Starting phenix.real_space_refine on Tue Feb 11 10:40:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aw3_15690/02_2025/8aw3_15690.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aw3_15690/02_2025/8aw3_15690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aw3_15690/02_2025/8aw3_15690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aw3_15690/02_2025/8aw3_15690.map" model { file = "/net/cci-nas-00/data/ceres_data/8aw3_15690/02_2025/8aw3_15690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aw3_15690/02_2025/8aw3_15690.cif" } resolution = 3.6 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 73 5.49 5 S 26 5.16 5 C 2899 2.51 5 N 903 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5059 Number of models: 1 Model: "" Number of chains: 5 Chain: "1" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1557 Classifications: {'RNA': 73} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 30, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 59} Chain: "2" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1341 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "3" Number of atoms: 2159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2159 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 260} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2293 SG CYS 2 136 45.404 41.101 78.006 1.00 52.15 S ATOM 2315 SG CYS 2 139 46.023 40.789 81.160 1.00 49.74 S ATOM 4670 SG CYS 3 291 40.792 29.700 77.854 1.00 52.47 S ATOM 4691 SG CYS 3 294 44.534 28.750 76.195 1.00 55.91 S Time building chain proxies: 4.42, per 1000 atoms: 0.87 Number of scatterers: 5059 At special positions: 0 Unit cell: (76.14, 76.95, 115.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 26 16.00 P 73 15.00 O 1156 8.00 N 903 7.00 C 2899 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 657.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 501 " pdb="ZN ZN 2 501 " - pdb=" ND1 HIS 2 90 " pdb="ZN ZN 2 501 " - pdb=" SG CYS 2 136 " pdb="ZN ZN 2 501 " - pdb=" SG CYS 2 139 " pdb=" ZN 3 501 " pdb="ZN ZN 3 501 " - pdb=" SG CYS 3 294 " pdb="ZN ZN 3 501 " - pdb=" ND1 HIS 3 252 " pdb="ZN ZN 3 501 " - pdb=" SG CYS 3 291 " 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 856 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 37.1% alpha, 12.1% beta 20 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain '2' and resid 24 through 42 removed outlier: 3.525A pdb=" N ALA 2 35 " --> pdb=" O ALA 2 31 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR 2 36 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N CYS 2 37 " --> pdb=" O LYS 2 33 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA 2 38 " --> pdb=" O GLU 2 34 " (cutoff:3.500A) Processing helix chain '2' and resid 53 through 56 removed outlier: 4.032A pdb=" N SER 2 56 " --> pdb=" O ALA 2 53 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 53 through 56' Processing helix chain '2' and resid 57 through 61 Processing helix chain '2' and resid 65 through 72 Processing helix chain '2' and resid 91 through 103 removed outlier: 3.620A pdb=" N VAL 2 96 " --> pdb=" O GLU 2 92 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU 2 97 " --> pdb=" O PHE 2 93 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA 2 103 " --> pdb=" O LEU 2 99 " (cutoff:3.500A) Processing helix chain '2' and resid 136 through 146 Processing helix chain '2' and resid 193 through 207 removed outlier: 3.712A pdb=" N LEU 2 201 " --> pdb=" O ALA 2 197 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE 2 204 " --> pdb=" O LEU 2 200 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR 2 205 " --> pdb=" O LEU 2 201 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG 2 207 " --> pdb=" O GLN 2 203 " (cutoff:3.500A) Processing helix chain '3' and resid 23 through 38 removed outlier: 3.592A pdb=" N CYS 3 27 " --> pdb=" O GLN 3 23 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER 3 32 " --> pdb=" O THR 3 28 " (cutoff:3.500A) Processing helix chain '3' and resid 41 through 45 removed outlier: 3.670A pdb=" N CYS 3 45 " --> pdb=" O PRO 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 129 Processing helix chain '3' and resid 147 through 154 removed outlier: 3.775A pdb=" N TRP 3 154 " --> pdb=" O GLU 3 150 " (cutoff:3.500A) Processing helix chain '3' and resid 172 through 186 removed outlier: 3.551A pdb=" N VAL 3 176 " --> pdb=" O SER 3 172 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY 3 177 " --> pdb=" O GLU 3 173 " (cutoff:3.500A) Processing helix chain '3' and resid 186 through 195 removed outlier: 3.838A pdb=" N ARG 3 195 " --> pdb=" O ALA 3 191 " (cutoff:3.500A) Processing helix chain '3' and resid 220 through 224 Processing helix chain '3' and resid 254 through 259 removed outlier: 3.669A pdb=" N LEU 3 258 " --> pdb=" O VAL 3 254 " (cutoff:3.500A) Processing helix chain '3' and resid 291 through 301 removed outlier: 3.506A pdb=" N MET 3 296 " --> pdb=" O VAL 3 292 " (cutoff:3.500A) Processing helix chain '3' and resid 323 through 327 Processing sheet with id=AA1, first strand: chain '2' and resid 73 through 78 removed outlier: 7.200A pdb=" N GLY 2 47 " --> pdb=" O VAL 2 132 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU 2 129 " --> pdb=" O TYR 2 152 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N GLY 2 154 " --> pdb=" O LEU 2 129 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N VAL 2 131 " --> pdb=" O GLY 2 154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '3' and resid 1 through 4 removed outlier: 4.868A pdb=" N VAL 3 336 " --> pdb=" O VAL 3 4 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL 3 306 " --> pdb=" O PHE 3 337 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N CYS 3 339 " --> pdb=" O VAL 3 306 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR 3 308 " --> pdb=" O CYS 3 339 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU 3 206 " --> pdb=" O LEU 3 216 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG 3 214 " --> pdb=" O ASP 3 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 106 through 111 removed outlier: 3.915A pdb=" N LEU 3 106 " --> pdb=" O VAL 3 21 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU 3 17 " --> pdb=" O LEU 3 110 " (cutoff:3.500A) 115 hydrogen bonds defined for protein. 312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 701 1.32 - 1.44: 1769 1.44 - 1.56: 2652 1.56 - 1.69: 145 1.69 - 1.81: 36 Bond restraints: 5303 Sorted by residual: bond pdb=" C1' G 1 70 " pdb=" N9 G 1 70 " ideal model delta sigma weight residual 1.475 1.383 0.092 1.50e-02 4.44e+03 3.72e+01 bond pdb=" C1' U 1 73 " pdb=" N1 U 1 73 " ideal model delta sigma weight residual 1.480 1.561 -0.081 1.50e-02 4.44e+03 2.89e+01 bond pdb=" C1' C 1 20 " pdb=" N1 C 1 20 " ideal model delta sigma weight residual 1.480 1.558 -0.078 1.50e-02 4.44e+03 2.73e+01 bond pdb=" C1' A 1 52 " pdb=" N9 A 1 52 " ideal model delta sigma weight residual 1.475 1.397 0.078 1.50e-02 4.44e+03 2.70e+01 bond pdb=" C1' C 1 65 " pdb=" N1 C 1 65 " ideal model delta sigma weight residual 1.480 1.556 -0.076 1.50e-02 4.44e+03 2.57e+01 ... (remaining 5298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 7177 2.44 - 4.88: 312 4.88 - 7.33: 41 7.33 - 9.77: 6 9.77 - 12.21: 5 Bond angle restraints: 7541 Sorted by residual: angle pdb=" C LEU 3 194 " pdb=" N ARG 3 195 " pdb=" CA ARG 3 195 " ideal model delta sigma weight residual 123.05 110.84 12.21 1.40e+00 5.10e-01 7.61e+01 angle pdb=" N THR 3 196 " pdb=" CA THR 3 196 " pdb=" C THR 3 196 " ideal model delta sigma weight residual 109.86 98.09 11.77 1.55e+00 4.16e-01 5.77e+01 angle pdb=" N ARG 3 195 " pdb=" CA ARG 3 195 " pdb=" C ARG 3 195 " ideal model delta sigma weight residual 108.52 120.41 -11.89 1.63e+00 3.76e-01 5.32e+01 angle pdb=" C THR 3 199 " pdb=" CA THR 3 199 " pdb=" CB THR 3 199 " ideal model delta sigma weight residual 109.80 121.45 -11.65 1.65e+00 3.67e-01 4.98e+01 angle pdb=" N GLU 3 198 " pdb=" CA GLU 3 198 " pdb=" C GLU 3 198 " ideal model delta sigma weight residual 111.28 117.87 -6.59 1.09e+00 8.42e-01 3.66e+01 ... (remaining 7536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.21: 3061 34.21 - 68.42: 239 68.42 - 102.62: 26 102.62 - 136.83: 1 136.83 - 171.04: 1 Dihedral angle restraints: 3328 sinusoidal: 2008 harmonic: 1320 Sorted by residual: dihedral pdb=" O4' U 1 36 " pdb=" C1' U 1 36 " pdb=" N1 U 1 36 " pdb=" C2 U 1 36 " ideal model delta sinusoidal sigma weight residual -128.00 43.04 -171.04 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" C THR 3 199 " pdb=" N THR 3 199 " pdb=" CA THR 3 199 " pdb=" CB THR 3 199 " ideal model delta harmonic sigma weight residual -122.00 -135.09 13.09 0 2.50e+00 1.60e-01 2.74e+01 dihedral pdb=" C PHE 2 204 " pdb=" N PHE 2 204 " pdb=" CA PHE 2 204 " pdb=" CB PHE 2 204 " ideal model delta harmonic sigma weight residual -122.60 -111.32 -11.28 0 2.50e+00 1.60e-01 2.04e+01 ... (remaining 3325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 801 0.111 - 0.222: 105 0.222 - 0.332: 10 0.332 - 0.443: 6 0.443 - 0.554: 1 Chirality restraints: 923 Sorted by residual: chirality pdb=" P G 1 1 " pdb=" OP1 G 1 1 " pdb=" OP2 G 1 1 " pdb=" O5' G 1 1 " both_signs ideal model delta sigma weight residual True 2.41 2.96 -0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" P C 1 71 " pdb=" OP1 C 1 71 " pdb=" OP2 C 1 71 " pdb=" O5' C 1 71 " both_signs ideal model delta sigma weight residual True 2.41 -2.80 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" P G 1 69 " pdb=" OP1 G 1 69 " pdb=" OP2 G 1 69 " pdb=" O5' G 1 69 " both_signs ideal model delta