Starting phenix.real_space_refine on Fri Dec 27 14:19:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aw3_15690/12_2024/8aw3_15690.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aw3_15690/12_2024/8aw3_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_15690/12_2024/8aw3_15690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aw3_15690/12_2024/8aw3_15690.map" model { file = "/net/cci-nas-00/data/ceres_data/8aw3_15690/12_2024/8aw3_15690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aw3_15690/12_2024/8aw3_15690.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 73 5.49 5 S 26 5.16 5 C 2899 2.51 5 N 903 2.21 5 O 1156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5059 Number of models: 1 Model: "" Number of chains: 5 Chain: "1" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1557 Classifications: {'RNA': 73} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 30, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 59} Chain: "2" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1341 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "3" Number of atoms: 2159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2159 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 260} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2293 SG CYS 2 136 45.404 41.101 78.006 1.00 52.15 S ATOM 2315 SG CYS 2 139 46.023 40.789 81.160 1.00 49.74 S ATOM 4670 SG CYS 3 291 40.792 29.700 77.854 1.00 52.47 S ATOM 4691 SG CYS 3 294 44.534 28.750 76.195 1.00 55.91 S Time building chain proxies: 7.38, per 1000 atoms: 1.46 Number of scatterers: 5059 At special positions: 0 Unit cell: (76.14, 76.95, 115.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 26 16.00 P 73 15.00 O 1156 8.00 N 903 7.00 C 2899 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 691.8 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: 2.50 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: 2.24 Time building geometry restraints manager: 1.65 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: 7.730 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: 0.000 Extract box with map and model: 0.600 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 24.920 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 5303 Z= 0.496 Angle : 1.102 12.209 7541 Z= 0.715 Chirality : 0.079 0.554 923 Planarity : 0.005 0.039 695 Dihedral : 20.772 171.040 2472 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.12 % Allowed : 3.44 % Favored : 94.44 % Cbeta Deviations : 0.70 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.38), residues: 444 helix: -0.66 (0.47), residues: 137 sheet: -2.56 (0.81), residues: 44 loop : -1.41 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 3 158 HIS 0.007 0.001 HIS 3 300 PHE 0.013 0.002 PHE 3 256 TYR 0.045 0.004 TYR 2 130 ARG 0.007 0.001 ARG 3 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.434 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: 0.3271 time to fit residues: 28.8356 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 : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 44 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 211 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5303 Z= 0.235 Angle : 0.620 7.619 7541 Z= 0.321 Chirality : 0.039 0.170 923 Planarity : 0.004 0.035 695 Dihedral : 21.958 177.382 1662 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.44 % Allowed : 12.17 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.39), residues: 444 helix: -0.20 (0.45), residues: 148 sheet: -2.92 (0.74), residues: 44 loop : -1.12 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 3 158 HIS 0.004 0.001 HIS 3 300 PHE 0.016 0.002 PHE 3 256 TYR 0.016 0.002 TYR 2 23 ARG 0.005 0.001 ARG 3 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 23 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.7075 (t80) REVERT: 2 28 MET cc_start: 0.8276 (mmt) cc_final: 0.7875 (tpp) REVERT: 2 134 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.6229 (pt0) REVERT: 3 282 MET cc_start: 0.8724 (mmm) cc_final: 0.8421 (mmm) outliers start: 13 outliers final: 7 residues processed: 47 average time/residue: 0.2500 time to fit residues: 15.5150 Evaluate side-chains 37 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 23 TYR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 134 GLU Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 169 THR Chi-restraints excluded: chain 3 residue 278 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 50 optimal weight: 0.0470 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6080 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5303 Z= 0.144 Angle : 0.534 9.160 7541 Z= 0.271 Chirality : 0.037 0.181 923 Planarity : 0.004 0.035 695 Dihedral : 21.473 173.331 1662 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.70 % Allowed : 13.49 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.39), residues: 444 helix: -0.03 (0.45), residues: 149 sheet: -2.59 (0.66), residues: 50 loop : -0.75 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 3 158 HIS 0.003 0.001 HIS 3 300 PHE 0.016 0.002 PHE 3 256 TYR 0.017 0.001 TYR 2 23 ARG 0.007 0.001 ARG 2 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 