Starting phenix.real_space_refine on Wed Mar 12 18:10:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7agg_11779/03_2025/7agg_11779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7agg_11779/03_2025/7agg_11779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7agg_11779/03_2025/7agg_11779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7agg_11779/03_2025/7agg_11779.map" model { file = "/net/cci-nas-00/data/ceres_data/7agg_11779/03_2025/7agg_11779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7agg_11779/03_2025/7agg_11779.cif" } resolution = 3.3 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= 0.001 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 5206 2.51 5 N 1344 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8252 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1538 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "D" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1819 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1538 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "C" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1538 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1819 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Time building chain proxies: 5.36, per 1000 atoms: 0.65 Number of scatterers: 8252 At special positions: 0 Unit cell: (113.75, 110.5, 101.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1669 8.00 N 1344 7.00 C 5206 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: 1.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2018 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 17 sheets defined 7.5% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.558A pdb=" N GLY A 234 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 removed outlier: 5.642A pdb=" N LYS A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 296 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 231 through 236 removed outlier: 3.558A pdb=" N GLY B 234 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 252 removed outlier: 5.642A pdb=" N LYS B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 252 " --> pdb=" O ARG B 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 185 through 188 Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.557A pdb=" N GLY C 234 " --> pdb=" O ASN C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 removed outlier: 5.642A pdb=" N LYS C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 252 " --> pdb=" O ARG C 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 296 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 135 removed outlier: 3.573A pdb=" N TYR A 320 " --> pdb=" O VAL A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 199 removed outlier: 5.896A pdb=" N ASN A 297 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA4, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.990A pdb=" N THR D 187 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 154 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR D 189 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 130 through 131 removed outlier: 3.579A pdb=" N MET D 130 " --> pdb=" O ILE D 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 222 through 223 Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 231 removed outlier: 6.723A pdb=" N SER D 302 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 133 through 135 removed outlier: 3.573A pdb=" N TYR B 320 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 190 through 199 removed outlier: 5.896A pdb=" N ASN B 297 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AB2, first strand: chain 'C' and resid 133 through 135 removed outlier: 3.572A pdb=" N TYR C 320 " --> pdb=" O VAL C 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 190 through 199 removed outlier: 5.897A pdb=" N ASN C 297 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 219 through 220 Processing sheet with id=AB5, first strand: chain 'F' and resid 114 through 120 removed outlier: 6.991A pdb=" N THR F 187 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU F 154 " --> pdb=" O