sigma weight residual True 2.41 -2.78 -0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 920 not shown) Planarity restraints: 695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN 2 203 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C GLN 2 203 " 0.067 2.00e-02 2.50e+03 pdb=" O GLN 2 203 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE 2 204 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 2 130 " -0.005 2.00e-02 2.50e+03 2.15e-02 9.23e+00 pdb=" CG TYR 2 130 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR 2 130 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR 2 130 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR 2 130 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR 2 130 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR 2 130 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR 2 130 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA 3 191 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.71e+00 pdb=" C ALA 3 191 " -0.045 2.00e-02 2.50e+03 pdb=" O ALA 3 191 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS 3 192 " 0.015 2.00e-02 2.50e+03 ... (remaining 692 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 15 2.48 - 3.08: 3272 3.08 - 3.69: 8450 3.69 - 4.29: 12081 4.29 - 4.90: 17548 Nonbonded interactions: 41366 Sorted by model distance: nonbonded pdb=" OH TYR 3 236 " pdb="ZN ZN 3 501 " model vdw 1.874 2.230 nonbonded pdb=" O ARG 3 181 " pdb=" OG1 THR 3 185 " model vdw 2.251 3.040 nonbonded pdb=" O ALA 3 143 " pdb=" NH1 ARG 3 145 " model vdw 2.303 3.120 nonbonded pdb=" O GLU 3 289 " pdb=" ND2 ASN 3 312 " model vdw 2.349 3.120 nonbonded pdb=" O ILE 3 327 " pdb=" NE2 HIS 3 333 " model vdw 2.350 3.120 ... (remaining 41361 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.880 Find NCS groups from input model: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 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 : 0.008 0.092 5303 Z= 0.496 Angle : 1.102 12.209 7541 Z= 0.715 Chirality : 0.079 0.554 923 Planarity : 0.005 0.039 695 Dihedral : 20.772 171.040 2472 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.12 % Allowed : 3.44 % Favored : 94.44 % Cbeta Deviations : 0.70 % Peptide Plane: Cis-proline : 0.00 % 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: -1.95 (0.38), residues: 444 helix: -0.66 (0.47), residues: 137 sheet: -2.56 (0.81), residues: 44 loop : -1.41 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 3 158 HIS 0.007 0.001 HIS 3 300 PHE 0.013 0.002 PHE 3 256 TYR 0.045 0.004 TYR 2 130 ARG 0.007 0.001 ARG 3 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 28 MET cc_start: 0.7808 (mmt) cc_final: 0.7552 (tpp) outliers start: 8 outliers final: 2 residues processed: 75 average time/residue: 0.2699 time to fit residues: 24.0090 Evaluate side-chains 35 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 44 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.078956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.054179 restraints weight = 29741.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.055160 restraints weight = 16735.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.055823 restraints weight = 12308.138| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5303 Z= 0.235 Angle : 0.620 7.619 7541 Z= 0.321 Chirality : 0.039 0.170 923 Planarity : 0.004 0.035 695 Dihedral : 21.958 177.382 1662 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.44 % Allowed : 12.17 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.53 (0.39), residues: 444 helix: -0.20 (0.45), residues: 148 sheet: -2.92 (0.74), residues: 44 loop : -1.12 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 3 158 HIS 0.004 0.001 HIS 3 300 PHE 0.016 0.002 PHE 3 256 TYR 0.016 0.002 TYR 2 23 ARG 0.005 0.001 ARG 3 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 23 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.7079 (t80) REVERT: 2 28 MET cc_start: 0.8863 (mmt) cc_final: 0.8414 (tpp) REVERT: 2 134 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6951 (pt0) outliers start: 13 outliers final: 7 residues processed: 47 average time/residue: 0.1913 time to fit residues: 11.6681 Evaluate side-chains 37 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 23 TYR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 134 GLU Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 169 THR Chi-restraints excluded: chain 3 residue 278 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 40.0000 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.2980 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 246 ASN ** 3 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.073319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.049942 restraints weight = 29768.