Starting phenix.real_space_refine on Sun Apr 27 10:05:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8exr_28660/04_2025/8exr_28660.cif Found real_map, /net/cci-nas-00/data/ceres_data/8exr_28660/04_2025/8exr_28660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8exr_28660/04_2025/8exr_28660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8exr_28660/04_2025/8exr_28660.map" model { file = "/net/cci-nas-00/data/ceres_data/8exr_28660/04_2025/8exr_28660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8exr_28660/04_2025/8exr_28660.cif" } resolution = 3.8 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= 0.014 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 5 5.49 5 S 20 5.16 5 C 3438 2.51 5 N 802 2.21 5 O 844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5111 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2496 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 6, 'TRANS': 288} Chain breaks: 1 Chain: "A" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 2051 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 6, 'TRANS': 234} Chain breaks: 1 Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 445 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' ZN': 1, 'P6L': 1, 'PO4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' ZN': 1, 'P6L': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.97, per 1000 atoms: 0.78 Number of scatterers: 5111 At special positions: 0 Unit cell: (72.38, 85.47, 93.94, 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 20 16.00 P 5 15.00 O 844 8.00 N 802 7.00 C 3438 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: 1.54 Conformation dependent library (CDL) restraints added in 598.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 205 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 201 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 205 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 201 " 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 70.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'B' and resid 2 through 29 removed outlier: 3.858A pdb=" N TYR B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE B 25 " --> pdb=" O PHE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 38 Processing helix chain 'B' and resid 39 through 48 removed outlier: 4.065A pdb=" N LEU B 43 " --> pdb=" O TRP B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 100 through 133 removed outlier: 4.624A pdb=" N VAL B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 133 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'B' and resid 194 through 208 removed outlier: 4.327A pdb=" N LEU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 224 removed outlier: 4.197A pdb=" N ILE B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 251 removed outlier: 3.501A pdb=" N ILE B 232 " --> pdb=" O PRO B 228 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 271 Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 308 through 329 removed outlier: 3.534A pdb=" N PHE B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 336 Processing helix chain 'A' and resid 2 through 31 removed outlier: 3.529A pdb=" N ILE A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 38 Processing helix chain 'A' and resid 39 through 47 removed outlier: 4.125A pdb=" N LEU A 43 " --> pdb=" O TRP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 134 removed outlier: 3.566A pdb=" N VAL A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 194 through 208 removed outlier: 3.814A pdb=" N ASN A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 224 Processing helix chain 'A' and resid 227 through 251 removed outlier: 3.857A pdb=" N HIS A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG A 235 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 253 No H-bonds generated for 'chain 'A' and resid 252 through 253' Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 257 through 271 removed outlier: 3.752A