THR F 187 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR F 189 " --> pdb=" O VAL F 152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 130 through 131 removed outlier: 3.578A pdb=" N MET F 130 " --> pdb=" O ILE F 171 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 222 through 223 Processing sheet with id=AB8, first strand: chain 'F' and resid 229 through 231 removed outlier: 6.725A pdb=" N SER F 302 " --> pdb=" O ALA F 264 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 537 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2700 1.34 - 1.46: 1662 1.46 - 1.57: 4002 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 8418 Sorted by residual: bond pdb=" CB TRP C 135 " pdb=" CG TRP C 135 " ideal model delta sigma weight residual 1.498 1.443 0.055 3.10e-02 1.04e+03 3.10e+00 bond pdb=" CB TRP A 135 " pdb=" CG TRP A 135 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.06e+00 bond pdb=" CB TRP B 135 " pdb=" CG TRP B 135 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.03e+00 bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.09e+00 bond pdb=" CG1 ILE A 273 " pdb=" CD1 ILE A 273 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.08e+00 ... (remaining 8413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 10498 1.26 - 2.52: 791 2.52 - 3.77: 144 3.77 - 5.03: 48 5.03 - 6.29: 9 Bond angle restraints: 11490 Sorted by residual: angle pdb=" N TRP A 135 " pdb=" CA TRP A 135 " pdb=" CB TRP A 135 " ideal model delta sigma weight residual 111.56 106.66 4.90 1.52e+00 4.33e-01 1.04e+01 angle pdb=" N TRP C 135 " pdb=" CA TRP C 135 " pdb=" CB TRP C 135 " ideal model delta sigma weight residual 111.56 106.66 4.90 1.52e+00 4.33e-01 1.04e+01 angle pdb=" N TRP B 135 " pdb=" CA TRP B 135 " pdb=" CB TRP B 135 " ideal model delta sigma weight residual 111.56 106.68 4.88 1.52e+00 4.33e-01 1.03e+01 angle pdb=" C LYS D 313 " pdb=" CA LYS D 313 " pdb=" CB LYS D 313 " ideal model delta sigma weight residual 110.96 106.03 4.93 1.54e+00 4.22e-01 1.03e+01 angle pdb=" C LYS F 313 " pdb=" CA LYS F 313 " pdb=" CB LYS F 313 " ideal model delta sigma weight residual 110.96 106.03 4.93 1.54e+00 4.22e-01 1.02e+01 ... (remaining 11485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 4637 17.28 - 34.56: 311 34.56 - 51.85: 44 51.85 - 69.13: 19 69.13 - 86.41: 8 Dihedral angle restraints: 5019 sinusoidal: 1907 harmonic: 3112 Sorted by residual: dihedral pdb=" CA GLU D 240 " pdb=" C GLU D 240 " pdb=" N VAL D 241 " pdb=" CA VAL D 241 " ideal model delta harmonic sigma weight residual 180.00 -154.69 -25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA GLU F 240 " pdb=" C GLU F 240 " pdb=" N VAL F 241 " pdb=" CA VAL F 241 " ideal model delta harmonic sigma weight residual -180.00 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ILE F 315 " pdb=" C ILE F 315 " pdb=" N ARG F 316 " pdb=" CA ARG F 316 " ideal model delta harmonic sigma weight residual 180.00 155.57 24.43 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 5016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1024 0.057 - 0.115: 292 0.115 - 0.172: 39 0.172 - 0.230: 0 0.230 - 0.287: 2 Chirality restraints: 1357 Sorted by residual: chirality pdb=" CB VAL D 204 " pdb=" CA VAL D 204 " pdb=" CG1 VAL D 204 " pdb=" CG2 VAL D 204 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB VAL F 204 " pdb=" CA VAL F 204 " pdb=" CG1 VAL F 204 " pdb=" CG2 VAL F 204 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA TYR F 158 " pdb=" N TYR F 158 " pdb=" C TYR F 158 " pdb=" CB TYR F 158 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 1354 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 135 " -0.040 2.00e-02 2.50e+03 4.40e-02 4.83e+01 pdb=" CG TRP A 135 " 0.113 2.00e-02 2.50e+03 pdb=" CD1 TRP A 135 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP A 135 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 135 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 135 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 135 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 135 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 