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.051142 restraints weight = 17265.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.051999 restraints weight = 12504.985| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5303 Z= 0.329 Angle : 0.671 10.700 7541 Z= 0.344 Chirality : 0.040 0.192 923 Planarity : 0.005 0.035 695 Dihedral : 22.000 175.966 1662 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.82 % Allowed : 10.85 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.84 (0.39), residues: 444 helix: -0.81 (0.41), residues: 165 sheet: -3.18 (0.62), residues: 48 loop : -0.96 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 3 138 HIS 0.004 0.001 HIS 3 223 PHE 0.018 0.002 PHE 3 256 TYR 0.017 0.003 TYR 2 205 ARG 0.007 0.001 ARG 2 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 29 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: 2 23 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7589 (t80) REVERT: 2 28 MET cc_start: 0.8695 (mmt) cc_final: 0.8245 (tpp) REVERT: 2 134 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6969 (pt0) REVERT: 3 188 MET cc_start: 0.7914 (tmm) cc_final: 0.7405 (ttm) outliers start: 22 outliers final: 14 residues processed: 49 average time/residue: 0.1524 time to fit residues: 10.1986 Evaluate side-chains 39 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 23 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 23 TYR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 134 GLU Chi-restraints excluded: chain 2 residue 173 TYR Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 15 SER Chi-restraints excluded: chain 3 residue 169 THR Chi-restraints excluded: chain 3 residue 202 ILE Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 286 VAL Chi-restraints excluded: chain 3 residue 324 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 40 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.074891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.052336 restraints weight = 30710.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.053379 restraints weight = 16735.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.054357 restraints weight = 11849.379| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5303 Z= 0.142 Angle : 0.547 9.423 7541 Z= 0.277 Chirality : 0.037 0.156 923 Planarity : 0.004 0.030 695 Dihedral : 21.610 170.175 1662 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.70 % Allowed : 15.61 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.43 (0.39), residues: 444 helix: -0.32 (0.43), residues: 160 sheet: -2.73 (0.61), residues: 50 loop : -0.90 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 3 151 HIS 0.003 0.001 HIS 3 300 PHE 0.014 0.002 PHE 3 307 TYR 0.016 0.001 TYR 2 23 ARG 0.004 0.001 ARG 2 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 27 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: 2 23 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.7295 (t80) REVERT: 2 28 MET cc_start: 0.8668 (mmt) cc_final: 0.7807 (tpp) REVERT: 3 188 MET cc_start: 0.7792 (tmm) cc_final: 0.7331 (ttm) outliers start: 14 outliers final: 9 residues processed: 37 average time/residue: 0.1617 time to fit residues: 8.1968 Evaluate side-chains 34 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 23 TYR Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 169 THR Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 286 VAL Chi-restraints excluded: chain 3 residue 321 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 11 optimal weight: 0.0970 chunk 2 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 0.4980 chunk 49 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.075843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.052701 restraints weight = 30748.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.053150 restraints weight = 16711.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.054174 restraints weight = 12699.087| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5303 Z= 0.186 Angle : 0.563 11.610 7541 Z= 0.282 Chirality : 0.037 0.152 923 Planarity : 0.004 0.028 695 Dihedral : 21.582 172.114 1661 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.50 % Allowed : 15.87 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.27 (0.39), residues: 444 helix: -0.20 (0.44), residues: 159 sheet: -2.46 (0.63), residues: 50 loop : -0.83 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP 3 158 HIS 0.002 0.001 HIS 3 315 PHE 0.009 0.001 PHE 3 256 TYR 0.015 0.002 TYR 2 23 ARG 0.003 0.000 ARG 2 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 24 time to evaluate : 0.462 Fit side-chains REVERT: 2 23 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.7317 (t80) REVERT: 2 28 MET cc_start: 0.8695 (mmt) cc_final: 0.7856 (tpp) REVERT: 3 188 MET cc_start: 0.7821 (tmm) cc_final: 0.7556 (tmm) outliers start: 17 outliers final: 9 residues processed: 38 average time/residue: 0.1328 time to fit residues: 7.4128 Evaluate side-chains 33 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 23 TYR Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 169 THR Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 286 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 0.4980 chunk 13 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 0.0970 overall best weight: 4.