Starting phenix.real_space_refine on Fri Aug 22 15:49:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aw3_15690/08_2025/8aw3_15690.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aw3_15690/08_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_15690/08_2025/8aw3_15690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aw3_15690/08_2025/8aw3_15690.map" model { file = "/net/cci-nas-00/data/ceres_data/8aw3_15690/08_2025/8aw3_15690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aw3_15690/08_2025/8aw3_15690.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'PHE: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: 1.51, per 1000 atoms: 0.30 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: 0.33 Conformation dependent library (CDL) restraints added in 107.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.43 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: 0.58 Time building geometry restraints manager: 0.44 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: 1.750 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.320 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.230 ------------------------------------------------------------------------------- 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 5309 Z= 0.519 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG 3 214 TYR 0.045 0.004 TYR 2 130 PHE 0.013 0.002 PHE 3 256 TRP 0.021 0.002 TRP 3 158 HIS 0.007 0.001 HIS 3 300 Details of bonding type rmsd covalent geometry : bond 0.00789 ( 5303) covalent geometry : angle 1.10164 ( 7541) hydrogen bonds : bond 0.22117 ( 165) hydrogen bonds : angle 9.67033 ( 400) metal coordination : bond 0.00737 ( 6) *********************** 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 : 0.150 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: 0.1069 time to fit residues: 9.5714 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 : 0.108 ------------------------------------------------------------------------------- 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 24 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 7.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.078135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.053371 restraints weight = 30580.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.054354 restraints weight = 17254.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.054887 restraints weight = 12557.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.055444 restraints weight = 10618.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.056145 restraints weight = 9525.558| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 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 = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5309 Z= 0.189 Angle : 0.646 7.433 7541 Z= 0.332 Chirality : 0.040 0.176 923 Planarity : 0.005 0.036 695 Dihedral : 22.014 178.376 1662 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.97 % Allowed : 11.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.39), residues: 444 helix: -0.37 (0.43), residues: 154 sheet: -3.06 (0.73), residues: 44 loop : -1.06 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 3 214 TYR 0.017 0.002 TYR 2 23 PHE 0.018 0.002 PHE 3 256 TRP 0.012 0.002 TRP 3 158 HIS 0.004 0.001 HIS 3 300 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 5303) covalent geometry : angle 0.64583 ( 7541) hydrogen bonds : bond 0.05225 ( 165) hydrogen bonds : angle 4.65352 ( 400) metal coordination : bond 0.01087 ( 6) *********************** 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: 15 poor density : 34 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 23 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.7290 (t80) REVERT: 2 28 MET cc_start: 0.8870 (mmt) cc_final: 0.8438 (tpp) REVERT: 2 134 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6870 (pt0) outliers start: 15 outliers final: 8 residues processed: 47 average time/residue: 0.0720 time to fit residues: 4.3999 Evaluate side-chains 39 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 188 SER 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 39 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 25 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 42 optimal weight: 0.3980 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.078910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.054155 restraints weight = 30112.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.055195 restraints weight = 16826.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.055723 restraints weight = 12315.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.056233 restraints weight = 10552.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.056247 restraints weight = 9564.438| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 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 = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5309 Z= 0.100 Angle : 0.532 8.856 7541 Z= 0.272 Chirality : 0.037 0.153 923 Planarity : 0.004 0.031 695 Dihedral : 21.541 173.349 1662 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.44 % Allowed : 14.02 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.40), residues: 444 helix: 0.03 (0.45), residues: 149 sheet: -2.91 (0.64), residues: 50 loop : -0.79 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 206 TYR 0.016 0.001 TYR 2 23 PHE 0.013 0.002 PHE 3 256 TRP 0.007 0.001 TRP 3 158 HIS 0.002 0.001 HIS 3 300 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 5303) covalent geometry : angle 0.53183 ( 7541) hydrogen bonds : bond 0.04207 ( 165) hydrogen bonds : angle 4.22865 ( 400) metal coordination : bond 0.00573 ( 6) *********************** 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 45 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 23 TYR cc_start: 0.7722 (OUTLIER) cc_final: 0.7077 (t80) REVERT: 2 28 MET cc_start: 0.8757 (mmt) cc_final: 0.8159 (tpp) outliers start: 13 outliers final: 8 residues processed: 41 average time/residue: 0.0666 time to fit residues: 3.6871 Evaluate side-chains 36 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 86 HIS Chi-restraints excluded: chain 3 residue 1 MET Chi-restraints excluded: chain 3 residue 3 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 Chi-restraints excluded: chain 3 residue 286 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 6 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 11 optimal weight: 0.0030 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 44 optimal weight: 0.0980 chunk 29 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.7994 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.074961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.052239 restraints weight = 29841.