pdb=" N VAL A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.734A pdb=" N LYS C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 329 removed outlier: 4.354A pdb=" N LEU C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 336 removed outlier: 4.040A pdb=" N THR C 335 " --> pdb=" O GLN C 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 160 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.685A pdb=" N VAL A 160 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE A 182 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG A 162 " --> pdb=" O ILE A 182 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 870 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: 1.23 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 1301 1.33 - 1.47: 1570 1.47 - 1.61: 2315 1.61 - 1.75: 3 1.75 - 1.89: 34 Bond restraints: 5223 Sorted by residual: bond pdb=" CB HIS B 213 " pdb=" CG HIS B 213 " ideal model delta sigma weight residual 1.497 1.371 0.126 1.40e-02 5.10e+03 8.05e+01 bond pdb=" CB HIS B 153 " pdb=" CG HIS B 153 " ideal model delta sigma weight residual 1.497 1.372 0.125 1.40e-02 5.10e+03 7.94e+01 bond pdb=" CB PHE A 173 " pdb=" CG PHE A 173 " ideal model delta sigma weight residual 1.502 1.321 0.181 2.30e-02 1.89e+03 6.18e+01 bond pdb=" NE1 TRP B 39 " pdb=" CE2 TRP B 39 " ideal model delta sigma weight residual 1.370 1.285 0.085 1.10e-02 8.26e+03 6.00e+01 bond pdb=" CB HIS A 205 " pdb=" CG HIS A 205 " ideal model delta sigma weight residual 1.497 1.389 0.108 1.40e-02 5.10e+03 5.93e+01 ... (remaining 5218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 6387 3.28 - 6.57: 574 6.57 - 9.85: 51 9.85 - 13.13: 6 13.13 - 16.42: 3 Bond angle restraints: 7021 Sorted by residual: angle pdb=" N VAL A 160 " pdb=" CA VAL A 160 " pdb=" C VAL A 160 " ideal model delta sigma weight residual 108.46 122.06 -13.60 1.49e+00 4.50e-01 8.33e+01 angle pdb=" N ARG A 194 " pdb=" CA ARG A 194 " pdb=" C ARG A 194 " ideal model delta sigma weight residual 114.04 102.97 11.07 1.24e+00 6.50e-01 7.97e+01 angle pdb=" N VAL B 160 " pdb=" CA VAL B 160 " pdb=" C VAL B 160 " ideal model delta sigma weight residual 108.46 121.66 -13.20 1.49e+00 4.50e-01 7.84e+01 angle pdb=" CA PHE B 30 " pdb=" CB PHE B 30 " pdb=" CG PHE B 30 " ideal model delta sigma weight residual 113.80 105.18 8.62 1.00e+00 1.00e+00 7.44e+01 angle pdb=" N TRP B 174 " pdb=" CA TRP B 174 " pdb=" C TRP B 174 " ideal model delta sigma weight residual 110.56 126.98 -16.42 1.94e+00 2.66e-01 7.16e+01 ... (remaining 7016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.09: 2907 14.09 - 28.17: 148 28.17 - 42.25: 49 42.25 - 56.34: 30 56.34 - 70.42: 11 Dihedral angle restraints: 3145 sinusoidal: 1362 harmonic: 1783 Sorted by residual: dihedral pdb=" C PHE B 258 " pdb=" N PHE B 258 " pdb=" CA PHE B 258 " pdb=" CB PHE B 258 " ideal model delta harmonic sigma weight residual -122.60 -114.82 -7.78 0 2.50e+00 1.60e-01 9.68e+00 dihedral pdb=" N TYR B 155 " pdb=" C TYR B 155 " pdb=" CA TYR B 155 " pdb=" CB TYR B 155 " ideal model delta harmonic sigma weight residual 122.80 130.57 -7.77 0 2.50e+00 1.60e-01 9.66e+00 dihedral pdb=" CG ARG A 235 " pdb=" CD ARG A 235 " pdb=" NE ARG A 235 " pdb=" CZ ARG A 235 " ideal model delta sinusoidal sigma weight residual 180.00 143.09 36.91 2 1.50e+01 4.44e-03 7.69e+00 ... (remaining 3142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 564 0.117 - 0.234: 200 0.234 - 0.351: 31 0.351 - 0.468: 4 0.468 - 0.584: 1 Chirality restraints: 800 Sorted by residual: chirality pdb=" C5 P6L A 702 " pdb=" C6 P6L A 702 " pdb=" C7 P6L A 702 " pdb=" O4 P6L A 702 " both_signs ideal model delta sigma weight residual False -2.31 -1.73 -0.58 2.00e-01 2.50e+01 8.54e+00 chirality pdb=" CA TRP B 174 " pdb=" N TRP B 174 " pdb=" C TRP B 174 " pdb=" CB TRP B 174 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CA TYR B 155 " pdb=" N TYR B 155 " pdb=" C TYR B 155 " pdb=" CB TYR B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 