Starting phenix.real_space_refine on Sat Dec 28 08:19:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ddy_27382/12_2024/8ddy_27382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ddy_27382/12_2024/8ddy_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_27382/12_2024/8ddy_27382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ddy_27382/12_2024/8ddy_27382.map" model { file = "/net/cci-nas-00/data/ceres_data/8ddy_27382/12_2024/8ddy_27382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ddy_27382/12_2024/8ddy_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-5532/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: 4.56, per 1000 atoms: 0.57 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: 2.73 Conformation dependent library (CDL) restraints added in 901.6 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: 0.71 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: 2.17 Time building geometry restraints manager: 2.59 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: 0.00 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: 2.220 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.700 Find NCS groups from input model: 0.310 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:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.450 ------------------------------------------------------------------------------- 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 : 0.917 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: 2.0444 time to fit residues: 389.5772 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 : 0.884 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 : 0.982 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7705 (tttm) cc_final: 0.7429 (ttpt) REVERT: A 79 GLN cc_start: 0.6714 (mm-40) cc_final: 0.6398 (pt0) REVERT: A 141 ILE cc_start: 0.8386 (mt) cc_final: 0.8176 (mm) REVERT: A 158 LYS cc_start: 0.8222 (tttt) cc_final: 0.7926 (ttpt) REVERT: B 14 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6840 (pt0) REVERT: B 54 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8211 (mtmt) REVERT: B 133 MET cc_start: 0.8576 (ttm) cc_final: 0.8264 (ttm) REVERT: C 76 LYS cc_start: 0.8091 (tttm) cc_final: 0.7889 (ttpt) REVERT: C 84 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7370 (mtt180) REVERT: C 168 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.5538 (tp30) REVERT: D 107 ARG cc_start: 0.7505 (mmt90) cc_final: 0.7102 (mmt-90) REVERT: E 28 MET cc_start: 0.7393 (ttm) cc_final: 0.6986 (ttm) REVERT: E 54 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6692 (mm-30) REVERT: F 106 GLU cc_start: 0.6928 (pp20) cc_final: 0.6556 (pp20) REVERT: F 107 ARG cc_start: 0.7609 (mmt90) cc_final: 0.7133 (mpt180) outliers start: 18 outliers final: 1 residues processed: 153 average time/residue: 1.9985 time to fit residues: 317.4865 Evaluate side-chains 137 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 133 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 46 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 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 106 GLN A 109 GLN ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7764 Z= 0.171 Angle : 0.633 10.895 10518 Z= 0.295 Chirality : 0.038 0.123 1176 Planarity : 0.005 0.054 1335 Dihedral : 9.040 77.137 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 : 13.10 % Favored : 84.99 % 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: 1.04 (0.27), residues: 933 helix: 1.30 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -3.11 (0.47), 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 0.011 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 : 0.986 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7690 (tttm) cc_final: 0.7411 (ttpt) REVERT: A 79 GLN cc_start: 0.6642 (mm-40) cc_final: 0.6214 (pt0) REVERT: A 179 ARG cc_start: 0.8224 (tpt-90) cc_final: 0.7658 (tpt170) REVERT: B 14 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6862 (mm-30) REVERT: B 54 LYS cc_start: 0.8517 (mtmt) cc_final: 0.8234 (mtmt) REVERT: B 133 MET cc_start: 0.8563 (ttm) cc_final: 0.8239 (ttm) REVERT: C 76 LYS cc_start: 0.8150 (tttm) cc_final: 0.7820 (ttpt) REVERT: C 168 GLU