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.053279 restraints weight = 16714.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.054085 restraints weight = 11936.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.054435 restraints weight = 9835.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.054990 restraints weight = 8853.342| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 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 = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5309 Z= 0.150 Angle : 0.566 9.878 7541 Z= 0.288 Chirality : 0.037 0.143 923 Planarity : 0.004 0.030 695 Dihedral : 21.514 174.089 1661 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.76 % Allowed : 15.08 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.39), residues: 444 helix: -0.37 (0.43), residues: 164 sheet: -2.45 (0.65), residues: 50 loop : -0.84 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 2 206 TYR 0.014 0.002 TYR 2 23 PHE 0.010 0.002 PHE 3 256 TRP 0.010 0.002 TRP 3 158 HIS 0.002 0.001 HIS 3 315 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 5303) covalent geometry : angle 0.56602 ( 7541) hydrogen bonds : bond 0.04798 ( 165) hydrogen bonds : angle 3.83989 ( 400) metal coordination : bond 0.00988 ( 6) *********************** 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 48 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: 2 23 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.7335 (t80) REVERT: 2 28 MET cc_start: 0.8745 (mmt) cc_final: 0.8252 (tpp) REVERT: 3 188 MET cc_start: 0.7892 (tmm) cc_final: 0.7409 (ttm) outliers start: 18 outliers final: 12 residues processed: 44 average time/residue: 0.0575 time to fit residues: 3.6300 Evaluate side-chains 39 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 26 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 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 6 VAL Chi-restraints excluded: chain 3 residue 110 LEU 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 324 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 43 optimal weight: 0.0870 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.5162 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.074868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.051939 restraints weight = 30234.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.053133 restraints weight = 16902.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.053728 restraints weight = 12032.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.054517 restraints weight = 10015.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.054676 restraints weight = 8911.557| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 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 = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5309 Z= 0.128 Angle : 0.538 9.232 7541 Z= 0.274 Chirality : 0.036 0.151 923 Planarity : 0.004 0.032 695 Dihedral : 21.471 171.833 1661 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.70 % Allowed : 16.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.40), residues: 444 helix: -0.21 (0.44), residues: 160 sheet: -2.44 (0.64), residues: 50 loop : -0.85 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 206 TYR 0.015 0.002 TYR 2 23 PHE 0.013 0.001 PHE 3 256 TRP 0.023 0.002 TRP 3 158 HIS 0.002 0.001 HIS 3 223 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 5303) covalent geometry : angle 0.53802 ( 7541) hydrogen bonds : bond 0.04296 ( 165) hydrogen bonds : angle 3.83171 ( 400) metal coordination : bond 0.00787 ( 6) *********************** 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 42 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 28 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: 2 23 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7293 (t80) REVERT: 2 28 MET cc_start: 0.8723 (mmt) cc_final: 0.7963 (tpp) REVERT: 2 70 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8809 (mp-120) outliers start: 14 outliers final: 9 residues processed: 40 average time/residue: 0.0532 time to fit residues: 2.9914 Evaluate side-chains 35 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.101 ------------------------------------------------------------------------------- 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 70 GLN Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 2 residue 99 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 70 GLN ** 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 = 0.3904 r_free = 0.3904 target = 0.073927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.050881 restraints weight = 32230.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.051364 restraints weight = 17561.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.052137 restraints weight = 13254.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.052443 restraints weight = 10969.