797 not shown) Planarity restraints: 823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 P6L B 702 " 0.079 2.00e-02 2.50e+03 1.61e-01 2.59e+02 pdb=" C22 P6L B 702 " -0.213 2.00e-02 2.50e+03 pdb=" C23 P6L B 702 " 0.213 2.00e-02 2.50e+03 pdb=" C24 P6L B 702 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C21 P6L A 702 " 0.077 2.00e-02 2.50e+03 1.53e-01 2.35e+02 pdb=" C22 P6L A 702 " -0.203 2.00e-02 2.50e+03 pdb=" C23 P6L A 702 " 0.203 2.00e-02 2.50e+03 pdb=" C24 P6L A 702 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C32 P6L A 702 " -0.074 2.00e-02 2.50e+03 1.48e-01 2.18e+02 pdb=" C33 P6L A 702 " 0.195 2.00e-02 2.50e+03 pdb=" C34 P6L A 702 " -0.195 2.00e-02 2.50e+03 pdb=" C35 P6L A 702 " 0.074 2.00e-02 2.50e+03 ... (remaining 820 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 76 2.59 - 3.17: 5122 3.17 - 3.75: 7615 3.75 - 4.32: 10357 4.32 - 4.90: 15033 Nonbonded interactions: 38203 Sorted by model distance: nonbonded pdb=" OE2 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.016 2.230 nonbonded pdb=" OE2 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.017 2.230 nonbonded pdb=" OE1 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.038 2.230 nonbonded pdb=" OE1 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.050 2.230 nonbonded pdb=" O GLY B 286 " pdb=" CG LYS B 287 " model vdw 2.142 3.440 ... (remaining 38198 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.900 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 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 : 0.026 0.181 5227 Z= 1.487 Angle : 1.944 16.416 7021 Z= 1.328 Chirality : 0.115 0.584 800 Planarity : 0.013 0.161 823 Dihedral : 12.156 70.423 1981 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.76 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -0.66 (0.32), residues: 580 helix: -0.13 (0.24), residues: 383 sheet: -0.25 (0.87), residues: 26 loop : -0.87 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.009 TRP B 99 HIS 0.012 0.003 HIS A 153 PHE 0.033 0.006 PHE B 284 TYR 0.099 0.012 TYR A 203 ARG 0.006 0.001 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.25172 ( 299) hydrogen bonds : angle 8.15000 ( 870) metal coordination : bond 0.05433 ( 4) covalent geometry : bond 0.02593 ( 5223) covalent geometry : angle 1.94400 ( 7021) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 41 LEU cc_start: 0.8542 (mt) cc_final: 0.7864 (tt) REVERT: B 136 LEU cc_start: 0.6840 (tp) cc_final: 0.6454 (tp) REVERT: B 255 LYS cc_start: 0.8736 (mttt) cc_final: 0.8205 (mmtm) REVERT: A 141 ASN cc_start: 0.7362 (m-40) cc_final: 0.6924 (p0) REVERT: A 187 PHE cc_start: 0.8156 (m-80) cc_final: 0.7907 (m-80) REVERT: A 219 ILE cc_start: 0.8605 (mm) cc_final: 0.8397 (mt) REVERT: A 276 ASN cc_start: 0.6779 (p0) cc_final: 0.6314 (m-40) REVERT: C 295 LEU cc_start: 0.8700 (mt) cc_final: 0.8423 (tt) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1868 time to fit residues: 43.2227 Evaluate side-chains 119 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 ASN A 271 ASN C 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.187039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.165314 restraints weight = 10810.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.169483 restraints weight = 6706.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.172477 restraints weight = 4654.422| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5227 Z= 0.189 Angle : 0.711 6.755 7021 Z= 0.398 Chirality : 0.045 0.179 800 Planarity : 0.005 0.048 823 Dihedral : 13.288 73.931 725 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.24 % Favored : 97.41 % Rotamer: Outliers : 3.19 % Allowed : 11.70 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.34), residues: 580 helix: 1.45 (0.25), residues: 376 sheet: 0.08 (1.02), residues: 35 loop : -0.78 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 110 HIS 0.006 0.001 HIS B 213 PHE 0.024 0.002 PHE B 16 TYR 