Starting phenix.real_space_refine on Thu Jul 2 01:28:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8aw3_15690/07_2026/8aw3_15690.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aw3_15690/07_2026/8aw3_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_15690/07_2026/8aw3_15690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aw3_15690/07_2026/8aw3_15690.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8aw3_15690/07_2026/8aw3_15690.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8aw3_15690/07_2026/8aw3_15690.cif" model { file = "/net/cci-nas-00/data/ceres_data/8aw3_15690/07_2026/8aw3_15690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aw3_15690/07_2026/8aw3_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-dev-6108/lib/python3.11/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: 1.09, per 1000 atoms: 0.22 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: 0.40 Conformation dependent library (CDL) restraints added in 129.1 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: 0.58 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: 0.66 Time building geometry restraints manager: 0.55 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: 2932 34.21 - 68.42: 97 68.42 - 102.62: 5 102.62 - 136.83: 1 136.83 - 171.04: 1 Dihedral angle restraints: 3036 sinusoidal: 1716 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 3033 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.700 Find NCS groups from input model: 0.020 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 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 : 15.186 171.040 2180 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 are 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/Z covalent geometry : bond 0.00789 / 0.52 ( 5303) covalent geometry : angle 1.10164 / 0.71 ( 7541) hydrogen bonds : bond 0.22117 / 13.14 ( 165) hydrogen bonds : angle 9.67033 / 5.54 ( 400) metal coordination : bond 0.00737 / 0.46 ( 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 : 0.154 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: 0.1096 time to fit residues: 9.8535 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 : 0.131 ------------------------------------------------------------------------------- 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: 9.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 8.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3954 r_free = 0.3954 target = 0.078176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.053417 restraints weight = 30342.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.054471 restraints weight = 17060.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.055046 restraints weight = 12479.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.055799 restraints weight = 10529.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.055954 restraints weight = 9510.991| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 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 = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5309 Z= 0.198 Angle : 0.646 6.152 7541 Z= 0.333 Chirality : 0.040 0.172 923 Planarity : 0.005 0.036 695 Dihedral : 13.902 178.326 1370 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.97 % Allowed : 11.38 % Favored : 84.66 % 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 are not related in a simple way. whole: -1.62 (0.39), residues: 444 helix: -0.37 (0.43), residues: 154 sheet: -3.14 (0.72), residues: 44 loop : -1.09 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 3 214 TYR 0.019 0.002 TYR 2 23 PHE 0.017 0.002 PHE 3 256 TRP 0.010 0.002 TRP 3 158 HIS 0.003 0.001 HIS 3 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 ( 5303) covalent geometry : angle 0.64650 / 0.33 ( 7541) hydrogen bonds : bond 0.05468 / 3.16 ( 165) hydrogen bonds : angle 4.73567 / 2.61 ( 400) metal coordination : bond 0.01102 / 0.67 ( 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 : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 23 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.7173 (t80) REVERT: 2 28 MET cc_start: 0.8887 (mmt) cc_final: 0.8471 (tpp) REVERT: 2 134 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6958 (pt0) outliers start: 15 outliers final: 8 residues processed: 46 average time/residue: 0.0743 time to fit residues: 4.5333 Evaluate side-chains 38 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 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 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 28 THR 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: 0.7980 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 40.0000 chunk 1 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.077509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.052200 restraints weight = 30534.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.053294 restraints weight = 17313.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.054245 restraints weight = 12536.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.054891 restraints weight = 10437.