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.052800 restraints weight = 9922.152| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 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 = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5309 Z= 0.286 Angle : 0.707 7.422 7541 Z= 0.356 Chirality : 0.041 0.203 923 Planarity : 0.005 0.031 695 Dihedral : 21.920 174.021 1661 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.23 % Allowed : 15.87 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.39), residues: 444 helix: -0.59 (0.42), residues: 166 sheet: -2.49 (0.61), residues: 48 loop : -0.94 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 2 193 TYR 0.016 0.003 TYR 2 205 PHE 0.018 0.002 PHE 3 285 TRP 0.019 0.002 TRP 3 158 HIS 0.003 0.001 HIS 3 223 Details of bonding type rmsd covalent geometry : bond 0.00608 ( 5303) covalent geometry : angle 0.70731 ( 7541) hydrogen bonds : bond 0.06778 ( 165) hydrogen bonds : angle 4.13721 ( 400) metal coordination : bond 0.01133 ( 6) *********************** 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 40 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 24 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: 2 23 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7684 (t80) REVERT: 2 28 MET cc_start: 0.8711 (mmt) cc_final: 0.8360 (tpp) REVERT: 3 188 MET cc_start: 0.7988 (tmm) cc_final: 0.7514 (ttm) outliers start: 16 outliers final: 11 residues processed: 39 average time/residue: 0.0543 time to fit residues: 3.0962 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 : 0.153 ------------------------------------------------------------------------------- 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 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 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 17 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 48 optimal weight: 0.1980 chunk 47 optimal weight: 4.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.073291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.050312 restraints weight = 31437.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.050983 restraints weight = 17382.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.052020 restraints weight = 13076.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.052212 restraints weight = 10540.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.052690 restraints weight = 9577.961| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 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 = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5309 Z= 0.126 Angle : 0.568 9.023 7541 Z= 0.288 Chirality : 0.037 0.163 923 Planarity : 0.004 0.029 695 Dihedral : 21.738 170.664 1661 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.44 % Allowed : 16.67 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.40), residues: 444 helix: -0.17 (0.44), residues: 160 sheet: -2.33 (0.64), residues: 50 loop : -0.82 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 184 TYR 0.016 0.001 TYR 2 23 PHE 0.012 0.002 PHE 3 256 TRP 0.009 0.002 TRP 3 151 HIS 0.004 0.001 HIS 3 223 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 5303) covalent geometry : angle 0.56769 ( 7541) hydrogen bonds : bond 0.04626 ( 165) hydrogen bonds : angle 3.81025 ( 400) metal coordination : bond 0.00635 ( 6) *********************** 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 36 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 23 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: 2 23 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.7483 (t80) REVERT: 2 28 MET cc_start: 0.8714 (mmt) cc_final: 0.7827 (tpp) REVERT: 3 188 MET cc_start: 0.7858 (tmm) cc_final: 0.7432 (ttm) REVERT: 3 256 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7564 (t80) outliers start: 13 outliers final: 8 residues processed: 35 average time/residue: 0.0581 time to fit residues: 2.8315 Evaluate side-chains 32 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.100 ------------------------------------------------------------------------------- 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 6 VAL Chi-restraints excluded: chain 3 residue 169 THR Chi-restraints excluded: chain 3 residue 202 ILE 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 47 optimal weight: 0.0020 chunk 35 optimal weight: 0.0170 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 7 optimal weight: 0.0980 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 29 optimal weight: 0.0060 chunk 10 optimal weight: 0.8980 overall best weight: 0.2042 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.089742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.060392 restraints weight = 35467.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.061269 restraints weight = 19443.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.061889 restraints weight = 14199.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.062241 restraints weight = 12240.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.062339 restraints weight = 11204.015| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5309 Z= 0.101 Angle : 0.578 9.607 7541 Z= 0.286 Chirality : 0.036 0.171 923 Planarity : 0.003 0.030 695 Dihedral : 21.456 168.143 1661 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.85 % Allowed : 19.58 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.40), residues: 444 helix: -0.07 (0.44), residues: 160 sheet: -1.79 (0.71), residues: 50 loop : -0.71 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 25 TYR 0.016 0.001 TYR 2 23 PHE 0.011 0.002 PHE 3 160 TRP 0.009 0.001 TRP 3 158 HIS 0.006 0.001 HIS 2 170 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 5303) covalent geometry : angle 0.57821 ( 7541) hydrogen bonds : bond 0.03777 ( 165) hydrogen bonds : angle 3.70422 ( 400) metal coordination : bond 0.00135 ( 6) *********************** 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 32 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 28 MET cc_start: 0.8492 (mmt) cc_final: 0.8035 (tpp) REVERT: 3 188 MET cc_start: 0.7836 (tmm) cc_final: 0.7456 (ttm) outliers start: 7 outliers final: 4 residues processed: 31 average time/residue: 0.0622 time to fit residues: 2.7740 Evaluate side-chains 27 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 3 residue 169 THR Chi-restraints excluded: chain 3 residue 278 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 26 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 0.0470 chunk 43 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 overall best weight: 0.6882 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.074570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.051795 restraints weight = 31327.