135 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 135 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 135 " -0.040 2.00e-02 2.50e+03 4.39e-02 4.82e+01 pdb=" CG TRP C 135 " 0.113 2.00e-02 2.50e+03 pdb=" CD1 TRP C 135 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP C 135 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C 135 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 135 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 135 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 135 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 135 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP C 135 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 135 " 0.040 2.00e-02 2.50e+03 4.39e-02 4.81e+01 pdb=" CG TRP B 135 " -0.113 2.00e-02 2.50e+03 pdb=" CD1 TRP B 135 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP B 135 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 135 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 135 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 135 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 135 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 135 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP B 135 " 0.002 2.00e-02 2.50e+03 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 74 2.56 - 3.15: 6661 3.15 - 3.73: 12795 3.73 - 4.32: 18999 4.32 - 4.90: 30816 Nonbonded interactions: 69345 Sorted by model distance: nonbonded pdb=" OH TYR A 319 " pdb=" OH TYR B 319 " model vdw 1.980 3.040 nonbonded pdb=" O HIS F 273 " pdb=" OG1 THR F 286 " model vdw 2.236 3.040 nonbonded pdb=" O HIS D 273 " pdb=" OG1 THR D 286 " model vdw 2.237 3.040 nonbonded pdb=" OG SER A 238 " pdb=" OE1 GLN B 222 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR B 165 " pdb=" OG1 THR B 170 " model vdw 2.292 3.040 ... (remaining 69340 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.170 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 : 0.007 0.056 8418 Z= 0.463 Angle : 0.785 6.289 11490 Z= 0.455 Chirality : 0.052 0.287 1357 Planarity : 0.005 0.050 1484 Dihedral : 13.158 86.411 3001 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -1.18 (0.26), residues: 1046 helix: -2.40 (0.61), residues: 54 sheet: -0.53 (0.26), residues: 370 loop : -0.73 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.010 TRP A 135 HIS 0.007 0.002 HIS F 312 PHE 0.016 0.002 PHE B 199 TYR 0.038 0.003 TYR F 293 ARG 0.008 0.002 ARG C 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 174 THR cc_start: 0.8912 (p) cc_final: 0.8559 (t) REVERT: B 156 CYS cc_start: 0.6660 (p) cc_final: 0.6230 (p) REVERT: F 189 THR cc_start: 0.7935 (m) cc_final: 0.7224 (p) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2650 time to fit residues: 78.9536 Evaluate side-chains 147 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.0980 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN D 206 GLN D 208 GLN B 188 HIS ** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.116475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.089836 restraints weight = 17679.407| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.86 r_work: 0.3290 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8418 Z= 0.232 Angle : 0.580 5.549 11490 Z= 0.315 Chirality : 0.046 0.160 1357 Planarity : 0.004 0.050 1484 Dihedral : 5.603 24.359 1121 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.75 % Allowed : 9.37 % Favored : 89.88 % 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: -0.92 (0.26), residues: 1046 helix: -1.81 (0.79), residues: 36 sheet: -0.42 (0.27), residues: 376 loop : -0.59 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP A 135 HIS 0.003 0.001 HIS F 183 PHE 0.018 0.002 PHE D 301 TYR 0.019 0.001 TYR D 293 ARG 0.006 0.001 ARG F 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 196 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7332 (mm-30) REVERT: A 323 GLU cc_start: 0.8641 (tp30) cc_final: 0.8334 (tp30) REVERT: A 325 ASP cc_start: 0.8058 (m-30) cc_final: 0.7810 (m-30) REVERT: D 154 LEU cc_start: 0.8855 (mp) cc_final: 0.8591 (mp) REVERT: D 174 THR cc_start: 0.9024 (p) cc_final: 0.8714 (t) REVERT: B 276 MET cc_start: 0.8060 (mtm) cc_final: 0.7628 (ttt) REVERT: B 325 ASP cc_start: 0.7698 (m-30) cc_final: 0.7446 (m-30) REVERT: C 200 ASP cc_start: 0.7920 (t0) cc_final: 0.7712 (t0) REVERT: C 250 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8246 (mt-10) REVERT: C 280 ARG cc_start: 0.8071 (ttp80) cc_final: 0.7695 (ttp-110) REVERT: F 150 ARG cc_start: 0.7501 (ptt180) cc_final: 0.6529 (ptt180) REVERT: F 189 THR cc_start: 0.7693 (m) cc_final: 0.6996 (p) REVERT: F 191 GLU cc_start: 0.7985 (tt0) cc_final: 0.7418 (tt0) REVERT: F 206 GLN cc_start: 0.7621 (mt0) cc_final: 0.7254 (mp10) REVERT: F 300 ASP cc_start: 0.8734 (t0) cc_final: 0.7971 (p0) REVERT: F 301 PHE cc_start: 0.8484 (p90) cc_final: 0.7945 (p90) outliers start: 7 outliers final: 6 residues processed: 167 average time/residue: 0.2214 time to fit residues: 50.7009 Evaluate side-chains 149 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain F residue 177 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 0.0670 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN B 146 GLN B 305 GLN C 188 HIS C 231 ASN F 106 ASN F 236 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.113484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.087290 restraints weight = 18297.573| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.91 r_work: 0.3240 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8418 Z= 0.259 Angle : 0.558 6.413 11490 Z= 0.301 Chirality : 0.045 0.154 1357 Planarity : 0.004 0.040 1484 Dihedral : 5.304 21.733 1121 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.81 % Allowed : 11.40 % Favored : 86.79 % 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: -0.92 (0.26), residues: 1046 helix: -0.93 (1.14), residues: 21 sheet: -0.42 (0.26), residues: 370 loop : -0.67 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 135 HIS 0.005 0.001 HIS F 183 PHE 0.017 0.002 PHE A 199 TYR 0.018 0.001 TYR D 293 ARG 0.003 0.001 ARG F 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 1.070 Fit side-chains REVERT: A 146 GLN cc_start: 0.9133 (tt0) cc_final: 0.8610 (tt0) REVERT: A 196 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7353 (mm-30) REVERT: A 323 GLU cc_start: 0.8745 (tp30) cc_final: 0.8498 (tp30) REVERT: D 154 LEU cc_start: 0.8776 (mp) cc_final: 0.8562 (mp) REVERT: B 129 ASP cc_start: 0.8326 (t0) cc_final: 0.7872 (t0) REVERT: B 184 MET cc_start: 0.8137 (ppp) cc_final: 0.7934 (ppp) REVERT: B 192 ASN cc_start: 0.9040 (t0) cc_final: 0.8438 (p0) REVERT: B 276 MET cc_start: 0.8089 (mtm) cc_final: 0.7625 (ttt) REVERT: B 323 GLU cc_start: 0.8177 (tp30) cc_final: 0.7782 (tp30) REVERT: B 325 ASP cc_start: 0.7753 (m-30) cc_final: 0.7515 (m-30) REVERT: C 250 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8145 (mt-10) REVERT: C 276 MET cc_start: 0.8405 (mtm) cc_final: 0.8087 (mtt) REVERT: C 291 ARG cc_start: 0.8597 (ttm170) cc_final: 0.8268 (ttm-80) REVERT: F 150 ARG cc_start: 0.7542 (ptt180) cc_final: 0.6675 (ptt180) REVERT: F 167 ASP cc_start: 0.8184 (p0) cc_final: 0.7901 (p0) REVERT: F 189 THR cc_start: 0.7623 (m) cc_final: 0.6982 (p) REVERT: F 191 GLU cc_start: 0.7856 (tt0) cc_final: 0.7291 (tt0) REVERT: F 301 PHE cc_start: 0.8381 (p90) cc_final: 0.8050 (p90) REVERT: F 327 LYS cc_start: 0.7901 (ptpp) cc_final: 0.7565 (pttm) outliers start: 17 outliers final: 14 residues processed: 164 average time/residue: 0.2823 time to fit residues: 62.6823 Evaluate side-chains 153 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 177 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 98 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 206 GLN B 305 GLN ** F 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 ASN F 236 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.108398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.082068 restraints weight = 18555.955| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.91 r_work: 0.3148 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 8418 Z= 0.483 Angle : 0.669 6.914 11490 Z= 0.360 Chirality : 0.048 