Starting phenix.real_space_refine on Wed Mar 12 17:16:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ddy_27382/03_2025/8ddy_27382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ddy_27382/03_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_27382/03_2025/8ddy_27382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ddy_27382/03_2025/8ddy_27382.map" model { file = "/net/cci-nas-00/data/ceres_data/8ddy_27382/03_2025/8ddy_27382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ddy_27382/03_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-5624/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: 4.62, per 1000 atoms: 0.58 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: 2.40 Conformation dependent library (CDL) restraints added in 931.0 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: 0.74 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: 2.27 Time building geometry restraints manager: 2.62 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: 1.030 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.400 Find NCS groups from input model: 0.170 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:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- 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 7764 Z= 1.001 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 *********************** 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 : 1.119 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: 1.9614 time to fit residues: 373.9193 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 : 0.918 ------------------------------------------------------------------------------- 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 = 0.110902 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: 0.2980 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 7764 Z= 0.175 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 *********************** 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 : 0.921 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7721 (tttm) cc_final: 0.7350 (ttpt) REVERT: A 79 GLN cc_start: 0.6915 (mm-40) cc_final: 0.6279 (pt0) REVERT: A 158 LYS cc_start: 0.8135 (tttt) cc_final: 0.7817 (ttpt) REVERT: B 14 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7061 (pt0) REVERT: B 54 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8510 (mtmt) REVERT: B 133 MET cc_start: 0.8703 (ttm) cc_final: 0.8389 (ttm) REVERT: C 76 LYS cc_start: 0.8177 (tttm) cc_final: 0.7899 (ttpt) REVERT: C 84 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7423 (mtt180) REVERT: C 159 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6926 (mt-10) REVERT: C 168 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5807 (tp30) REVERT: D 107 ARG cc_start: 0.7799 (mmt90) cc_final: 0.7328 (mmt-90) REVERT: E 28 MET cc_start: 0.7650 (ttm) cc_final: 0.7433 (ttm) REVERT: E 54 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7125 (mm-30) REVERT: F 106 GLU cc_start: 0.7063 (pp20) cc_final: 0.6631 (pp20) REVERT: F 107 ARG cc_start: 0.7930 (mmt90) cc_final: 0.7441 (mpt180) outliers start: 18 outliers final: 1 residues processed: 153 average time/residue: 1.9908 time to fit residues: 316.3643 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 : 0.908 ------------------------------------------------------------------------------- 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: 0.9990 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: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.129038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.108976 restraints weight = 9478.124| |-----------------------------------------------------------------------------| 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: 0.2937 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7764 Z= 0.181 Angle : 0.640 10.911 10518 Z= 0.299 Chirality : 0.038 0.123 1176 Planarity : 0.005 0.055 1335 Dihedral : 9.096 77.934 1317 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.77 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: 0.94 (0.27), residues: 933 helix: 1.23 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -3.15 (0.46), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 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 *********************** 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 166 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7673 (tttm) cc_final: 0.7262 (ttpt) REVERT: A 79 GLN cc_start: 0.6825 (mm-40) cc_final: 0.6031 (pt0) REVERT: A 179 ARG cc_start: 0.8229 (tpt-90) cc_final: 0.7578 (tmt170) REVERT: B 14 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7405 (mm-30) REVERT: B 54 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8509 (mtmt) REVERT: B 133 MET cc_start: 0.8707 (ttm) cc_final: 0.8461 (ttm) REVERT: C 55 ASP cc_start: 0.7102 (m-30) cc_final: 0.6828 (t70) REVERT: C 76 LYS cc_start: 0.8225 (tttm) cc_final: 0.7814 (ttpt) REVERT: C 84 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7528 (mmm-85) REVERT: C 159 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6835 (mt-10) REVERT: C 168 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.5927 (tp30) REVERT: E 28 MET cc_start: 0.7785 (ttm) cc_final: 0.7548 (ttm) REVERT: E 54 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7179 (mm-30) REVERT: E 79 GLN cc_start: 0.7333 (mm-40) cc_final: 0.7094 (mm-40) REVERT: F 106 GLU cc_start: 0.7051 (pp20) cc_final: 0.6678 (pp20) REVERT: F 107 ARG cc_start: 0.7958 (mmt90) cc_final: 0.7429 (mpt180) outliers start: 15 outliers final: 1 residues processed: 157 average time/residue: 1.7107 time to fit residues: 279.9704 Evaluate side-chains 142 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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: 1.9990 chunk 71 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 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: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 33 GLN ** 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 = 0.128601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.108642 restraints weight = 9336.269| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.12 r_work: 0.3049 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7764 Z= 0.182 Angle : 0.632 10.758 10518 Z= 0.294 Chirality : 0.038 0.146 1176 Planarity : 0.004 0.038 1335 Dihedral : 8.965 76.016 1317 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.04 % Allowed : 14.89 % Favored : 83.08 % 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: 1.57 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.87 (0.48), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 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 F 87 ARG 0.006 0.000 ARG E 151 *********************** 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 164 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.908 Fit side-chains REVERT: A 43 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.6635 (ptt180) REVERT: A 76 LYS cc_start: 0.7706 (tttm) cc_final: 0.7244 (ttpt) REVERT: A 79 GLN cc_start: 0.6805 (mm-40) cc_final: 0.6033 (pt0) REVERT: B 54 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8529 (mtmt) REVERT: B 133 MET cc_start: 0.8713 (ttm) cc_final: 0.8479 (ttm) REVERT: C 43 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.6495 (ptt180) REVERT: C 76 LYS cc_start: 0.8242 (tttm) cc_final: 0.7831 (ttpt) REVERT: C 159 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6901 (mt-10) REVERT: C 168 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5951 (tp30) REVERT: D 42 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.7937 (ttpt) REVERT: D 107 ARG cc_start: 0.7795 (mmt90) cc_final: 0.7462 (mpt180) REVERT: E 28 MET cc_start: 0.7742 (ttm) cc_final: 0.7508 (ttm) REVERT: E 54 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7215 (mm-30) REVERT: E 73 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7686 (p0) REVERT: E 74 GLU cc_start: 0.7772 (tt0) cc_final: 0.7405 (tt0) REVERT: F 106 GLU cc_start: 0.6995 (pp20) cc_final: 0.6685 (pp20) REVERT: F 107 ARG cc_start: 0.7959 (mmt90) cc_final: 0.7434 (mpt180) REVERT: F 128 GLN cc_start: 0.7942 (tt0) cc_final: 0.7401 (tt0) REVERT: F 154 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7394 (m-30) outliers start: 16 outliers final: 1 residues processed: 156 average time/residue: 1.7633 time to fit residues: 286.9923 Evaluate side-chains 147 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG 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 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: 0.8980 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 33 GLN ** 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 = 0.3425 r_free = 0.3425 target = 0.129136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109203 restraints weight = 