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.052873 restraints weight = 16885.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.053708 restraints weight = 11902.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.054256 restraints weight = 9811.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.054689 restraints weight = 8695.752| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5309 Z= 0.099 Angle : 0.582 11.843 7541 Z= 0.289 Chirality : 0.035 0.185 923 Planarity : 0.003 0.030 695 Dihedral : 21.446 171.561 1660 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.32 % Allowed : 20.63 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.40), residues: 444 helix: 0.00 (0.44), residues: 159 sheet: -1.70 (0.73), residues: 50 loop : -0.72 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 206 TYR 0.015 0.001 TYR 2 23 PHE 0.011 0.002 PHE 3 256 TRP 0.006 0.001 TRP 3 151 HIS 0.006 0.001 HIS 3 223 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 5303) covalent geometry : angle 0.58167 ( 7541) hydrogen bonds : bond 0.03678 ( 165) hydrogen bonds : angle 3.67322 ( 400) metal coordination : bond 0.00378 ( 6) *********************** 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 28 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: 2 28 MET cc_start: 0.8628 (mmt) cc_final: 0.8229 (tpp) REVERT: 3 188 MET cc_start: 0.7856 (tmm) cc_final: 0.7453 (ttm) outliers start: 5 outliers final: 5 residues processed: 27 average time/residue: 0.0434 time to fit residues: 1.7021 Evaluate side-chains 28 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 3 residue 169 THR Chi-restraints excluded: chain 3 residue 202 ILE Chi-restraints excluded: chain 3 residue 278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.074104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.051528 restraints weight = 31397.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.052604 restraints weight = 17137.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.053457 restraints weight = 12057.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.054143 restraints weight = 9914.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.054341 restraints weight = 8677.695| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5309 Z= 0.120 Angle : 0.591 11.306 7541 Z= 0.295 Chirality : 0.036 0.176 923 Planarity : 0.003 0.030 695 Dihedral : 21.471 172.598 1660 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.32 % Allowed : 20.37 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.40), residues: 444 helix: 0.08 (0.44), residues: 159 sheet: -1.77 (0.73), residues: 50 loop : -0.68 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 206 TYR 0.013 0.001 TYR 2 23 PHE 0.009 0.001 PHE 3 30 TRP 0.007 0.001 TRP 3 138 HIS 0.005 0.001 HIS 3 223 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5303) covalent geometry : angle 0.59081 ( 7541) hydrogen bonds : bond 0.04012 ( 165) hydrogen bonds : angle 3.68403 ( 400) metal coordination : bond 0.00573 ( 6) ********************** 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 28 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: 2 28 MET cc_start: 0.8621 (mmt) cc_final: 0.8231 (tpp) REVERT: 3 188 MET cc_start: 0.7884 (tmm) cc_final: 0.7477 (ttm) outliers start: 5 outliers final: 5 residues processed: 27 average time/residue: 0.0581 time to fit residues: 2.1842 Evaluate side-chains 27 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 3 residue 169 THR Chi-restraints excluded: chain 3 residue 202 ILE Chi-restraints excluded: chain 3 residue 278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 17 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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** 3 315 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.074240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.052112 restraints weight = 31961.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.053156 restraints weight = 17151.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.054085 restraints weight = 12086.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.054702 restraints weight = 9887.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.054943 restraints weight = 8666.583| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5309 Z= 0.125 Angle : 0.598 11.238 7541 Z= 0.300 Chirality : 0.036 0.169 923 Planarity : 0.003 0.031 695 Dihedral : 21.491 172.534 1660 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.32 % Allowed : 20.63 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.41), residues: 444 helix: 0.12 (0.44), residues: 160 sheet: -1.83 (0.72), residues: 50 loop : -0.68 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 206 TYR 0.013 0.001 TYR 2 23 PHE 0.011 0.002 PHE 3 256 TRP 0.007 0.001 TRP 3 138 HIS 0.017 0.001 HIS 3 223 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 5303) covalent geometry : angle 0.59771 ( 7541) hydrogen bonds : bond 0.04041 ( 165) hydrogen bonds : angle 3.73196 ( 400) metal coordination : bond 0.00588 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1275.87 seconds wall clock time: 22 minutes 29.09 seconds (1349.09 seconds total)