23 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.7007 (t80) REVERT: 2 28 MET cc_start: 0.8084 (mmt) cc_final: 0.7593 (tpp) REVERT: 3 29 MET cc_start: 0.6959 (mpp) cc_final: 0.6729 (ptp) REVERT: 3 321 THR cc_start: 0.7971 (p) cc_final: 0.7727 (t) outliers start: 14 outliers final: 8 residues processed: 43 average time/residue: 0.1686 time to fit residues: 9.7108 Evaluate side-chains 37 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 34 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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** ** 3 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5303 Z= 0.367 Angle : 0.681 5.887 7541 Z= 0.347 Chirality : 0.039 0.158 923 Planarity : 0.005 0.039 695 Dihedral : 21.899 173.619 1661 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.50 % Allowed : 15.08 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.39), residues: 444 helix: -0.77 (0.41), residues: 166 sheet: -2.59 (0.63), residues: 48 loop : -0.99 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP 3 158 HIS 0.004 0.001 HIS 3 223 PHE 0.020 0.002 PHE 3 285 TYR 0.022 0.003 TYR 2 205 ARG 0.004 0.001 ARG 2 193 *********************** 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: 17 poor density : 26 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: 2 28 MET cc_start: 0.8339 (mmt) cc_final: 0.7990 (tpp) REVERT: 3 29 MET cc_start: 0.6951 (mpp) cc_final: 0.6730 (ptp) REVERT: 3 188 MET cc_start: 0.7835 (tmm) cc_final: 0.7480 (ttm) outliers start: 17 outliers final: 13 residues processed: 41 average time/residue: 0.1788 time to fit residues: 9.9682 Evaluate side-chains 34 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 21 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 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 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 0 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 20 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5303 Z= 0.146 Angle : 0.519 6.169 7541 Z= 0.265 Chirality : 0.036 0.188 923 Planarity : 0.003 0.031 695 Dihedral : 21.592 170.173 1661 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.17 % Allowed : 16.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.39), residues: 444 helix: -0.24 (0.43), residues: 160 sheet: -2.48 (0.62), residues: 50 loop : -0.90 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 3 158 HIS 0.003 0.001 HIS 3 46 PHE 0.008 0.001 PHE 3 256 TYR 0.020 0.002 TYR 2 23 ARG 0.003 0.000 ARG 2 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: 2 28 MET cc_start: 0.8307 (mmt) cc_final: 0.7833 (tpp) REVERT: 3 188 MET cc_start: 0.7692 (tmm) cc_final: 0.7426 (ttm) outliers start: 12 outliers final: 7 residues processed: 37 average time/residue: 0.1717 time to fit residues: 8.6466 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 : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 169 THR Chi-restraints excluded: chain 3 residue 278 LEU Chi-restraints excluded: chain 3 residue 286 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.0000 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5303 Z= 0.172 Angle : 0.537 8.067 7541 Z= 0.271 Chirality : 0.036 0.153 923 Planarity : 0.003 0.030 695 Dihedral : 21.548 171.513 1661 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.65 % Allowed : 18.52 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.39), residues: 444 helix: -0.14 (0.44), residues: 159 sheet: -2.22 (0.66), residues: 50 loop : -0.91 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 3 138 HIS 0.002 0.001 HIS 3 315 PHE 0.009 0.001 PHE 3 256 TYR 0.016 0.002 TYR 2 23 ARG 0.003 0.000 ARG 2 206 *********************** 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 35 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: 2 28 MET cc_start: 0.8276 (mmt) cc_final: 0.7864 (tpp) REVERT: 3 188 MET cc_start: 0.7716 (tmm) cc_final: 0.7454 (ttm) REVERT: 3 284 MET cc_start: 0.7647 (tpp) cc_final: 0.7385 (tpp) outliers start: 10 outliers final: 7 residues processed: 33 average time/residue: 0.1507 time to fit residues: 7.1749 Evaluate side-chains 31 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 49 VAL 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 278 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 29 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 0.0170 chunk 31 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5303 Z= 0.182 Angle : 0.561 14.772 7541 Z= 0.280 Chirality : 0.037 0.158 923 Planarity : 0.003 0.030 695 Dihedral : 21.580 171.923 1661 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.70 % Allowed : 17.20 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.39), residues: 444 helix: -0.12 (0.43), residues: 159 sheet: -2.05 (0.67), residues: 52 loop : -0.82 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 3 138 HIS 0.002 0.001 HIS 3 332 PHE 0.010 0.002 PHE 3 30 TYR 0.016 0.002 TYR 2 23 ARG 0.003 0.000 ARG 2 206 *********************** 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 37 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: 2 28 MET cc_start: 0.8284 (mmt) cc_final: 0.7837 (tpp) REVERT: 3 188 MET cc_start: 0.7717 (tmm) cc_final: 0.7456 (ttm) outliers start: 14 outliers final: 10 residues processed: 35 average time/residue: 0.1522 time to fit residues: 7.4181 Evaluate side-chains 33 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 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 324 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 0.0010 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 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 0.027 5303 Z= 0.181 Angle : 0.570 9.305 7541 Z= 0.284 Chirality : 0.036 0.161 923 Planarity : 0.003 0.029 695 Dihedral : 21.584 171.916 1661 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.44 % Allowed : 17.72 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.40), residues: 444 helix: -0.15 (0.43), residues: 160 sheet: -1.97 (0.69), residues: 52 loop : -0.80 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 3 138 HIS 0.003 0.001 HIS 3 252 PHE 0.007 0.002 PHE 3 307 TYR 0.014 0.002 TYR 2 23 ARG 0.002 0.000 ARG 2 206 *********************** 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 38 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 25 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 28 MET cc_start: 0.8280 (mmt) cc_final: 0.7857 (tpp) REVERT: 3 188 MET cc_start: 0.7715 (tmm) cc_final: 0.7454 (ttm) outliers start: 13 outliers final: 10 residues processed: 36 average time/residue: 0.1481 time to fit residues: 7.6671 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 : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 21 VAL Chi-restraints excluded: chain 2 residue 49 VAL Chi-restraints excluded: chain 2 residue 86 HIS Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 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 324 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 45 optimal weight: 0.0070 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5303 Z= 0.135 Angle : 0.548 11.080 7541 Z= 0.277 Chirality : 0.035 0.159 923 Planarity : 0.003 0.028 695 Dihedral : 21.461 170.421 1661 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.65 % Allowed : 18.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.40), residues: 444 helix: -0.12 (0.43), residues: 160 sheet: -1.77 (0.73), residues: 50 loop : -0.85 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 3 151 HIS 0.007 0.001 HIS 3 223 PHE 0.008 0.001 PHE 3 256 TYR 0.015 0.001 TYR 2 23 ARG 0.003 0.000 ARG 2 206 *********************** 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 35 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 28 MET cc_start: 0.8188 (mmt) cc_final: 0.7808 (tpp) REVERT: 3 188 MET cc_start: 0.7697 (tmm) cc_final: 0.7428 (ttm) outliers start: 10 outliers final: 8 residues processed: 32 average time/residue: 0.1611 time to fit residues: 7.2133 Evaluate side-chains 31 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain 3 residue 324 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5303 Z= 0.174 Angle : 0.570 9.266 7541 Z= 0.285 Chirality : 0.036 0.151 923 Planarity : 0.003 0.030 695 Dihedral : 21.496 172.648 1660 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.12 % Allowed : 19.05 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.40), residues: 444 helix: -0.03 (0.43), residues: 160 sheet: -1.80 (0.71), residues: 50 loop : -0.83 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 3 138 HIS 0.006 0.001 HIS 3 223 PHE 0.011 0.001 PHE 3 256 TYR 0.015 0.002 TYR 2 127 ARG 0.002 0.000 ARG 2 206 ********************** 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 31 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 28 MET cc_start: 0.8191 (mmt) cc_final: 0.7820 (tpp) REVERT: 3 188 MET cc_start: 0.7736 (tmm) cc_final: 0.7458 (ttm) outliers start: 8 outliers final: 8 residues processed: 29 average time/residue: 0.1552 time to fit residues: 6.4641 Evaluate side-chains 30 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain 3 residue 324 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 29 optimal weight: 0.0370 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 32 optimal weight: 30.0000 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 332 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.089142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.059363 restraints weight = 35240.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.060258 restraints weight = 20242.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.060913 restraints weight = 15240.563| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5303 Z= 0.175 Angle : 0.591 12.535 7541 Z= 0.296 Chirality : 0.036 0.167 923 Planarity : 0.003 0.030 695 Dihedral : 21.520 172.242 1660 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.12 % Allowed : 19.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.40), residues: 444 helix: 0.05 (0.43), residues: 160 sheet: -1.85 (0.70), residues: 50 loop : -0.80 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 3 138 HIS 0.012 0.001 HIS 3 223 PHE 0.024 0.002 PHE 3 256 TYR 0.016 0.002 TYR 2 127 ARG 0.002 0.000 ARG 2 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1360.15 seconds wall clock time: 26 minutes 36.36 seconds (1596.36 seconds total)