9250.602| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.12 r_work: 0.3056 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7764 Z= 0.172 Angle : 0.623 10.739 10518 Z= 0.290 Chirality : 0.038 0.124 1176 Planarity : 0.004 0.030 1335 Dihedral : 8.585 69.583 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 : 2.67 % Allowed : 16.28 % Favored : 81.04 % 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: 1.80 (0.27), residues: 933 helix: 1.83 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -2.87 (0.48), 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 0.016 0.002 TYR F 87 ARG 0.006 0.000 ARG B 107 *********************** 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 173 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.825 Fit side-chains REVERT: A 43 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.6642 (ptt180) REVERT: A 76 LYS cc_start: 0.7702 (tttm) cc_final: 0.7237 (ttpt) REVERT: A 79 GLN cc_start: 0.6757 (mm-40) cc_final: 0.5956 (pt0) REVERT: A 164 ILE cc_start: 0.6905 (OUTLIER) cc_final: 0.6611 (mt) REVERT: B 54 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8559 (mtmt) REVERT: B 133 MET cc_start: 0.8723 (ttm) cc_final: 0.8475 (ttm) REVERT: B 149 MET cc_start: 0.8041 (mmm) cc_final: 0.7819 (mmm) REVERT: C 43 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.6455 (ptt180) REVERT: C 76 LYS cc_start: 0.8236 (tttm) cc_final: 0.7850 (ttpt) REVERT: C 84 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.7445 (mtt180) REVERT: C 159 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6810 (mt-10) REVERT: C 168 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.6027 (tp30) REVERT: E 28 MET cc_start: 0.7744 (ttm) cc_final: 0.7441 (ttm) REVERT: E 54 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7190 (mm-30) REVERT: E 74 GLU cc_start: 0.7767 (tt0) cc_final: 0.7391 (tt0) REVERT: F 32 GLN cc_start: 0.6850 (pt0) cc_final: 0.6623 (mt0) REVERT: F 106 GLU cc_start: 0.6930 (pp20) cc_final: 0.6468 (pp20) REVERT: F 107 ARG cc_start: 0.7951 (mmt90) cc_final: 0.7380 (mpt180) REVERT: F 128 GLN cc_start: 0.7968 (tt0) cc_final: 0.7422 (tt0) REVERT: F 154 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7412 (m-30) outliers start: 21 outliers final: 2 residues processed: 162 average time/residue: 1.8436 time to fit residues: 310.9902 Evaluate side-chains 151 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 168 GLU Chi-restraints excluded: chain D residue 117 ILE 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: 3.9990 chunk 90 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 0.0040 chunk 73 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 33 GLN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.130958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111032 restraints weight = 9352.884| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.13 r_work: 0.3089 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7764 Z= 0.144 Angle : 0.592 10.613 10518 Z= 0.277 Chirality : 0.037 0.124 1176 Planarity : 0.004 0.029 1335 Dihedral : 8.499 72.463 1314 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.29 % Allowed : 17.18 % Favored : 80.53 % 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: 2.07 (0.28), residues: 933 helix: 2.00 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.87 (0.50), residues: 129 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 0.001 TYR D 87 ARG 0.007 0.000 ARG E 137 *********************** 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 167 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 1.668 Fit side-chains REVERT: A 74 GLU cc_start: 0.7895 (tt0) cc_final: 0.7610 (tt0) REVERT: A 76 LYS cc_start: 0.7590 (tttm) cc_final: 0.7140 (ttpt) REVERT: A 79 GLN cc_start: 0.6705 (mm-40) cc_final: 0.5890 (pt0) REVERT: A 164 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6709 (mt) REVERT: B 54 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8522 (mtmt) REVERT: B 149 MET cc_start: 0.7987 (mmm) cc_final: 0.7787 (mmm) REVERT: C 43 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.6387 (ptt180) REVERT: C 50 ILE cc_start: 0.7809 (mm) cc_final: 0.7565 (mp) REVERT: C 76 LYS cc_start: 0.8179 (tttm) cc_final: 0.7841 (ttpt) REVERT: C 79 GLN cc_start: 0.7272 (pt0) cc_final: 0.7028 (mt0) REVERT: C 84 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7391 (mtt180) REVERT: C 159 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6787 (mt-10) REVERT: C 168 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.6032 (tp30) REVERT: D 107 ARG cc_start: 0.7848 (mmt-90) cc_final: 0.6906 (mmt180) REVERT: E 73 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7673 (p0) REVERT: F 106 GLU cc_start: 0.6949 (pp20) cc_final: 0.6525 (pp20) REVERT: F 107 ARG cc_start: 0.7905 (mmt90) cc_final: 0.7352 (mpt180) REVERT: F 128 GLN cc_start: 0.7947 (tt0) cc_final: 0.7375 (tt0) outliers start: 18 outliers final: 4 residues processed: 156 average time/residue: 2.1218 time to fit residues: 346.1068 Evaluate side-chains 155 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain B residue 29 ARG 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 117 ILE Chi-restraints excluded: chain E residue 73 ASN 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: 6.9990 chunk 25 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 0.2980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.105942 restraints weight = 9479.411| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.28 r_work: 0.2997 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7764 Z= 0.227 Angle : 0.668 10.964 10518 Z= 0.313 Chirality : 0.040 0.135 1176 Planarity : 0.004 0.028 1335 Dihedral : 8.551 67.427 1314 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.16 % Allowed : 17.68 % Favored : 80.15 % 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: 1.85 (0.27), residues: 933 helix: 1.83 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.78 (0.49), residues: 129 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 0.018 0.002 TYR D 87 ARG 0.007 0.001 ARG E 137 *********************** 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 163 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.898 Fit side-chains REVERT: A 52 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7422 (ttmt) REVERT: A 76 LYS cc_start: 0.7577 (tttm) cc_final: 0.7150 (ttmt) REVERT: A 125 ASP cc_start: 0.8053 (p0) cc_final: 0.7451 (p0) REVERT: A 164 ILE cc_start: 0.6915 (OUTLIER) cc_final: 0.6712 (mt) REVERT: C 43 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.6409 (ptt180) REVERT: C 68 GLN cc_start: 0.7273 (tp-100) cc_final: 0.6974 (mm110) REVERT: C 73 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7304 (p0) REVERT: C 76 LYS cc_start: 0.8179 (tttm) cc_final: 0.7761 (ttpt) REVERT: C 84 ARG cc_start: 0.7622 (mmm-85) cc_final: 0.7399 (mtt180) REVERT: C 159 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6936 (mt-10) REVERT: C 168 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.6039 (tp30) REVERT: D 14 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: D 107 ARG cc_start: 0.7925 (mmt-90) cc_final: 0.7042 (mmt180) REVERT: D 114 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: E 54 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7208 (mm-30) REVERT: E 73 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7585 (p0) REVERT: E 74 GLU cc_start: 0.7862 (tt0) cc_final: 0.7572 (tt0) REVERT: F 106 GLU cc_start: 0.6913 (pp20) cc_final: 0.6482 (pp20) REVERT: F 107 ARG cc_start: 0.7956 (mmt90) cc_final: 0.7380 (mpt180) REVERT: F 128 GLN cc_start: 0.7915 (tt0) cc_final: 0.7398 (tt0) REVERT: F 154 ASP cc_start: 0.7825 (m-30) cc_final: 0.7482 (m-30) outliers start: 17 outliers final: 5 residues processed: 153 average time/residue: 1.6316 time to fit residues: 260.5844 Evaluate side-chains 157 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 43 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 31 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.129109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.108323 restraints weight = 9395.896| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.24 r_work: 0.3090 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7764 Z= 0.189 Angle : 0.640 10.756 10518 Z= 0.300 Chirality : 0.039 0.143 1176 Planarity : 0.004 0.029 1335 Dihedral : 8.466 68.118 1314 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.91 % Allowed : 18.07 % 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: 1.96 (0.27), residues: 933 helix: 1.91 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.76 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 111 HIS 0.001 0.000 HIS D 155 PHE 0.011 0.001 PHE C 85 TYR 0.021 0.002 TYR D 87 ARG 0.007 0.001 ARG B 107 *********************** 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 159 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.846 