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 315 HIS ** 3 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.073382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.049874 restraints weight = 31650.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.050563 restraints weight = 17651.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.051271 restraints weight = 12881.488| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 5303 Z= 0.421 Angle : 0.723 8.039 7541 Z= 0.367 Chirality : 0.041 0.175 923 Planarity : 0.005 0.033 695 Dihedral : 22.062 174.658 1661 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.44 % Allowed : 17.72 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.53 (0.39), residues: 444 helix: -0.57 (0.42), residues: 160 sheet: -2.46 (0.64), residues: 48 loop : -0.92 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP 3 158 HIS 0.004 0.001 HIS 3 315 PHE 0.020 0.003 PHE 3 256 TYR 0.017 0.003 TYR 2 205 ARG 0.004 0.001 ARG 2 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 20 time to evaluate : 0.444 Fit side-chains REVERT: 2 28 MET cc_start: 0.8737 (mmt) cc_final: 0.8146 (tpp) REVERT: 3 188 MET cc_start: 0.7935 (tmm) cc_final: 0.7641 (tmm) outliers start: 13 outliers final: 11 residues processed: 31 average time/residue: 0.1133 time to fit residues: 5.3942 Evaluate side-chains 29 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 18 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 188 SER Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 169 THR Chi-restraints excluded: chain 3 residue 202 ILE Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 286 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.072506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.049358 restraints weight = 30471.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.050595 restraints weight = 17274.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.050947 restraints weight = 12284.167| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5303 Z= 0.211 Angle : 0.602 10.990 7541 Z= 0.307 Chirality : 0.038 0.171 923 Planarity : 0.004 0.029 695 Dihedral : 21.909 172.227 1661 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.17 % Allowed : 19.05 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.40), residues: 444 helix: -0.33 (0.43), residues: 160 sheet: -2.33 (0.67), residues: 50 loop : -0.83 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 3 158 HIS 0.005 0.001 HIS 3 223 PHE 0.010 0.002 PHE 3 256 TYR 0.020 0.002 TYR 2 23 ARG 0.003 0.000 ARG 3 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 0.435 Fit side-chains REVERT: 2 28 MET cc_start: 0.8735 (mmt) cc_final: 0.8051 (tpp) REVERT: 3 188 MET cc_start: 0.7839 (tmm) cc_final: 0.7350 (ttm) REVERT: 3 256 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7935 (t80) outliers start: 12 outliers final: 8 residues processed: 30 average time/residue: 0.1128 time to fit residues: 5.3234 Evaluate side-chains 26 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 17 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 169 THR Chi-restraints excluded: chain 3 residue 256 PHE Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 286 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.0670 chunk 13 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.075504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.051772 restraints weight = 31098.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.052588 restraints weight = 16915.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.053091 restraints weight = 12276.458| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5303 Z= 0.159 Angle : 0.566 10.372 7541 Z= 0.283 Chirality : 0.036 0.159 923 Planarity : 0.003 0.029 695 Dihedral : 21.703 172.456 1661 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.91 % Allowed : 20.11 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.07 (0.40), residues: 444 helix: -0.07 (0.43), residues: 160 sheet: -2.00 (0.69), residues: 50 loop : -0.78 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 3 138 HIS 0.003 0.001 HIS 3 332 PHE 0.008 0.001 PHE 3 307 TYR 0.017 0.002 TYR 2 23 ARG 0.003 0.000 ARG 3 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 19 time to evaluate : 0.368 Fit