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.055051 restraints weight = 9395.725| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 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 = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5309 Z= 0.154 Angle : 0.565 11.300 7541 Z= 0.290 Chirality : 0.037 0.153 923 Planarity : 0.004 0.036 695 Dihedral : 13.477 174.740 1370 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.97 % Allowed : 13.76 % Favored : 82.28 % 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 are not related in a simple way. whole: -1.54 (0.39), residues: 444 helix: -0.39 (0.42), residues: 161 sheet: -2.88 (0.63), residues: 50 loop : -0.94 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 2 206 TYR 0.016 0.002 TYR 2 23 PHE 0.018 0.002 PHE 3 256 TRP 0.008 0.001 TRP 3 151 HIS 0.003 0.001 HIS 3 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 5303) covalent geometry : angle 0.56496 / 0.29 ( 7541) hydrogen bonds : bond 0.04960 / 2.93 ( 165) hydrogen bonds : angle 4.05343 / 2.22 ( 400) metal coordination : bond 0.01020 / 0.63 ( 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 44 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: 2 23 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7290 (t80) REVERT: 2 28 MET cc_start: 0.8758 (mmt) cc_final: 0.8270 (tpp) REVERT: 2 134 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6919 (pt0) REVERT: 3 29 MET cc_start: 0.6140 (mpp) cc_final: 0.5836 (ptp) REVERT: 3 188 MET cc_start: 0.7851 (tmm) cc_final: 0.7331 (ttm) outliers start: 15 outliers final: 8 residues processed: 41 average time/residue: 0.0641 time to fit residues: 3.5970 Evaluate side-chains 37 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 134 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 6 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 44 optimal weight: 0.0770 chunk 29 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 70 GLN 3 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.075856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.052286 restraints weight = 30748.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.053210 restraints weight = 17165.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.053992 restraints weight = 12431.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.054309 restraints weight = 10554.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.055110 restraints weight = 9632.793| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5309 Z= 0.158 Angle : 0.553 6.279 7541 Z= 0.283 Chirality : 0.036 0.155 923 Planarity : 0.004 0.031 695 Dihedral : 13.491 173.191 1369 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.23 % Allowed : 16.14 % 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 are not related in a simple way. whole: -1.38 (0.39), residues: 444 helix: -0.33 (0.43), residues: 163 sheet: -2.65 (0.63), residues: 50 loop : -0.84 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 335 TYR 0.015 0.002 TYR 2 23 PHE 0.014 0.002 PHE 3 337 TRP 0.007 0.001 TRP 3 151 HIS 0.003 0.001 HIS 3 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 5303) covalent geometry : angle 0.55252 / 0.28 ( 7541) hydrogen bonds : bond 0.04999 / 2.86 ( 165) hydrogen bonds : angle 3.73902 / 2.04 ( 400) metal coordination : bond 0.00926 / 0.58 ( 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 43 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 27 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 23 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.7391 (t80) REVERT: 2 28 MET cc_start: 0.8695 (mmt) cc_final: 0.8251 (tpp) REVERT: 3 29 MET cc_start: 0.6297 (mpp) cc_final: 0.6056 (ptp) REVERT: 3 188 MET cc_start: 0.7891 (tmm) cc_final: 0.7671 (tmm) outliers start: 16 outliers final: 12 residues processed: 40 average time/residue: 0.0641 time to fit residues: 3.5700 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 : 0.163 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 1 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3948 r_free = 0.3948 target = 0.075540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.052456 restraints weight = 30939.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.053218 restraints weight = 17055.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.053961 restraints weight = 12350.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.054222 restraints weight = 10366.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.054612 restraints weight = 9453.587| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5309 Z= 0.140 Angle : 0.537 6.876 7541 Z= 0.275 Chirality : 0.036 0.156 923 Planarity : 0.004 0.028 695 Dihedral : 13.510 172.044 1369 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.29 % Allowed : 16.67 % 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 are not related in a simple way. whole: -1.20 (0.40), residues: 444 helix: -0.23 (0.42), residues: 165 sheet: -2.26 (0.64), residues: 50 loop : -0.77 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 3 263 TYR 0.015 0.002 TYR 2 23 PHE 0.014 0.001 PHE 3 256 TRP 0.007 0.001 TRP 3 151 HIS 0.003 0.001 HIS 3 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 5303) covalent geometry : angle 0.53679 / 0.27 ( 7541) hydrogen bonds : bond 0.04711 / 2.74 ( 165) hydrogen bonds : angle 3.59162 / 1.97 ( 400) metal coordination : bond 0.00718 / 0.44 ( 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 47 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 27 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: 2 23 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7355 (t80) REVERT: 2 28 MET cc_start: 0.8713 (mmt) cc_final: 0.7803 (tpp) REVERT: 3 188 MET cc_start: 0.7836 (tmm) cc_final: 0.7568 (tmm) outliers start: 20 outliers final: 12 residues processed: 43 average time/residue: 0.0435 time to fit residues: 2.7315 Evaluate side-chains 40 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 188 SER Chi-restraints excluded: chain 3 residue 1 MET 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 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: 2.9990 chunk 3 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 70 GLN ** 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 = 0.3862 r_free = 0.3862 target = 0.071336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.048542 restraints weight = 31253.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.049499 restraints weight = 17811.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 87)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.050217 restraints weight = 12766.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.050562 restraints weight = 10436.