cc_start: 0.5950 (OUTLIER) cc_final: 0.5609 (tp30) REVERT: E 28 MET cc_start: 0.7450 (ttm) cc_final: 0.7105 (ttm) REVERT: E 54 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6745 (mm-30) REVERT: E 84 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7349 (mtt180) REVERT: F 106 GLU cc_start: 0.6921 (pp20) cc_final: 0.6586 (pp20) REVERT: F 107 ARG cc_start: 0.7656 (mmt90) cc_final: 0.7115 (mpt180) outliers start: 15 outliers final: 1 residues processed: 157 average time/residue: 1.7388 time to fit residues: 284.7402 Evaluate side-chains 143 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 84 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.9980 chunk 63 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 75 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7764 Z= 0.141 Angle : 0.589 10.615 10518 Z= 0.275 Chirality : 0.036 0.125 1176 Planarity : 0.004 0.038 1335 Dihedral : 8.870 74.046 1317 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.78 % Allowed : 15.78 % Favored : 82.44 % 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: 1.73 (0.27), residues: 933 helix: 1.79 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -2.97 (0.47), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 111 HIS 0.000 0.000 HIS D 155 PHE 0.011 0.001 PHE C 85 TYR 0.014 0.001 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 166 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.877 Fit side-chains REVERT: A 76 LYS cc_start: 0.7675 (tttm) cc_final: 0.7334 (ttpt) REVERT: A 79 GLN cc_start: 0.6540 (mm-40) cc_final: 0.6180 (pt0) REVERT: B 54 LYS cc_start: 0.8511 (mtmt) cc_final: 0.8227 (mtmt) REVERT: B 133 MET cc_start: 0.8581 (ttm) cc_final: 0.8320 (ttm) REVERT: C 76 LYS cc_start: 0.8114 (tttm) cc_final: 0.7882 (ttpt) REVERT: C 154 MET cc_start: 0.8019 (mmp) cc_final: 0.7656 (mmp) REVERT: C 168 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.5734 (tp30) REVERT: D 107 ARG cc_start: 0.7458 (mmt90) cc_final: 0.7173 (mpt180) REVERT: D 110 GLN cc_start: 0.6807 (OUTLIER) cc_final: 0.6454 (tt0) REVERT: E 28 MET cc_start: 0.7477 (ttm) cc_final: 0.7158 (ttm) REVERT: E 54 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6712 (mm-30) REVERT: E 73 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7663 (p0) REVERT: E 74 GLU cc_start: 0.7607 (tt0) cc_final: 0.7364 (tt0) REVERT: F 106 GLU cc_start: 0.6796 (pp20) cc_final: 0.6481 (pp20) REVERT: F 107 ARG cc_start: 0.7612 (mmt90) cc_final: 0.7081 (mpt180) REVERT: F 148 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7121 (mm-30) outliers start: 14 outliers final: 2 residues processed: 157 average time/residue: 1.6989 time to fit residues: 278.4522 Evaluate side-chains 147 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 142 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 73 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 124 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 7764 Z= 0.352 Angle : 0.752 11.143 10518 Z= 0.353 Chirality : 0.043 0.146 1176 Planarity : 0.005 0.039 1335 Dihedral : 8.931 65.685 1314 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.42 % Allowed : 17.18 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.27), residues: 933 helix: 1.40 (0.17), residues: 807 sheet: None (None), residues: 0 loop : -2.94 (0.48), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 111 HIS 0.002 0.001 HIS D 155 PHE 0.011 0.002 PHE C 85 TYR 0.016 0.002 TYR F 152 ARG 0.007 0.001 ARG E 137 *********************** 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 174 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.899 Fit side-chains REVERT: A 43 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.6448 (ptt180) REVERT: A 52 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7463 (ttmt) REVERT: A 76 LYS cc_start: 0.7812 (tttm) cc_final: 0.7381 (ttpt) REVERT: A 79 GLN cc_start: 0.6619 (mm-40) cc_final: 0.6158 (pt0) REVERT: A 125 ASP cc_start: 0.7541 (p0) cc_final: 0.7051 (p0) REVERT: A 129 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6737 (mt-10) REVERT: B 54 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8323 (mtmt) REVERT: C 43 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.6594 (ptt180) REVERT: C 76 LYS cc_start: 0.8154 (tttm) cc_final: 0.7772 (ttpt) REVERT: C 168 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5793 (tp30) REVERT: E 54 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6763 (mm-30) REVERT: E 73 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7725 (p0) REVERT: F 106 GLU cc_start: 0.6882 (pp20) cc_final: 0.6646 (pp20) REVERT: F 107 ARG cc_start: 0.7728 (mmt90) cc_final: 0.7171 (mpt180) REVERT: F 128 GLN cc_start: 0.7616 (tt0) cc_final: 0.7034 (tt0) outliers start: 19 outliers final: 4 residues processed: 164 average time/residue: 1.8309 time to fit residues: 314.0548 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 : 0.986 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 75 GLN E 98 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2616 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= 0.220 Angle : 0.666 10.818 10518 Z= 0.311 Chirality : 0.039 0.133 1176 Planarity : 0.004 0.031 1335 Dihedral : 8.688 67.137 1314 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.42 % Allowed : 18.07 % 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: 1.60 (0.27), residues: 933 helix: 1.65 (0.18), residues: 807 sheet: None (None), residues: 0 loop : -2.86 (0.49), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 86 HIS 0.001 0.001 HIS D 155 PHE 0.010 0.001 PHE C 85 TYR 0.019 0.002 TYR D 152 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 166 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.954 Fit side-chains REVERT: A 76 LYS cc_start: 0.7740 (tttm) cc_final: 0.7407 (ttpt) REVERT: A 125 ASP cc_start: 0.7458 (p0) cc_final: 0.6928 (p0) REVERT: A 158 LYS cc_start: 0.8221 (tttt) cc_final: 0.7954 (ttpt) REVERT: A 164 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6832 (mt) REVERT: C 73 ASN cc_start: 0.7879 (OUTLIER) cc_final: 0.7412 (p0) REVERT: C 76 LYS cc_start: 0.8148 (tttm) cc_final: 0.7784 (ttpt) REVERT: C 168 GLU cc_start: 0.6036 (OUTLIER) cc_final: 0.5721 (tp30) REVERT: D 14 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: D 107 ARG cc_start: 0.7583 (mmt90) cc_final: 0.7208 (mmt180) REVERT: D 114 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6726 (tm-30) REVERT: E 54 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6699 (mm-30) REVERT: E 73 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7568 (p0) REVERT: F 107 ARG cc_start: 0.7690 (mmt90) cc_final: 0.7134 (mmp80) REVERT: F 128 GLN cc_start: 0.7619 (tt0) cc_final: 0.7033 (tt0) REVERT: F 154 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7180 (m-30) outliers start: 19 outliers final: 6 residues processed: 155 average time/residue: 1.7255 time to fit residues: 279.0617 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 : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 73 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 chunk 54 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 75 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 98 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7764 Z= 0.149 Angle : 0.605 10.576 10518 Z= 0.283 Chirality : 0.037 0.125 1176 Planarity : 0.004 0.031 1335 Dihedral : 8.534 70.668 1314 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.16 % Allowed : 18.70 % 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: 2.04 (0.28), residues: 933 helix: 1.97 (0.18), residues: 807 sheet: None (None), residues: 0 loop : -2.88 (0.51), residues: 126 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 0.017 0.001 TYR B 87 ARG 0.007 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.932 Fit side-chains REVERT: A 43 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.6340 (ptt180) REVERT: A 76 LYS cc_start: 0.7646 (tttm) cc_final: 0.7332 (ttpt) REVERT: A 141 ILE cc_start: 0.8334 (mt) cc_final: 0.8118 (mm) REVERT: A 164 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6978 (mt) REVERT: B 14 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6671 (tp30) REVERT: B 54 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8345 (mtmt) REVERT: C 68 GLN cc_start: 0.6964 (tp-100) cc_final: 0.6627 (mm110) REVERT: C 73 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7323 (p0) REVERT: C 76 LYS