Fit side-chains REVERT: A 52 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7463 (ttmt) REVERT: A 74 GLU cc_start: 0.7863 (tt0) cc_final: 0.7583 (tt0) REVERT: A 76 LYS cc_start: 0.7578 (tttm) cc_final: 0.7226 (ttmt) REVERT: A 164 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6842 (mt) REVERT: B 14 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7021 (tp30) REVERT: B 54 LYS cc_start: 0.8833 (mtmm) cc_final: 0.8614 (mtmt) REVERT: C 43 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.6403 (ptt180) REVERT: C 68 GLN cc_start: 0.7274 (tp-100) cc_final: 0.6964 (mm110) REVERT: C 73 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7233 (p0) REVERT: C 76 LYS cc_start: 0.8172 (tttm) cc_final: 0.7766 (ttpt) REVERT: C 84 ARG cc_start: 0.7616 (mmm-85) cc_final: 0.7392 (mtt180) REVERT: C 159 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6823 (mt-10) REVERT: C 168 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.6088 (tp30) REVERT: D 14 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: D 107 ARG cc_start: 0.7920 (mmt-90) cc_final: 0.7111 (mmt180) REVERT: E 54 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7181 (mm-30) REVERT: E 73 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7603 (p0) REVERT: E 74 GLU cc_start: 0.7777 (tt0) cc_final: 0.7498 (tt0) REVERT: F 106 GLU cc_start: 0.6940 (pp20) cc_final: 0.6590 (pp20) REVERT: F 107 ARG cc_start: 0.7957 (mmt90) cc_final: 0.7410 (mpt180) REVERT: F 128 GLN cc_start: 0.7949 (tt0) cc_final: 0.7446 (tt0) REVERT: F 154 ASP cc_start: 0.7811 (m-30) cc_final: 0.7491 (m-30) outliers start: 15 outliers final: 7 residues processed: 151 average time/residue: 1.6063 time to fit residues: 253.3835 Evaluate side-chains 156 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 B residue 117 ILE Chi-restraints excluded: chain C residue 43 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 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 59 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.128197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.107140 restraints weight = 9499.097| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.26 r_work: 0.3010 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7764 Z= 0.210 Angle : 0.660 10.835 10518 Z= 0.310 Chirality : 0.039 0.137 1176 Planarity : 0.004 0.029 1335 Dihedral : 8.483 67.638 1314 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.80 % Allowed : 17.81 % Favored : 79.39 % 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: 1.91 (0.27), residues: 933 helix: 1.90 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -2.82 (0.49), residues: 132 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 0.024 0.002 TYR D 87 ARG 0.006 0.001 ARG B 107 *********************** 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 167 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.955 Fit side-chains REVERT: A 52 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7429 (ttmt) REVERT: A 76 LYS cc_start: 0.7584 (tttm) cc_final: 0.7197 (ttmt) REVERT: A 141 ILE cc_start: 0.8566 (mt) cc_final: 0.8359 (mm) REVERT: B 14 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7002 (tp30) REVERT: B 54 LYS cc_start: 0.8824 (mtmm) cc_final: 0.8612 (mtmt) REVERT: C 43 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.6392 (ptt180) REVERT: C 68 GLN cc_start: 0.7270 (tp-100) cc_final: 0.6963 (mm110) REVERT: C 73 ASN cc_start: 0.7703 (OUTLIER) cc_final: 0.7167 (p0) REVERT: C 76 LYS cc_start: 0.8142 (tttm) cc_final: 0.7726 (ttpt) REVERT: C 84 ARG cc_start: 0.7600 (mmm-85) cc_final: 0.7380 (mtt180) REVERT: C 159 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6851 (mt-10) REVERT: C 168 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6151 (tp30) REVERT: D 14 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: D 107 ARG cc_start: 0.7916 (mmt-90) cc_final: 0.7142 (mmt180) REVERT: E 43 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7075 (ptt90) REVERT: E 54 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7222 (mm-30) REVERT: E 73 ASN cc_start: 0.7868 (OUTLIER) cc_final: 0.7594 (p0) REVERT: E 74 GLU cc_start: 0.7821 (tt0) cc_final: 0.7367 (tt0) REVERT: E 126 LYS cc_start: 0.8285 (tppt) cc_final: 0.8030 (tptp) REVERT: F 106 GLU cc_start: 0.6898 (pp20) cc_final: 0.6571 (pp20) REVERT: F 107 ARG cc_start: 0.7966 (mmt90) cc_final: 0.7416 (mpt180) REVERT: F 128 GLN cc_start: 0.7959 (tt0) cc_final: 0.7447 (tt0) REVERT: F 154 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7499 (m-30) outliers start: 22 outliers final: 9 residues processed: 155 average time/residue: 1.8695 time to fit residues: 301.8224 Evaluate side-chains 160 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 43 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 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 29 ARG 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: 0.9990 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 0.0070 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 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 = 0.3458 r_free = 0.3458 target = 0.131779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.111119 restraints weight = 9367.931| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.23 r_work: 0.3115 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7764 Z= 0.149 Angle : 0.606 10.578 10518 Z= 0.286 Chirality : 0.037 0.125 1176 Planarity : 0.004 0.030 1335 Dihedral : 8.376 71.827 1314 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.78 % Allowed : 18.32 % 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: 2.18 (0.28), residues: 933 helix: 2.08 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.80 (0.52), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 111 HIS 0.000 0.000 HIS D 155 PHE 0.012 0.001 PHE C 85 TYR 0.026 0.001 TYR D 87 ARG 0.007 0.000 ARG B 107 ********************** 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 163 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 1.116 Fit side-chains REVERT: A 74 GLU cc_start: 0.7598 (tt0) cc_final: 0.7341 (tt0) REVERT: A 76 LYS cc_start: 0.7621 (tttm) cc_final: 0.7287 (ttmt) REVERT: A 141 ILE cc_start: 0.8504 (mt) cc_final: 0.8290 (mm) REVERT: B 14 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6940 (tp30) REVERT: B 54 LYS cc_start: 0.8821 (mtmm) cc_final: 0.8585 (mtmt) REVERT: C 68 GLN cc_start: 0.7210 (tp-100) cc_final: 0.6921 (mm110) REVERT: C 73 ASN cc_start: 0.7706 (OUTLIER) cc_final: 0.7167 (p0) REVERT: C 76 LYS cc_start: 0.8066 (tttm) cc_final: 0.7756 (ttpt) REVERT: C 137 ARG cc_start: 0.8014 (mtt90) cc_final: 0.7727 (ttt180) REVERT: C 159 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6817 (mt-10) REVERT: C 168 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6196 (tp30) REVERT: D 14 GLU cc_start: 0.8030 (mp0) cc_final: 0.7707 (mm-30) REVERT: D 107 ARG cc_start: 0.7869 (mmt-90) cc_final: 0.7146 (mmt180) REVERT: E 73 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7554 (p0) REVERT: E 76 LYS cc_start: 0.8505 (tttm) cc_final: 0.8059 (ttpt) REVERT: E 80 GLU cc_start: 0.8494 (tp30) cc_final: 0.8280 (tp30) REVERT: F 106 GLU cc_start: 0.6906 (pp20) cc_final: 0.6555 (pp20) REVERT: F 107 ARG cc_start: 0.7927 (mmt90) cc_final: 0.7372 (mpt180) REVERT: F 128 GLN cc_start: 0.7893 (tt0) cc_final: 0.7390 (tt0) REVERT: F 144 GLU cc_start: 0.7293 (pt0) cc_final: 0.6968 (tt0) outliers start: 14 outliers final: 8 residues processed: 155 average time/residue: 1.7860 time to fit residues: 288.9715 Evaluate side-chains 154 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 79 GLN Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 26 GLN 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 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 58 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 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 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.129137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.108151 restraints weight = 9518.842| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.25 r_work: 0.3078 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7764 Z= 0.197 Angle : 0.648 10.817 10518 Z= 0.305 Chirality : 0.039 0.129 1176 Planarity : 0.004 0.029 1335 Dihedral : 8.367 69.265 1314 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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 (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: 2.06 (0.28), residues: 933 helix: 2.00 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -2.75 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 86 HIS 0.001 0.000 HIS D 155 PHE 0.013 0.001 PHE C 85 TYR 0.032 0.002 TYR B 87 ARG 0.007 0.001 ARG B 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7847.52 seconds wall clock time: 137 minutes 40.89 seconds (8260.89 seconds total)