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.050821 restraints weight = 9312.929| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 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 = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5309 Z= 0.264 Angle : 0.677 7.329 7541 Z= 0.344 Chirality : 0.040 0.175 923 Planarity : 0.004 0.031 695 Dihedral : 14.380 174.382 1369 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.50 % Allowed : 17.46 % 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 are not related in a simple way. whole: -1.43 (0.39), residues: 444 helix: -0.52 (0.42), residues: 160 sheet: -2.41 (0.63), residues: 48 loop : -0.84 (0.41), residues: 236 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 0.022 0.002 PHE 3 285 TRP 0.008 0.002 TRP 3 138 HIS 0.005 0.001 HIS 3 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.26 ( 5303) covalent geometry : angle 0.67683 / 0.34 ( 7541) hydrogen bonds : bond 0.07091 / 4.05 ( 165) hydrogen bonds : angle 4.00941 / 2.25 ( 400) metal coordination : bond 0.01048 / 0.69 ( 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: 17 poor density : 23 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: 2 28 MET cc_start: 0.8709 (mmt) cc_final: 0.8385 (tpp) REVERT: 3 188 MET cc_start: 0.7935 (tmm) cc_final: 0.7626 (tmm) outliers start: 17 outliers final: 12 residues processed: 38 average time/residue: 0.0665 time to fit residues: 3.5389 Evaluate side-chains 32 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 20 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 VAL 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 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 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 32 optimal weight: 40.0000 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 0.0470 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 70 GLN 3 315 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.075576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.051520 restraints weight = 31229.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.052382 restraints weight = 17197.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.053100 restraints weight = 12480.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.053938 restraints weight = 10470.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.053830 restraints weight = 9445.464| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 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 = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5309 Z= 0.102 Angle : 0.539 8.315 7541 Z= 0.275 Chirality : 0.037 0.164 923 Planarity : 0.003 0.026 695 Dihedral : 13.785 169.427 1369 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.70 % Allowed : 18.25 % 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 are not related in a simple way. whole: -1.12 (0.40), residues: 444 helix: -0.11 (0.43), residues: 158 sheet: -2.21 (0.67), residues: 50 loop : -0.76 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 184 TYR 0.021 0.001 TYR 2 23 PHE 0.012 0.001 PHE 3 256 TRP 0.008 0.001 TRP 3 151 HIS 0.006 0.001 HIS 3 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 5303) covalent geometry : angle 0.53872 / 0.27 ( 7541) hydrogen bonds : bond 0.04391 / 2.57 ( 165) hydrogen bonds : angle 3.48216 / 1.92 ( 400) metal coordination : bond 0.00426 / 0.27 ( 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: 14 poor density : 22 time to evaluate : 0.121 Fit side-chains REVERT: 2 28 MET cc_start: 0.8687 (mmt) cc_final: 0.8004 (tpp) REVERT: 3 188 MET cc_start: 0.7791 (tmm) cc_final: 0.7322 (ttm) outliers start: 14 outliers final: 9 residues processed: 35 average time/residue: 0.0617 time to fit residues: 3.0560 Evaluate side-chains 30 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 57 THR 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 202 ILE Chi-restraints excluded: chain 3 residue 278 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 49 optimal weight: 0.0980 chunk 45 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3912 r_free = 0.3912 target = 0.075294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.051125 restraints weight = 31332.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.052022 restraints weight = 17521.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.052708 restraints weight = 12734.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.053475 restraints weight = 10784.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.053585 restraints weight = 9673.178| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 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 = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5309 Z= 0.114 Angle : 0.533 7.896 7541 Z= 0.268 Chirality : 0.036 0.158 923 Planarity : 0.003 0.026 695 Dihedral : 13.701 171.518 1368 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.65 % Allowed : 19.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.40), residues: 444 helix: 0.01 (0.43), residues: 158 sheet: -1.94 (0.71), residues: 50 loop : -0.72 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 166 TYR 0.018 0.001 TYR 2 23 PHE 0.010 0.001 PHE 3 256 TRP 0.007 0.001 TRP 3 138 HIS 0.003 0.001 HIS 3 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 5303) covalent geometry : angle 0.53264 / 0.27 ( 7541) hydrogen bonds : bond 0.04526 / 2.60 ( 165) hydrogen bonds : angle 3.49496 / 1.94 ( 400) metal coordination : bond 0.00535 / 0.35 ( 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 31 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 21 time to evaluate : 0.198 Fit side-chains REVERT: 2 28 MET cc_start: 0.8668 (mmt) cc_final: 0.8018 (tpp) REVERT: 3 29 MET cc_start: 0.4739 (mmm) cc_final: 0.4515 (ptp) REVERT: 3 188 MET cc_start: 0.7816 (tmm) cc_final: 0.7493 (tmm) outliers start: 10 outliers final: 8 residues processed: 30 average time/residue: 0.0632 time to fit residues: 2.7519 Evaluate side-chains 29 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 26 optimal weight: 7.9990 chunk 10 optimal weight: 0.0870 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 2 optimal weight: 9.9990 chunk 46 optimal weight: 0.4980 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3923 r_free = 0.3923 target = 0.075866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.051483 restraints weight = 31577.