0.18), residues: 807 sheet: None (None), residues: 0 loop : -2.77 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 111 HIS 0.000 0.000 HIS D 155 PHE 0.011 0.001 PHE C 85 TYR 0.013 0.001 TYR F 87 ARG 0.007 0.000 ARG E 137 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 564) hydrogen bonds : angle 3.72624 ( 1692) covalent geometry : bond 0.00210 ( 7764) covalent geometry : angle 0.58366 (10518) Misc. bond : bond 0.00019 ( 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 172 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.843 Fit side-chains REVERT: A 43 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.6394 (ptt180) REVERT: A 50 ILE cc_start: 0.7968 (mm) cc_final: 0.7753 (mp) REVERT: A 52 LYS cc_start: 0.7700 (mtmm) cc_final: 0.7391 (ttmt) REVERT: A 74 GLU cc_start: 0.7890 (tt0) cc_final: 0.7600 (tt0) REVERT: A 76 LYS cc_start: 0.7591 (tttm) cc_final: 0.7144 (ttpt) REVERT: A 79 GLN cc_start: 0.6702 (mm-40) cc_final: 0.5895 (pt0) REVERT: A 141 ILE cc_start: 0.8464 (mt) cc_final: 0.8262 (mm) REVERT: A 164 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6629 (mt) REVERT: B 54 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8529 (mtmt) REVERT: C 50 ILE cc_start: 0.7816 (mm) cc_final: 0.7585 (mp) REVERT: C 76 LYS cc_start: 0.8182 (tttm) cc_final: 0.7864 (ttpt) REVERT: C 84 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7414 (mtt180) REVERT: C 159 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6792 (mt-10) REVERT: C 168 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.6016 (tp30) REVERT: D 14 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: F 107 ARG cc_start: 0.7920 (mmt90) cc_final: 0.7355 (mpt180) REVERT: F 115 THR cc_start: 0.7794 (m) cc_final: 0.7550 (p) REVERT: F 128 GLN cc_start: 0.7940 (tt0) cc_final: 0.7368 (tt0) outliers start: 19 outliers final: 4 residues processed: 161 average time/residue: 1.6230 time to fit residues: 272.7376 Evaluate side-chains 156 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 29 ARG 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 F residue 29 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 0 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 56 optimal weight: 0.0770 chunk 21 optimal weight: 0.0470 overall best weight: 1.0438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 98 ASN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.129335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.109308 restraints weight = 9439.378| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.12 r_work: 0.3054 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7770 Z= 0.129 Angle : 0.630 10.766 10518 Z= 0.295 Chirality : 0.038 0.125 1176 Planarity : 0.004 0.031 1335 Dihedral : 8.446 70.567 1314 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.29 % Allowed : 17.94 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.28), residues: 933 helix: 2.03 (0.18), residues: 798 sheet: None (None), residues: 0 loop : -2.79 (0.49), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 111 HIS 0.001 0.000 HIS D 155 PHE 0.011 0.001 PHE C 85 TYR 0.016 0.002 TYR D 87 ARG 0.007 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 564) hydrogen bonds : angle 3.80016 ( 1692) covalent geometry : bond 0.00291 ( 7764) covalent geometry : angle 0.62981 (10518) Misc. bond : bond 0.00025 ( 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 161 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.810 Fit side-chains REVERT: A 43 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.6508 (ptt180) REVERT: A 52 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7475 (ttmt) REVERT: A 74 GLU cc_start: 0.7941 (tt0) cc_final: 0.7676 (tt0) REVERT: A 76 LYS cc_start: 0.7653 (tttm) cc_final: 0.7344 (ttpt) REVERT: B 54 LYS cc_start: 0.8807 (mtmt) cc_final: 0.8564 (mtmt) REVERT: C 68 GLN cc_start: 0.7285 (tp-100) cc_final: 0.6998 (mm110) REVERT: C 76 LYS cc_start: 0.8238 (tttm) cc_final: 0.7838 (ttpt) REVERT: C 79 GLN cc_start: 0.7373 (mt0) cc_final: 0.6555 (pt0) REVERT: C 159 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6963 (mt-10) REVERT: C 168 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5941 (tp30) REVERT: D 14 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: D 114 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: E 73 ASN cc_start: 0.7969 (OUTLIER) cc_final: 0.7671 (p0) REVERT: F 107 ARG cc_start: 0.7959 (mmt90) cc_final: 0.7525 (mpt180) REVERT: F 128 GLN cc_start: 0.7907 (tt0) cc_final: 0.7412 (tt0) REVERT: F 154 ASP cc_start: 0.7777 (m-30) cc_final: 0.7480 (m-30) outliers start: 18 outliers final: 6 residues processed: 151 average time/residue: 1.5258 time to fit residues: 240.8676 Evaluate side-chains 154 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 1 MET Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 117 ILE 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 F residue 1 MET 