0.019 0.002 TYR B 127 ARG 0.006 0.001 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.08576 ( 299) hydrogen bonds : angle 5.15958 ( 870) metal coordination : bond 0.00364 ( 4) covalent geometry : bond 0.00350 ( 5223) covalent geometry : angle 0.71128 ( 7021) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 MET cc_start: 0.7409 (mmt) cc_final: 0.6797 (ptp) REVERT: B 22 PHE cc_start: 0.7062 (m-80) cc_final: 0.6788 (m-80) REVERT: B 136 LEU cc_start: 0.7409 (tp) cc_final: 0.6700 (mp) REVERT: B 168 GLN cc_start: 0.6748 (mp10) cc_final: 0.6216 (mm-40) REVERT: B 240 ASP cc_start: 0.8443 (m-30) cc_final: 0.8045 (t0) REVERT: A 122 LEU cc_start: 0.8400 (mt) cc_final: 0.8141 (tp) REVERT: A 141 ASN cc_start: 0.7719 (m-40) cc_final: 0.7271 (p0) REVERT: A 194 ARG cc_start: 0.6969 (ptt180) cc_final: 0.6661 (ptt180) REVERT: C 295 LEU cc_start: 0.8547 (mt) cc_final: 0.7858 (tt) outliers start: 18 outliers final: 7 residues processed: 162 average time/residue: 0.1580 time to fit residues: 33.1880 Evaluate side-chains 120 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 328 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 0.0980 chunk 45 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4292 r_free = 0.4292 target = 0.185836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.164296 restraints weight = 10186.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.168767 restraints weight = 6404.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.172063 restraints weight = 4394.430| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5227 Z= 0.157 Angle : 0.648 10.706 7021 Z= 0.351 Chirality : 0.043 0.225 800 Planarity : 0.004 0.052 823 Dihedral : 11.835 85.974 725 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.01 % Allowed : 16.13 % Favored : 80.85 % 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: 1.16 (0.34), residues: 580 helix: 1.65 (0.25), residues: 374 sheet: -0.34 (1.00), residues: 37 loop : -0.92 (0.46), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 174 HIS 0.003 0.001 HIS B 231 PHE 0.020 0.002 PHE B 14 TYR 0.024 0.002 TYR A 186 ARG 0.004 0.001 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.06993 ( 299) hydrogen bonds : angle 4.67857 ( 870) metal coordination : bond 0.00151 ( 4) covalent geometry : bond 0.00300 ( 5223) covalent geometry : angle 0.64789 ( 7021) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: B 22 PHE cc_start: 0.7071 (m-80) cc_final: 0.6766 (m-80) REVERT: B 136 LEU cc_start: 0.7539 (tp) cc_final: 0.7146 (mp) REVERT: B 162 ARG cc_start: 0.6384 (mtt180) cc_final: 0.6110 (ttm170) REVERT: B 240 ASP cc_start: 0.8474 (m-30) cc_final: 0.8142 (t0) REVERT: B 266 MET cc_start: 0.6984 (tpt) cc_final: 0.6704 (tpt) REVERT: A 22 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7767 (t80) REVERT: A 100 ASP cc_start: 0.4988 (m-30) cc_final: 0.4433 (t0) REVERT: A 122 LEU cc_start: 0.8495 (mt) cc_final: 0.8280 (tp) REVERT: A 141 ASN cc_start: 0.7612 (m-40) cc_final: 0.7304 (p0) REVERT: A 165 GLU cc_start: 0.6898 (pm20) cc_final: 0.6619 (pt0) REVERT: A 186 TYR cc_start: 0.7546 (m-10) cc_final: 0.7341 (m-80) REVERT: A 246 ASP cc_start: 0.7186 (m-30) cc_final: 0.6970 (t0) REVERT: C 300 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7659 (tm-30) outliers start: 17 outliers final: 9 residues processed: 147 average time/residue: 0.1586 time to fit residues: 30.2038 Evaluate side-chains 128 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 328 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.185019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.164273 restraints weight = 10548.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.168448 restraints weight = 6793.