0.150 1357 Planarity : 0.004 0.052 1484 Dihedral : 5.772 26.519 1121 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.73 % Allowed : 12.03 % Favored : 84.24 % 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: -1.41 (0.25), residues: 1046 helix: -2.36 (0.72), residues: 36 sheet: -0.77 (0.26), residues: 376 loop : -0.91 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 135 HIS 0.007 0.001 HIS F 183 PHE 0.023 0.002 PHE A 199 TYR 0.024 0.002 TYR F 293 ARG 0.003 0.001 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 1.037 Fit side-chains REVERT: A 276 MET cc_start: 0.7990 (mtp) cc_final: 0.7669 (ttp) REVERT: D 243 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8068 (mtp85) REVERT: B 129 ASP cc_start: 0.8427 (t0) cc_final: 0.8084 (t0) REVERT: B 276 MET cc_start: 0.8367 (mtm) cc_final: 0.7952 (ttt) REVERT: B 325 ASP cc_start: 0.7742 (m-30) cc_final: 0.7494 (m-30) REVERT: C 250 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8200 (mt-10) REVERT: C 280 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.7913 (ttp-110) REVERT: F 150 ARG cc_start: 0.8016 (ptt180) cc_final: 0.7495 (ptt180) REVERT: F 189 THR cc_start: 0.7682 (m) cc_final: 0.7086 (p) REVERT: F 206 GLN cc_start: 0.7614 (mt0) cc_final: 0.7148 (mp10) REVERT: F 293 TYR cc_start: 0.4039 (p90) cc_final: 0.3500 (p90) REVERT: F 301 PHE cc_start: 0.8384 (p90) cc_final: 0.8037 (p90) REVERT: F 327 LYS cc_start: 0.8075 (ptpp) cc_final: 0.7782 (ptpp) outliers start: 35 outliers final: 23 residues processed: 169 average time/residue: 0.2082 time to fit residues: 48.2267 Evaluate side-chains 158 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 300 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 67 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 106 ASN F 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.111915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.086099 restraints weight = 18363.983| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.87 r_work: 0.3219 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8418 Z= 0.206 Angle : 0.541 7.844 11490 Z= 0.288 Chirality : 0.044 0.154 1357 Planarity : 0.003 0.044 1484 Dihedral : 5.103 21.592 1121 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.66 % Allowed : 13.95 % Favored : 83.39 % 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: -1.21 (0.26), residues: 1046 helix: -1.96 (0.77), residues: 36 sheet: -0.64 (0.26), residues: 376 loop : -0.79 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 296 HIS 0.002 0.000 HIS F 183 PHE 0.015 0.002 PHE F 110 TYR 0.018 0.001 TYR D 293 ARG 0.004 0.001 ARG D 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 146 GLN cc_start: 0.9117 (tt0) cc_final: 0.8686 (tt0) REVERT: A 276 MET cc_start: 0.7861 (mtp) cc_final: 0.7368 (mtt) REVERT: D 170 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8361 (mt-10) REVERT: D 206 GLN cc_start: 0.8106 (tt0) cc_final: 0.7802 (pm20) REVERT: D 208 GLN cc_start: 0.7115 (mm-40) cc_final: 0.6901 (mm-40) REVERT: B 129 ASP cc_start: 0.8410 (t0) cc_final: 0.8047 (t0) REVERT: B 192 ASN cc_start: 0.9067 (t0) cc_final: 0.8408 (p0) REVERT: B 251 LYS cc_start: 0.9188 (mttm) cc_final: 0.8913 (mttm) REVERT: B 276 MET cc_start: 0.8154 (mtm) cc_final: 0.7893 (ttt) REVERT: B 323 GLU cc_start: 0.8244 (tp30) cc_final: 0.7799 (tp30) REVERT: C 189 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8538 (mtmm) REVERT: C 250 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8301 (mt-10) REVERT: C 280 ARG cc_start: 0.8262 (ttp-110) cc_final: 0.7979 (ttp-110) REVERT: C 291 ARG cc_start: 0.8608 (ttm170) cc_final: 0.8221 (ttm170) REVERT: C 303 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8472 (mm-30) REVERT: F 167 ASP cc_start: 0.8391 (p0) cc_final: 0.8003 (p0) REVERT: F 293 TYR cc_start: 0.3928 (p90) cc_final: 0.3530 (p90) outliers start: 25 outliers final: 17 residues processed: 175 average time/residue: 0.2248 time to fit residues: 53.3620 Evaluate side-chains 157 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 300 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 5 