cc_start: 0.8080 (tttm) cc_final: 0.7854 (ttpt) REVERT: C 154 MET cc_start: 0.8075 (mmp) cc_final: 0.7561 (mmp) REVERT: C 168 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5803 (tp30) REVERT: D 14 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: D 107 ARG cc_start: 0.7503 (mmt90) cc_final: 0.7122 (mmt180) REVERT: E 43 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.6740 (ptt180) REVERT: E 54 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6693 (mm-30) REVERT: F 107 ARG cc_start: 0.7604 (mmt90) cc_final: 0.7332 (mpt180) REVERT: F 128 GLN cc_start: 0.7644 (tt0) cc_final: 0.7129 (tt0) outliers start: 17 outliers final: 4 residues processed: 156 average time/residue: 1.8498 time to fit residues: 301.0149 Evaluate side-chains 150 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 73 ASN Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain F residue 36 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 75 GLN E 98 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7764 Z= 0.199 Angle : 0.646 10.815 10518 Z= 0.303 Chirality : 0.039 0.127 1176 Planarity : 0.004 0.032 1335 Dihedral : 8.484 68.696 1314 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.29 % Allowed : 18.70 % 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: 2.02 (0.28), residues: 933 helix: 1.98 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -2.87 (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 0.021 0.002 TYR B 87 ARG 0.006 0.000 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 166 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.970 Fit side-chains REVERT: A 43 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.6372 (ptt180) REVERT: A 76 LYS cc_start: 0.7702 (tttm) cc_final: 0.7352 (ttpt) REVERT: B 14 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6661 (tp30) REVERT: B 54 LYS cc_start: 0.8608 (mtmm) cc_final: 0.8351 (mtmt) REVERT: C 73 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7304 (p0) REVERT: C 76 LYS cc_start: 0.8100 (tttm) cc_final: 0.7777 (ttpt) REVERT: C 154 MET cc_start: 0.8094 (mmp) cc_final: 0.7642 (mmp) REVERT: C 168 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5683 (tp30) REVERT: D 14 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: D 107 ARG cc_start: 0.7527 (mmt90) cc_final: 0.7054 (mmt180) REVERT: E 43 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.6845 (ptt90) REVERT: E 54 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6713 (mm-30) REVERT: E 73 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7541 (p0) REVERT: E 80 GLU cc_start: 0.8091 (tp30) cc_final: 0.7703 (tp30) REVERT: F 107 ARG cc_start: 0.7661 (mmt90) cc_final: 0.7107 (mmp80) REVERT: F 128 GLN cc_start: 0.7606 (tt0) cc_final: 0.7087 (tt0) outliers start: 18 outliers final: 6 residues processed: 156 average time/residue: 1.7045 time to fit residues: 277.4537 Evaluate side-chains 155 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.0670 chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7764 Z= 0.159 Angle : 0.616 10.667 10518 Z= 0.290 Chirality : 0.037 0.124 1176 Planarity : 0.004 0.031 1335 Dihedral : 8.404 71.236 1314 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.91 % Allowed : 19.08 % 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: 2.18 (0.28), residues: 933 helix: 2.08 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.84 (0.52), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 111 HIS 0.000 0.000 HIS D 155 PHE 0.011 0.001 PHE C 85 TYR 0.023 0.001 TYR D 87 ARG 0.006 0.000 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 160 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.932 Fit side-chains REVERT: A 43 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.6376 (ptt180) REVERT: A 76 LYS cc_start: 0.7702 (tttm) cc_final: 0.7454 (ttmt) REVERT: A 141 ILE cc_start: 0.8424 (mt) cc_final: 0.8192 (mm) REVERT: B 14 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6635 (tp30) REVERT: B 54 LYS cc_start: 0.8610 (mtmm) cc_final: 0.8356 (mtmt) REVERT: C 68 GLN cc_start: 0.6943 (tp-100) cc_final: 0.6734 (mm110) REVERT: C 73 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7247 (p0) REVERT: C 76 LYS cc_start: 0.8036 (tttm) cc_final: 0.7828 (ttpt) REVERT: C 137 ARG cc_start: 0.7438 (mtt90) cc_final: 0.7118 (ttt180) REVERT: C 168 GLU cc_start: 0.5993 (OUTLIER) cc_final: 0.5702 (tp30) REVERT: D 14 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7172 (mm-30) REVERT: E 43 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.6805 (ptt90) REVERT: E 54 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6717 (mm-30) REVERT: E 73 ASN cc_start: 0.7749 (OUTLIER) cc_final: 0.7436 (p0) REVERT: E 80 GLU cc_start: 0.8072 (tp30) cc_final: 0.7709 (tp30) REVERT: F 107 ARG cc_start: 0.7632 (mmt90) cc_final: 0.7333 (mpt180) REVERT: F 128 GLN cc_start: 0.7555 (tt0) cc_final: 0.7047 (tt0) REVERT: F 154 ASP cc_start: 0.7293 (m-30) cc_final: 0.6959 (m-30) outliers start: 15 outliers final: 7 residues processed: 153 average time/residue: 1.7073 time to fit residues: 272.7247 Evaluate side-chains 151 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 73 ASN 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 53 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 0.3980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7764 Z= 0.189 Angle : 0.641 10.761 10518 Z= 0.302 Chirality : 0.038 0.125 1176 Planarity : 0.004 0.031 1335 Dihedral : 8.394 70.040 1314 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.04 % Allowed : 19.21 % 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: 2.14 (0.28), residues: 933 helix: 2.06 (0.18), residues: 801 sheet: None (None), residues: 0 loop : -2.78 (0.50), 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 0.013 0.001 PHE C 85 TYR 0.027 0.002 TYR D 87 ARG 0.007 0.000 ARG D 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 158 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.895 Fit side-chains REVERT: A 43 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.6375 (ptt180) REVERT: A 76 LYS cc_start: 0.7832 (tttm) cc_final: 0.7455 (ttpt) REVERT: A 141 ILE cc_start: 0.8474 (mt) cc_final: 0.8249 (mm) REVERT: B 14 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6640 (tp30) REVERT: B 54 LYS cc_start: 0.8614 (mtmm) cc_final: 0.8364 (mtmt) REVERT: C 68 GLN cc_start: 0.6932 (tp-100) cc_final: 0.6715 (mm110) REVERT: C 73 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7236 (p0) REVERT: C 76 LYS cc_start: 0.8004 (tttm) cc_final: 0.7763 (ttpt) REVERT: C 168 GLU cc_start: 0.6003 (OUTLIER) cc_final: 0.5770 (tp30) REVERT: D 14 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7176 (mm-30) REVERT: E 43 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.6839 (ptt90) REVERT: E 54 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6731 (mm-30) REVERT: E 73 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7532 (p0) REVERT: E 80 GLU cc_start: 0.8094 (tp30) cc_final: 0.7717 (tp30) REVERT: F 107 ARG cc_start: 0.7651 (mmt90) cc_final: 0.7336 (mpt180) REVERT: F 128 GLN cc_start: 0.7556 (tt0) cc_final: 0.7046 (tt0) outliers start: 16 outliers final: 8 residues processed: 149 average time/residue: 1.6722 time to fit residues: 260.2577 Evaluate side-chains 151 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 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 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 75 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 98 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.130991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.111086 restraints weight = 9235.293| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.11 r_work: 0.3081 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7764 Z= 0.169 Angle : 0.628 10.679 10518 Z= 0.297 Chirality : 0.038 0.123 1176 Planarity : 0.004 0.032 1335 Dihedral : 8.348 71.445 1314 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.16 % Allowed : 19.72 % Favored : 78.12 % 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: 2.22 (0.28), residues: 933 helix: 2.10 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.78 (0.52), 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 0.013 0.001 PHE C 85 TYR 0.028 0.002 TYR D 87 ARG 0.008 0.000 ARG D 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4363.98 seconds wall clock time: 78 minutes 23.54 seconds (4703.54 seconds total)