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.171436 restraints weight = 4773.165| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5227 Z= 0.145 Angle : 0.606 9.549 7021 Z= 0.329 Chirality : 0.042 0.209 800 Planarity : 0.004 0.053 823 Dihedral : 10.877 77.832 725 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.90 % Allowed : 17.20 % Favored : 78.90 % 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: 1.17 (0.34), residues: 580 helix: 1.76 (0.25), residues: 374 sheet: -0.70 (0.97), residues: 36 loop : -1.09 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 174 HIS 0.003 0.001 HIS B 213 PHE 0.020 0.002 PHE C 328 TYR 0.027 0.002 TYR B 127 ARG 0.004 0.001 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.06106 ( 299) hydrogen bonds : angle 4.57895 ( 870) metal coordination : bond 0.00411 ( 4) covalent geometry : bond 0.00285 ( 5223) covalent geometry : angle 0.60575 ( 7021) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: B 22 PHE cc_start: 0.6936 (m-80) cc_final: 0.6619 (m-80) REVERT: B 136 LEU cc_start: 0.7434 (tp) cc_final: 0.6585 (mp) REVERT: B 240 ASP cc_start: 0.8602 (m-30) cc_final: 0.8192 (t0) REVERT: B 266 MET cc_start: 0.6875 (tpt) cc_final: 0.6608 (tpt) REVERT: A 22 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7812 (t80) REVERT: A 100 ASP cc_start: 0.4684 (m-30) cc_final: 0.4062 (t0) REVERT: A 122 LEU cc_start: 0.8482 (mt) cc_final: 0.8252 (tp) REVERT: A 165 GLU cc_start: 0.6847 (pm20) cc_final: 0.6581 (pt0) REVERT: A 186 TYR cc_start: 0.7508 (m-10) cc_final: 0.7244 (m-80) REVERT: A 246 ASP cc_start: 0.7307 (m-30) cc_final: 0.7105 (t0) REVERT: A 271 ASN cc_start: 0.6443 (m-40) cc_final: 0.6160 (p0) REVERT: C 325 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8384 (tm-30) outliers start: 22 outliers final: 16 residues processed: 140 average time/residue: 0.1562 time to fit residues: 29.5266 Evaluate side-chains 133 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 53 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 47 optimal weight: 0.0870 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.4310 r_free = 0.4310 target = 0.189029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.167287 restraints weight = 10335.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.171831 restraints weight = 6518.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.175149 restraints weight = 4511.296| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5227 Z= 0.130 Angle : 0.597 9.238 7021 Z= 0.318 Chirality : 0.041 0.196 800 Planarity : 0.004 0.050 823 Dihedral : 9.985 65.912 725 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.84 % Allowed : 20.04 % Favored : 77.13 % 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: 1.17 (0.34), residues: 580 helix: 1.85 (0.26), residues: 374 sheet: -0.73 (0.98), residues: 36 loop : -1.33 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 174 HIS 0.002 0.001 HIS B 213 PHE 0.022 0.001 PHE C 328 TYR 0.017 0.001 TYR B 127 ARG 0.003 0.001 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.05258 ( 299) hydrogen bonds : angle 4.46039 ( 870) metal coordination : bond 0.00185 ( 4) covalent geometry : bond 0.00244 ( 5223) covalent geometry : angle 0.59718 ( 7021) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 PHE cc_start: 0.7097 (m-80) cc_final: 0.6751 (m-80) REVERT: B 136 LEU cc_start: 0.7513 (tp) cc_final: 0.7090 (mp) REVERT: B 203 TYR cc_start: 0.6867 (t80) cc_final: 0.6526 (t80) REVERT: B 240 ASP cc_start: 0.8622 (m-30) cc_final: 0.8230 (t0) REVERT: B 266 MET cc_start: 0.6942 (tpt) cc_final: 0.6695 (tpt) REVERT: A 100 ASP cc_start: 0.4419 (m-30) cc_final: 0.4009 (t0) REVERT: A 122 LEU cc_start: 0.8522 (mt) cc_final: 0.8305 (tp) REVERT: A 123 LYS cc_start: 0.7898 (tttt) cc_final: 0.7564 (pttm) REVERT: A 142 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7189 (mt-10) REVERT: A 246 ASP cc_start: 0.7115 (m-30) cc_final: 0.6890 (t0) outliers start: 16 outliers final: 8 residues processed: 140 average time/residue: 0.1476 time to fit residues: 27.5629 Evaluate side-chains 123 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 14 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.184310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.163887 restraints weight = 10050.