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 31 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3414 r_free = 0.3414 target = 0.128214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.108261 restraints weight = 9414.742| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.12 r_work: 0.3039 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2713 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= 0.144 Angle : 0.657 10.835 10518 Z= 0.308 Chirality : 0.039 0.132 1176 Planarity : 0.004 0.028 1335 Dihedral : 8.481 67.860 1314 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.42 % Allowed : 17.68 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.27), residues: 933 helix: 1.86 (0.18), residues: 807 sheet: None (None), residues: 0 loop : -2.65 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 111 HIS 0.001 0.000 HIS D 155 PHE 0.011 0.001 PHE C 85 TYR 0.020 0.002 TYR D 152 ARG 0.007 0.001 ARG E 137 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 564) hydrogen bonds : angle 3.88310 ( 1692) covalent geometry : bond 0.00333 ( 7764) covalent geometry : angle 0.65673 (10518) Misc. bond : bond 0.00035 ( 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: 19 poor density : 147 time to evaluate : 0.887 Fit side-chains REVERT: A 43 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.6560 (ptt180) REVERT: A 52 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7515 (ttmt) REVERT: A 74 GLU cc_start: 0.7964 (tt0) cc_final: 0.7697 (tt0) REVERT: A 76 LYS cc_start: 0.7733 (tttm) cc_final: 0.7372 (ttmt) REVERT: B 14 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7142 (tp30) REVERT: C 73 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7336 (p0) REVERT: C 76 LYS cc_start: 0.8242 (tttm) cc_final: 0.7821 (ttpt) REVERT: C 79 GLN cc_start: 0.7252 (mt0) cc_final: 0.6461 (pt0) REVERT: C 159 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6931 (mt-10) REVERT: C 168 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.6121 (tp30) REVERT: D 14 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: D 114 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7137 (tm-30) REVERT: E 43 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7077 (ptt90) REVERT: E 73 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7637 (p0) REVERT: F 107 ARG cc_start: 0.7987 (mmt90) cc_final: 0.7547 (mpt180) REVERT: F 128 GLN cc_start: 0.7951 (tt0) cc_final: 0.7464 (tt0) REVERT: F 154 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7491 (m-30) outliers start: 19 outliers final: 6 residues processed: 157 average time/residue: 1.5430 time to fit residues: 254.0197 Evaluate side-chains 159 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 B residue 117 ILE 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 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 F residue 1 MET Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 154 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 59 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3438 r_free = 0.3438 target = 0.130195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.109464 restraints weight = 9500.594| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.23 r_work: 0.3036 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2811 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= 0.122 Angle : 0.629 10.726 10518 Z= 0.295 Chirality : 0.038 0.125 1176 Planarity : 0.004 0.029 1335 Dihedral : 8.410 69.912 1314 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.04 % Allowed : 18.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.28), residues: 933 helix: 2.01 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -2.73 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 86 HIS 0.001 0.000 HIS D 155 PHE 0.011 0.001 PHE C 85 TYR 0.024 0.002 TYR D 87 ARG 0.007 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 564) hydrogen bonds : angle 3.82082 ( 1692) covalent geometry : bond 0.00274 ( 7764) covalent geometry : angle 0.62936 (10518) Misc. bond : bond 0.00026 ( 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 160 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.909 Fit side-chains REVERT: A 43 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.6512 (ptt180) REVERT: A 50 ILE cc_start: 0.7922 (mm) cc_final: 0.7702 (mp) REVERT: A 74 GLU cc_start: 0.7935 (tt0) cc_final: 0.7631 (tt0) REVERT: A 76 LYS cc_start: 0.7631 (tttm) cc_final: 0.7223 (ttmt) REVERT: A 141 ILE cc_start: 0.8516 (mt) cc_final: 0.8295 (mm) REVERT: B 14 GLU cc_start: 0.7784 (mm-30) cc_final: 0.6990 (tp30) REVERT: B 54 LYS cc_start: 0.8825 (mtmm) cc_final: 0.8601 (mtmt) REVERT: C 68 GLN cc_start: 0.7285 (tp-100) cc_final: 0.7073 (mm110) REVERT: C 73 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7158 (p0) REVERT: C 76 LYS cc_start: 0.8136 (tttm) cc_final: 0.7714 (ttpt) REVERT: C 79 GLN cc_start: 0.7079 (mt0) cc_final: 0.6177 (pt0) REVERT: C 159 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6823 (mt-10) REVERT: C 168 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6114 (tp30) REVERT: D 14 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: E 43 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.6940 (ptt90) REVERT: E 73 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7512 (p0) REVERT: F 107 ARG cc_start: 0.7950 (mmt90) cc_final: 0.7500 (mpt180) REVERT: F 128 GLN cc_start: 0.7888 (tt0) cc_final: 0.7358 (tt0) REVERT: F 154 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7435 (m-30) outliers start: 16 outliers final: 6 residues processed: 152 average time/residue: 1.6205 time to fit residues: 257.5528 Evaluate side-chains 156 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 117 ILE 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 43 ARG Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 154 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** 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 = 0.130213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.108678 restraints weight = 9435.776| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.31 r_work: 0.3041 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 0.034 7770 Z= 0.116 Angle : 0.618 10.731 10518 Z= 0.291 Chirality : 0.037 0.123 1176 Planarity : 0.004 0.029 1335 Dihedral : 8.347 71.493 1314 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.91 % Allowed : 18.96 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.28), residues: 933 helix: 2.06 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.79 (0.52), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 86 HIS 0.000 0.000 HIS D 155 PHE 0.011 0.001 PHE C 85 TYR 0.026 0.001 TYR D 87 ARG 0.007 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 564) hydrogen bonds : angle 3.79429 ( 1692) covalent geometry : bond 0.00258 ( 7764) covalent geometry : angle 0.61757 (10518) Misc. bond : bond 0.00022 ( 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 160 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.931 Fit side-chains REVERT: A 43 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.6502 (ptt180) REVERT: A 50 ILE cc_start: 0.7878 (mm) cc_final: 0.7667 (mp) REVERT: A 76 LYS cc_start: 0.7594 (tttm) cc_final: 0.7205 (ttmt) REVERT: A 141 ILE cc_start: 0.8508 (mt) cc_final: 0.8284 (mm) REVERT: B 14 GLU cc_start: 0.7725 (mm-30) cc_final: 0.6941 (tp30) REVERT: B 54 LYS cc_start: 0.8814 (mtmm) cc_final: 0.8588 (mtmt) REVERT: C 68 GLN cc_start: 0.7280 (tp-100) cc_final: 0.7061 (mm110) REVERT: C 73 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7122 (p0) REVERT: C 76 LYS cc_start: 0.8035 (tttm) cc_final: 0.7702 (ttpt) REVERT: C 80 GLU cc_start: 0.8012 (tp30) cc_final: 0.7586 (tp30) REVERT: C 137 ARG cc_start: 0.7967 (mtt90) cc_final: 0.7678 (ttt180) REVERT: C 159 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6859 (mt-10) REVERT: C 168 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6243 (tp30) REVERT: D 14 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: E 43 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.6934 (ptt90) REVERT: E 73 ASN cc_start: 0.7829 (OUTLIER) cc_final: 0.7535 (p0) REVERT: E 76 LYS cc_start: 0.8339 (tttm) cc_final: 0.7887 (ttpt) REVERT: F 107 ARG cc_start: 0.7933 (mmt90) cc_final: 0.7482 (mpt180) REVERT: F 128 GLN cc_start: 0.7876 (tt0) cc_final: 0.7348 (tt0) REVERT: F 154 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7407 (m-30) outliers start: 15 outliers final: 6 residues processed: 153 average time/residue: 1.5322 time to fit residues: 245.1903 Evaluate side-chains 154 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 26 GLN 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 F residue 1 MET Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 154 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 58 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.129653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.108086 restraints weight = 9557.604| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.32 r_work: 0.3038 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2877 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= 0.126 Angle : 0.638 10.727 10518 Z= 0.301 Chirality : 0.038 0.124 1176 Planarity : 0.004 0.029 1335 Dihedral : 8.331 70.933 1314 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.28), residues: 933 helix: 2.07 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -2.74 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 86 HIS 0.001 0.000 HIS D 155 PHE 0.013 0.001 PHE C 85 TYR 0.028 0.002 TYR D 87 ARG 0.006 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 564) hydrogen bonds : angle 3.80428 ( 1692) covalent geometry : bond 0.00284 ( 7764) covalent geometry : angle 0.63750 (10518) Misc. bond : bond 0.00025 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6916.26 seconds wall clock time: 119 minutes 27.49 seconds (7167.49 seconds total)