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 70 optimal weight: 0.0970 chunk 9 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 GLN F 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.109644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.083778 restraints weight = 18538.548| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.88 r_work: 0.3185 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 8418 Z= 0.302 Angle : 0.579 6.494 11490 Z= 0.308 Chirality : 0.045 0.150 1357 Planarity : 0.004 0.046 1484 Dihedral : 5.165 21.588 1121 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.88 % Allowed : 14.48 % Favored : 82.64 % 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: -1.25 (0.26), residues: 1046 helix: -1.74 (0.82), residues: 36 sheet: -0.74 (0.26), residues: 382 loop : -0.77 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 296 HIS 0.004 0.001 HIS F 183 PHE 0.017 0.002 PHE A 199 TYR 0.022 0.002 TYR D 293 ARG 0.002 0.000 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 146 GLN cc_start: 0.9141 (tt0) cc_final: 0.8714 (tt0) REVERT: A 276 MET cc_start: 0.7931 (mtp) cc_final: 0.7464 (mtt) REVERT: A 324 ASP cc_start: 0.7716 (m-30) cc_final: 0.7436 (t0) REVERT: D 170 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8438 (mt-10) REVERT: D 243 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8042 (mtp85) REVERT: B 129 ASP cc_start: 0.8451 (t0) cc_final: 0.8059 (t0) REVERT: B 251 LYS cc_start: 0.9191 (mttm) cc_final: 0.8931 (mttm) REVERT: B 276 MET cc_start: 0.8381 (mtm) cc_final: 0.8014 (ttt) REVERT: B 323 GLU cc_start: 0.8322 (tp30) cc_final: 0.7842 (tp30) REVERT: B 325 ASP cc_start: 0.7726 (m-30) cc_final: 0.7470 (m-30) REVERT: C 250 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8309 (mt-10) REVERT: C 280 ARG cc_start: 0.8303 (ttp-110) cc_final: 0.7895 (ttp-110) REVERT: C 291 ARG cc_start: 0.8594 (ttm170) cc_final: 0.8100 (ttm170) REVERT: C 303 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8496 (mm-30) REVERT: F 167 ASP cc_start: 0.8413 (p0) cc_final: 0.8164 (p0) REVERT: F 189 THR cc_start: 0.7630 (m) cc_final: 0.7015 (p) REVERT: F 301 PHE cc_start: 0.8353 (p90) cc_final: 0.8053 (p90) outliers start: 27 outliers final: 21 residues processed: 164 average time/residue: 0.2161 time to fit residues: 47.5956 Evaluate side-chains 158 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 300 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 61 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 63 optimal weight: 0.0980 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.114448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.088994 restraints weight = 18331.576| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.85 r_work: 0.3277 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8418 Z= 0.151 Angle : 0.519 5.856 11490 Z= 0.276 Chirality : 0.044 0.151 1357 Planarity : 0.003 0.040 1484 Dihedral : 4.618 20.517 1121 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.02 % Allowed : 15.12 % Favored : 82.85 % 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 (0.26), residues: 1046 helix: -1.40 (0.89), residues: 36 sheet: -0.56 (0.26), residues: 384 loop : -0.60 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 296 HIS 0.001 0.000 HIS B 188 PHE 0.016 0.002 PHE F 110 TYR 0.020 0.001 TYR D 293 ARG 0.003 0.000 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 146 GLN cc_start: 0.9063 (tt0) cc_final: 0.8654 (tt0) REVERT: A 276 MET cc_start: 0.7818 (mtp) cc_final: 0.7373 (mtt) REVERT: A 324 ASP cc_start: 0.7667 (m-30) cc_final: 0.7354 (t0) REVERT: D 170 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8384 (mt-10) REVERT: D 206 GLN cc_start: 0.8060 (tt0) cc_final: 0.7576 (tm-30) REVERT: B 129 ASP cc_start: 0.8393 (t0) cc_final: 0.8110 (t0) REVERT: B 192 ASN cc_start: 0.8998 (t0) cc_final: 0.8507 (p0) REVERT: B 251 LYS cc_start: 0.9208 (mttm) cc_final: 0.8900 (mttt) REVERT: B 276 MET cc_start: 0.8239 (mtm) cc_final: 0.7855 (ttt) REVERT: B 319 TYR cc_start: 0.8981 (m-80) cc_final: 0.8717 (m-80) REVERT: C 189 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8469 (mtmm) REVERT: C 250 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8123 (mt-10) REVERT: C 280 ARG cc_start: 0.8284 (ttp-110) cc_final: 0.8043 (ttp-110) REVERT: F 167 ASP cc_start: 0.8547 (p0) cc_final: 0.8244 (p0) outliers start: 19 outliers final: 13 residues processed: 170 average time/residue: 0.2229 time to fit residues: 51.6930 Evaluate side-chains 157 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 305 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 87 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 83 optimal weight: 7.