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.168119 restraints weight = 6307.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.171361 restraints weight = 4361.984| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5227 Z= 0.156 Angle : 0.648 13.058 7021 Z= 0.344 Chirality : 0.042 0.164 800 Planarity : 0.004 0.049 823 Dihedral : 10.284 73.270 725 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.43 % Allowed : 21.81 % Favored : 73.76 % 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: 1.08 (0.35), residues: 580 helix: 1.75 (0.26), residues: 374 sheet: -0.60 (0.96), residues: 36 loop : -1.32 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 174 HIS 0.005 0.001 HIS B 213 PHE 0.023 0.002 PHE C 328 TYR 0.018 0.002 TYR A 261 ARG 0.004 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.05741 ( 299) hydrogen bonds : angle 4.55441 ( 870) metal coordination : bond 0.00576 ( 4) covalent geometry : bond 0.00331 ( 5223) covalent geometry : angle 0.64807 ( 7021) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 LEU cc_start: 0.7466 (tp) cc_final: 0.7067 (mp) REVERT: B 162 ARG cc_start: 0.6247 (mtt180) cc_final: 0.5928 (ttm170) REVERT: B 240 ASP cc_start: 0.8650 (m-30) cc_final: 0.8284 (t0) REVERT: B 266 MET cc_start: 0.6955 (tpt) cc_final: 0.6686 (tpt) REVERT: A 100 ASP cc_start: 0.4381 (m-30) cc_final: 0.3806 (t0) REVERT: A 122 LEU cc_start: 0.8521 (mt) cc_final: 0.8266 (tp) REVERT: A 165 GLU cc_start: 0.7490 (pm20) cc_final: 0.7220 (pm20) REVERT: A 246 ASP cc_start: 0.7429 (m-30) cc_final: 0.7128 (t0) outliers start: 25 outliers final: 17 residues processed: 135 average time/residue: 0.1409 time to fit residues: 25.4107 Evaluate side-chains 132 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain C residue 296 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.0770 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.189724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.168829 restraints weight = 9761.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.173410 restraints weight = 6025.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.176587 restraints weight = 4081.920| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.6637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5227 Z= 0.126 Angle : 0.605 14.177 7021 Z= 0.315 Chirality : 0.042 0.177 800 Planarity : 0.004 0.049 823 Dihedral : 9.770 73.145 725 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.72 % Allowed : 22.70 % Favored : 73.58 % 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: 1.09 (0.35), residues: 580 helix: 1.88 (0.26), residues: 376 sheet: -0.57 (0.99), residues: 36 loop : -1.71 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 174 HIS 0.003 0.001 HIS B 213 PHE 0.021 0.001 PHE C 328 TYR 0.016 0.001 TYR A 261 ARG 0.003 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.04967 ( 299) hydrogen bonds : angle 4.31035 ( 870) metal coordination : bond 0.00260 ( 4) covalent geometry : bond 0.00247 ( 5223) covalent geometry : angle 0.60455 ( 7021) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7487 (mt) REVERT: B 127 TYR cc_start: 0.7776 (t80) cc_final: 0.7522 (t80) REVERT: B 136 LEU cc_start: 0.7469 (tp) cc_final: 0.7157 (mp) REVERT: B 240 ASP cc_start: 0.8707 (m-30) cc_final: 0.8287 (t0) REVERT: B 266 MET cc_start: 0.6941 (tpt) cc_final: 0.6707 (tpt) REVERT: A 122 LEU cc_start: 0.8521 (mt) cc_final: 0.8241 (tp) REVERT: A 142 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7132 (mt-10) REVERT: A 246 ASP cc_start: 0.7109 (m-30) cc_final: 0.6803 (t0) outliers start: 21 outliers final: 15 residues processed: 136 average time/residue: 0.1447 time to fit residues: 26.3493 Evaluate side-chains 133 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 178 TYR Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 275 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.187871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.167292 restraints weight = 9942.