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.051968 restraints weight = 17094.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.052902 restraints weight = 12931.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.053620 restraints weight = 10791.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.053620 restraints weight = 9687.235| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 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 = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5355 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= 0.105 Angle : 0.544 8.782 7541 Z= 0.271 Chirality : 0.035 0.148 923 Planarity : 0.003 0.028 695 Dihedral : 13.600 171.908 1368 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.38 % Allowed : 21.16 % Favored : 76.46 % 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 are not related in a simple way. whole: -0.87 (0.40), residues: 444 helix: 0.14 (0.43), residues: 158 sheet: -1.89 (0.71), residues: 50 loop : -0.68 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 206 TYR 0.018 0.001 TYR 2 23 PHE 0.007 0.001 PHE 3 307 TRP 0.007 0.001 TRP 3 138 HIS 0.006 0.001 HIS 3 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 5303) covalent geometry : angle 0.54360 / 0.27 ( 7541) hydrogen bonds : bond 0.04168 / 2.38 ( 165) hydrogen bonds : angle 3.50338 / 1.99 ( 400) metal coordination : bond 0.00350 / 0.23 ( 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 32 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.160 Fit side-chains REVERT: 2 28 MET cc_start: 0.8599 (mmt) cc_final: 0.8012 (tpp) REVERT: 3 29 MET cc_start: 0.4751 (mmm) cc_final: 0.4535 (ptp) REVERT: 3 188 MET cc_start: 0.7813 (tmm) cc_final: 0.7372 (ttm) REVERT: 3 284 MET cc_start: 0.8427 (mmm) cc_final: 0.8034 (tpp) outliers start: 9 outliers final: 7 residues processed: 30 average time/residue: 0.0649 time to fit residues: 2.8029 Evaluate side-chains 29 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 0.0570 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 overall best weight: 2.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 70 GLN ** 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 = 0.3886 r_free = 0.3886 target = 0.072376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.049440 restraints weight = 30723.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.050049 restraints weight = 17248.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.050972 restraints weight = 13075.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.051552 restraints weight = 10725.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.051866 restraints weight = 9362.516| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 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 = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5309 Z= 0.205 Angle : 0.618 7.414 7541 Z= 0.312 Chirality : 0.037 0.163 923 Planarity : 0.004 0.028 695 Dihedral : 14.007 174.545 1368 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.40), residues: 444 helix: 0.15 (0.44), residues: 158 sheet: -1.91 (0.68), residues: 48 loop : -0.78 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 193 TYR 0.017 0.002 TYR 2 23 PHE 0.014 0.002 PHE 3 285 TRP 0.011 0.001 TRP 3 138 HIS 0.018 0.002 HIS 3 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 ( 5303) covalent geometry : angle 0.61759 / 0.31 ( 7541) hydrogen bonds : bond 0.05673 / 3.20 ( 165) hydrogen bonds : angle 3.72466 / 2.14 ( 400) metal coordination : bond 0.00995 / 0.65 ( 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 30 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 21 time to evaluate : 0.107 Fit side-chains REVERT: 2 28 MET cc_start: 0.8644 (mmt) cc_final: 0.8125 (tpp) REVERT: 3 29 MET cc_start: 0.5274 (mmm) cc_final: 0.4964 (ptp) REVERT: 3 188 MET cc_start: 0.7879 (tmm) cc_final: 0.7550 (tmm) REVERT: 3 284 MET cc_start: 0.8559 (mmm) cc_final: 0.8183 (tpp) outliers start: 9 outliers final: 8 residues processed: 29 average time/residue: 0.0653 time to fit residues: 2.6512 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 : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 70 GLN ** 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 = 0.3929 r_free = 0.3929 target = 0.075914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.051895 restraints weight = 31363.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.052918 restraints weight = 17498.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.053437 restraints weight = 12712.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.054009 restraints weight = 10812.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.053944 restraints weight = 9680.402| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 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 = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5309 Z= 0.100 Angle : 0.549 8.486 7541 Z= 0.276 Chirality : 0.035 0.147 923 Planarity : 0.003 0.029 695 Dihedral : 13.665 170.451 1368 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.12 % Allowed : 21.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.40), residues: 444 helix: 0.18 (0.43), residues: 158 sheet: -1.96 (0.68), residues: 50 loop : -0.71 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 3 214 TYR 0.031 0.002 TYR 2 173 PHE 0.019 0.002 PHE 3 256 TRP 0.007 0.001 TRP 3 151 HIS 0.017 0.002 HIS 3 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 5303) covalent geometry : angle 0.54915 / 0.28 ( 7541) hydrogen bonds : bond 0.04140 / 2.38 ( 165) hydrogen bonds : angle 3.63272 / 2.10 ( 400) metal coordination : bond 0.00249 / 0.15 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1396.88 seconds wall clock time: 24 minutes 41.76 seconds (1481.76 seconds total)