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 217 ASN B 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.113909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.088346 restraints weight = 18474.996| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.90 r_work: 0.3264 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8418 Z= 0.176 Angle : 0.539 7.553 11490 Z= 0.282 Chirality : 0.044 0.154 1357 Planarity : 0.003 0.038 1484 Dihedral : 4.610 18.848 1121 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.02 % Allowed : 15.97 % Favored : 82.00 % 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: -0.94 (0.26), residues: 1046 helix: -1.59 (0.87), residues: 36 sheet: -0.47 (0.26), residues: 393 loop : -0.59 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 296 HIS 0.002 0.000 HIS F 183 PHE 0.017 0.002 PHE F 110 TYR 0.023 0.001 TYR D 293 ARG 0.002 0.000 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 1.001 Fit side-chains REVERT: A 146 GLN cc_start: 0.9061 (tt0) cc_final: 0.8652 (tt0) REVERT: A 276 MET cc_start: 0.7822 (mtp) cc_final: 0.7363 (mtt) REVERT: A 324 ASP cc_start: 0.7718 (m-30) cc_final: 0.7445 (t0) REVERT: D 170 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8358 (mt-10) REVERT: D 208 GLN cc_start: 0.7092 (mm-40) cc_final: 0.6317 (tm-30) REVERT: D 243 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8087 (mtp85) REVERT: B 129 ASP cc_start: 0.8378 (t0) cc_final: 0.7978 (t0) REVERT: B 192 ASN cc_start: 0.8994 (t0) cc_final: 0.8387 (p0) REVERT: B 251 LYS cc_start: 0.9190 (mttm) cc_final: 0.8888 (mttt) REVERT: C 145 CYS cc_start: 0.8967 (t) cc_final: 0.8623 (p) REVERT: C 189 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8496 (mtmm) REVERT: C 250 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8110 (mt-10) REVERT: C 280 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.8068 (ttp-110) REVERT: F 167 ASP cc_start: 0.8520 (p0) cc_final: 0.8233 (p0) REVERT: F 301 PHE cc_start: 0.8579 (p90) cc_final: 0.8349 (p90) outliers start: 19 outliers final: 15 residues processed: 164 average time/residue: 0.2575 time to fit residues: 56.7557 Evaluate side-chains 160 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 156 CYS Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 305 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 101 optimal weight: 4.9990 chunk 40 optimal weight: 0.0070 chunk 33 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 25 optimal weight: 0.0870 chunk 71 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.112141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.086618 restraints weight = 18694.573| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.93 r_work: 0.3221 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8418 Z= 0.250 Angle : 0.568 6.786 11490 Z= 0.299 Chirality : 0.044 0.155 1357 Planarity : 0.003 0.037 1484 Dihedral : 4.811 19.915 1121 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.92 % Allowed : 16.08 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.26), residues: 1046 helix: -1.81 (0.85), residues: 36 sheet: -0.48 (0.26), residues: 382 loop : -0.59 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 296 HIS 0.003 0.001 HIS F 183 PHE 0.020 0.002 PHE F 247 TYR 0.022 0.002 TYR D 293 ARG 0.005 0.001 ARG F 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.925 Fit side-chains REVERT: A 146 GLN cc_start: 0.9108 (tt0) cc_final: 0.8705 (tt0) REVERT: A 276 MET cc_start: 0.7888 (mtp) cc_final: 0.7439 (mtt) REVERT: A 324 ASP cc_start: 0.7720 (m-30) cc_final: 0.7459 (t0) REVERT: D 170 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8410 (mt-10) REVERT: D 243 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7968 (mtp85) REVERT: B 129 ASP cc_start: 0.8419 (t0) cc_final: 0.8110 (t0) REVERT: B 192 ASN cc_start: 0.9046 (t0) cc_final: 0.8328 (p0) REVERT: B 251 LYS cc_start: 0.9182 (mttm) cc_final: 0.8908 (mttt) REVERT: C 145 CYS cc_start: 0.8907 (t) cc_final: 0.8679 (p) REVERT: C 250 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8178 (mt-10) REVERT: F 167 ASP cc_start: 0.8538 (p0) cc_final: 0.8276 (p0) REVERT: F 301 PHE cc_start: 0.8566 (p90) cc_final: 0.8336 (p90) outliers start: 18 outliers final: 16 residues processed: 154 average time/residue: 0.2209 time to fit residues: 46.0130 Evaluate side-chains 157 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 305 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 80 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 40 optimal weight: 0.0670 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 70 optimal weight: 0.3980 chunk 35 optimal weight: 5.9990 overall best weight: 1.6924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.111711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.086147 restraints weight = 18392.931| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.87 r_work: 0.3225 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8418 Z= 0.241 Angle : 0.578 6.750 11490 Z= 0.302 Chirality : 0.044 0.155 1357 Planarity : 0.004 0.037 1484 Dihedral : 4.848 22.750 1121 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.02 % Allowed : 15.65 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.26), residues: 1046 helix: -1.50 (0.89), residues: 36 sheet: -0.51 (0.26), residues: 384 loop : -0.59 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 296 HIS 0.003 0.001 HIS F 183 PHE 0.020 0.002 PHE F 110 TYR 0.023 0.002 TYR C 256 ARG 0.009 0.001 ARG C 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.132 Fit side-chains REVERT: A 146 GLN cc_start: 0.9098 (tt0) cc_final: 0.8684 (tt0) REVERT: A 276 MET cc_start: 0.7898 (mtp) cc_final: 0.7437 (mtt) REVERT: A 324 ASP cc_start: 0.7711 (m-30) cc_final: 0.7447 (t0) REVERT: D 170 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8369 (mt-10) REVERT: D 243 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7964 (mtp85) REVERT: B 192 ASN cc_start: 0.9038 (t0) cc_final: 0.8320 (p0) REVERT: B 251 LYS cc_start: 0.9184 (mttm) cc_final: 0.8902 (mttt) REVERT: C 145 CYS cc_start: 0.8918 (t) cc_final: 0.8693 (p) REVERT: C 189 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8533 (mtmm) REVERT: C 250 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8170 (mt-10) REVERT: F 167 ASP cc_start: 0.8584 (p0) cc_final: 0.8342 (p0) REVERT: F 301 PHE cc_start: 0.8577 (p90) cc_final: 0.8350 (p90) outliers start: 19 outliers final: 18 residues processed: 157 average time/residue: 0.2439 time to fit residues: 52.8581 Evaluate side-chains 160 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 305 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 58 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.114659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.088786 restraints weight = 18751.467| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.97 r_work: 0.3280 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8418 Z= 0.186 Angle : 0.554 6.882 11490 Z= 0.291 Chirality : 0.044 0.156 1357 Planarity : 0.003 0.035 1484 Dihedral : 4.659 25.549 1121 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.02 % Allowed : 15.34 % Favored : 82.64 % 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: -0.88 (0.27), residues: 1046 helix: -1.33 (0.90), residues: 36 sheet: -0.47 (0.26), residues: 384 loop : -0.53 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 296 HIS 0.001 0.000 HIS B 188 PHE 0.020 0.002 PHE F 110 TYR 0.022 0.002 TYR D 293 ARG 0.008 0.001 ARG C 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4418.68 seconds wall clock time: 79 minutes 48.16 seconds (4788.16 seconds total)