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.171702 restraints weight = 6145.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.174927 restraints weight = 4194.822| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.6753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5227 Z= 0.134 Angle : 0.637 13.827 7021 Z= 0.329 Chirality : 0.042 0.181 800 Planarity : 0.004 0.047 823 Dihedral : 9.675 78.333 725 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.66 % Allowed : 24.47 % Favored : 72.87 % 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: 0.89 (0.35), residues: 580 helix: 1.66 (0.26), residues: 384 sheet: -0.33 (1.08), residues: 32 loop : -1.86 (0.43), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 174 HIS 0.004 0.001 HIS B 213 PHE 0.025 0.001 PHE B 151 TYR 0.027 0.002 TYR A 175 ARG 0.003 0.000 ARG B 162 Details of bonding type rmsd hydrogen bonds : bond 0.04984 ( 299) hydrogen bonds : angle 4.29961 ( 870) metal coordination : bond 0.00350 ( 4) covalent geometry : bond 0.00277 ( 5223) covalent geometry : angle 0.63738 ( 7021) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7447 (mt) REVERT: B 127 TYR cc_start: 0.7716 (t80) cc_final: 0.7514 (t80) REVERT: B 186 TYR cc_start: 0.7520 (m-80) cc_final: 0.7072 (m-80) REVERT: B 240 ASP cc_start: 0.8695 (m-30) cc_final: 0.8334 (t0) REVERT: B 266 MET cc_start: 0.6922 (tpt) cc_final: 0.6658 (tpt) REVERT: A 106 CYS cc_start: 0.7265 (m) cc_final: 0.6977 (m) REVERT: A 122 LEU cc_start: 0.8535 (mt) cc_final: 0.8257 (tp) REVERT: A 246 ASP cc_start: 0.7241 (m-30) cc_final: 0.6956 (t0) outliers start: 15 outliers final: 14 residues processed: 129 average time/residue: 0.1495 time to fit residues: 25.8410 Evaluate side-chains 134 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain C residue 296 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 7 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 0.0020 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.191300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.169673 restraints weight = 9899.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.174425 restraints weight = 5985.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.177800 restraints weight = 4005.745| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.7130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5227 Z= 0.122 Angle : 0.607 11.148 7021 Z= 0.313 Chirality : 0.042 0.182 800 Planarity : 0.004 0.051 823 Dihedral : 9.235 82.239 725 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.13 % Allowed : 24.47 % Favored : 73.40 % 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: 1.22 (0.35), residues: 580 helix: 1.90 (0.26), residues: 380 sheet: -0.26 (1.11), residues: 32 loop : -1.58 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 174 HIS 0.002 0.001 HIS B 213 PHE 0.022 0.001 PHE B 151 TYR 0.026 0.001 TYR A 175 ARG 0.004 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 299) hydrogen bonds : angle 4.20735 ( 870) metal coordination : bond 0.00168 ( 4) covalent geometry : bond 0.00243 ( 5223) covalent geometry : angle 0.60650 ( 7021) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7427 (mt) REVERT: B 110 TRP cc_start: 0.7895 (t60) cc_final: 0.7641 (t60) REVERT: B 127 TYR cc_start: 0.7648 (t80) cc_final: 0.7415 (t80) REVERT: B 162 ARG cc_start: 0.6198 (ttt180) cc_final: 0.5802 (ttt90) REVERT: B 240 ASP cc_start: 0.8681 (m-30) cc_final: 0.8322 (t0) REVERT: B 255 LYS cc_start: 0.8442 (mptt) cc_final: 0.8182 (mmtm) REVERT: B 266 MET cc_start: 0.6880 (tpt) cc_final: 0.6648 (tpt) REVERT: A 106 CYS cc_start: 0.7424 (m) cc_final: 0.7092 (m) REVERT: A 122 LEU cc_start: 0.8541 (mt) cc_final: 0.8272 (tp) REVERT: A 211 THR cc_start: 0.8344 (p) cc_final: 0.8022 (p) REVERT: A 246 ASP cc_start: 0.7116 (m-30) cc_final: 0.6879 (t0) REVERT: C 325 GLN cc_start: 0.8284 (pp30) cc_final: 0.7900 (pp30) outliers start: 12 outliers final: 9 residues processed: 136 average time/residue: 0.1473 time to fit residues: 26.7191 Evaluate side-chains 129 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 275 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 33 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.190061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.168479 restraints weight = 9828.