side-chains REVERT: 2 23 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7142 (t80) REVERT: 2 28 MET cc_start: 0.8607 (mmt) cc_final: 0.7730 (tpp) REVERT: 3 188 MET cc_start: 0.7797 (tmm) cc_final: 0.7356 (ttm) outliers start: 11 outliers final: 8 residues processed: 28 average time/residue: 0.1230 time to fit residues: 5.3719 Evaluate side-chains 28 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 23 TYR Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 169 THR Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 286 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 21 optimal weight: 4.9990 chunk 48 optimal weight: 0.0980 chunk 3 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 0.0060 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.075343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.051549 restraints weight = 30664.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.052467 restraints weight = 17044.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.053306 restraints weight = 12392.664| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5303 Z= 0.163 Angle : 0.560 9.128 7541 Z= 0.281 Chirality : 0.036 0.162 923 Planarity : 0.003 0.031 695 Dihedral : 21.703 172.998 1660 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.38 % Allowed : 20.63 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.40), residues: 444 helix: -0.00 (0.43), residues: 160 sheet: -1.96 (0.69), residues: 50 loop : -0.69 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 3 138 HIS 0.004 0.001 HIS 3 223 PHE 0.007 0.001 PHE 3 307 TYR 0.018 0.002 TYR 2 23 ARG 0.002 0.000 ARG 3 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.498 Fit side-chains REVERT: 2 23 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.7128 (t80) REVERT: 2 28 MET cc_start: 0.8645 (mmt) cc_final: 0.7708 (tpp) REVERT: 3 188 MET cc_start: 0.7833 (tmm) cc_final: 0.7383 (ttm) outliers start: 9 outliers final: 7 residues processed: 28 average time/residue: 0.1415 time to fit residues: 5.9643 Evaluate side-chains 28 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 23 TYR Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 169 THR Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.074532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.050447 restraints weight = 31010.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.050956 restraints weight = 17082.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.052057 restraints weight = 13077.540| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5303 Z= 0.237 Angle : 0.598 8.904 7541 Z= 0.301 Chirality : 0.037 0.157 923 Planarity : 0.004 0.032 695 Dihedral : 21.761 174.817 1660 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.65 % Allowed : 20.63 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.40), residues: 444 helix: 0.05 (0.44), residues: 160 sheet: -2.09 (0.67), residues: 50 loop : -0.71 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 3 138 HIS 0.005 0.001 HIS 3 223 PHE 0.009 0.002 PHE 3 256 TYR 0.016 0.002 TYR 2 23 ARG 0.003 0.000 ARG 2 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.360 Fit side-chains REVERT: 2 23 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.7305 (t80) REVERT: 2 28 MET cc_start: 0.8660 (mmt) cc_final: 0.7888 (tpp) REVERT: 3 188 MET cc_start: 0.7821 (tmm) cc_final: 0.7392 (ttm) outliers start: 10 outliers final: 9 residues processed: 27 average time/residue: 0.1432 time to fit residues: 5.7123 Evaluate side-chains 28 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 18 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 23 TYR Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 169 THR Chi-restraints excluded: chain 3 residue 202 ILE Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.075222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.050923 restraints weight = 32001.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.051435 restraints weight = 17252.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.052347 restraints weight = 13051.008| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5303 Z= 0.167 Angle : 0.570 8.907 7541 Z= 0.284 Chirality : 0.036 0.165 923 Planarity : 0.003 0.032 695 Dihedral : 21.683 172.706 1660 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.38 % Allowed : 21.43 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.95 (0.40), residues: 444 helix: 0.08 (0.44), residues: 160 sheet: -2.08 (0.68), residues: 50 loop : -0.70 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 3 138 HIS 0.004 0.001 HIS 3 223 PHE 0.007 0.001 PHE 3 307 TYR 0.018 0.002 TYR 2 23 ARG 0.003 0.000 ARG 3 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2235.52 seconds wall clock time: 40 minutes 30.68 seconds (2430.68 seconds total)