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.172973 restraints weight = 5995.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.176167 restraints weight = 4070.566| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.7259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5227 Z= 0.128 Angle : 0.620 10.883 7021 Z= 0.328 Chirality : 0.042 0.173 800 Planarity : 0.004 0.050 823 Dihedral : 9.222 84.510 725 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.48 % Allowed : 25.00 % Favored : 72.52 % 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 (0.35), residues: 580 helix: 1.96 (0.26), residues: 373 sheet: -0.37 (1.03), residues: 36 loop : -1.52 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 174 HIS 0.004 0.001 HIS B 213 PHE 0.022 0.001 PHE B 151 TYR 0.020 0.002 TYR A 175 ARG 0.005 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 299) hydrogen bonds : angle 4.22681 ( 870) metal coordination : bond 0.00230 ( 4) covalent geometry : bond 0.00269 ( 5223) covalent geometry : angle 0.61987 ( 7021) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7381 (mt) REVERT: B 127 TYR cc_start: 0.7622 (t80) cc_final: 0.7397 (t80) REVERT: B 149 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7383 (mt) REVERT: B 151 PHE cc_start: 0.7160 (p90) cc_final: 0.6924 (p90) REVERT: B 240 ASP cc_start: 0.8690 (m-30) cc_final: 0.8359 (t0) REVERT: B 255 LYS cc_start: 0.8481 (mptt) cc_final: 0.8245 (mmtm) REVERT: B 266 MET cc_start: 0.6867 (tpt) cc_final: 0.6621 (tpt) REVERT: A 106 CYS cc_start: 0.7331 (m) cc_final: 0.7039 (m) REVERT: A 122 LEU cc_start: 0.8549 (mt) cc_final: 0.8269 (tp) REVERT: A 134 GLN cc_start: 0.7612 (mm-40) cc_final: 0.6562 (mt0) REVERT: A 194 ARG cc_start: 0.6561 (ptt180) cc_final: 0.6276 (ptt180) REVERT: A 211 THR cc_start: 0.8396 (p) cc_final: 0.8086 (p) REVERT: A 246 ASP cc_start: 0.7269 (m-30) cc_final: 0.6997 (t0) REVERT: C 325 GLN cc_start: 0.8302 (pp30) cc_final: 0.7960 (pp30) outliers start: 14 outliers final: 11 residues processed: 128 average time/residue: 0.1486 time to fit residues: 25.0192 Evaluate side-chains 129 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 275 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 278 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.187649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.166005 restraints weight = 10074.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.170417 restraints weight = 6107.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.173631 restraints weight = 4138.613| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.7201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5227 Z= 0.141 Angle : 0.646 10.427 7021 Z= 0.343 Chirality : 0.043 0.176 800 Planarity : 0.004 0.042 823 Dihedral : 9.616 89.828 725 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.48 % Allowed : 25.18 % Favored : 72.34 % 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 (0.35), residues: 580 helix: 1.70 (0.26), residues: 381 sheet: -0.33 (1.08), residues: 32 loop : -1.76 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 174 HIS 0.005 0.001 HIS B 213 PHE 0.021 0.001 PHE B 151 TYR 0.018 0.002 TYR A 261 ARG 0.004 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.04902 ( 299) hydrogen bonds : angle 4.30729 ( 870) metal coordination : bond 0.00456 ( 4) covalent geometry : bond 0.00308 ( 5223) covalent geometry : angle 0.64600 ( 7021) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1972.24 seconds wall clock time: 34 minutes 59.25 seconds (2099.25 seconds total)