Starting phenix.real_space_refine on Thu Jul 2 01:31:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8exr_28660/07_2026/8exr_28660.cif Found real_map, /net/cci-nas-00/data/ceres_data/8exr_28660/07_2026/8exr_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8exr_28660/07_2026/8exr_28660.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8exr_28660/07_2026/8exr_28660.cif" model { file = "/net/cci-nas-00/data/ceres_data/8exr_28660/07_2026/8exr_28660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8exr_28660/07_2026/8exr_28660.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8exr_28660/07_2026/8exr_28660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8exr_28660/07_2026/8exr_28660.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.07, per 1000 atoms: 0.21 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: 0.38 Conformation dependent library (CDL) restraints added in 163.3 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: 0.14 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: 0.51 Time building geometry restraints manager: 0.46 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: 2901 14.09 - 28.17: 139 28.17 - 42.25: 48 42.25 - 56.34: 23 56.34 - 70.42: 8 Dihedral angle restraints: 3119 sinusoidal: 1336 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 3116 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: 2.560 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.330 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 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 : 11.539 70.423 1955 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (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 ARG 0.006 0.001 ARG A 23 TYR 0.099 0.012 TYR A 203 PHE 0.033 0.006 PHE B 284 TRP 0.043 0.009 TRP B 99 HIS 0.012 0.003 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.02593 / 1.49 ( 5223) covalent geometry : angle 1.94400 / 1.33 ( 7021) hydrogen bonds : bond 0.25172 / 16.22 ( 299) hydrogen bonds : angle 8.15000 / 5.92 ( 870) metal coordination : bond 0.05433 / 2.66 ( 4) *********************** 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 : 0.186 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: 0.7363 (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: 0.6780 (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: 0.0692 time to fit residues: 16.4956 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 : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 271 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4309 r_free = 0.4309 target = 0.186518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.164778 restraints weight = 11090.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.169004 restraints weight = 6843.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.172032 restraints weight = 4719.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.174209 restraints weight = 3503.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.175835 restraints weight = 2749.137| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5227 Z= 0.191 Angle : 0.723 6.843 7021 Z= 0.404 Chirality : 0.045 0.189 800 Planarity : 0.005 0.049 823 Dihedral : 11.855 67.213 699 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.24 % Favored : 97.59 % Rotamer: Outliers : 3.19 % Allowed : 12.41 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.34), residues: 580 helix: 1.46 (0.25), residues: 373 sheet: 0.04 (1.02), residues: 35 loop : -0.68 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 247 TYR 0.019 0.002 TYR B 127 PHE 0.025 0.002 PHE B 16 TRP 0.010 0.002 TRP A 110 HIS 0.007 0.002 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.19 ( 5223) covalent geometry : angle 0.72289 / 0.40 ( 7021) hydrogen bonds : bond 0.08499 / 5.57 ( 299) hydrogen bonds : angle 5.17577 / 3.71 ( 870) metal coordination : bond 0.00436 / 0.22 ( 4) *********************** 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 : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 MET cc_start: 0.7304 (mmt) cc_final: 0.6749 (ptp) REVERT: B 22 PHE cc_start: 0.6963 (m-80) cc_final: 0.6705 (m-80) REVERT: B 136 LEU cc_start: 0.7335 (tp) cc_final: 0.6659 (mp) REVERT: B 168 GLN cc_start: 0.6731 (mp10) cc_final: 0.6203 (mm-40) REVERT: B 240 ASP cc_start: 0.8521 (m-30) cc_final: 0.8082 (t0) REVERT: A 122 LEU cc_start: 0.8397 (mt) cc_final: 0.8187 (tp) REVERT: A 141 ASN cc_start: 0.7619 (m-40) cc_final: 0.7217 (p0) REVERT: A 194 ARG cc_start: 0.6940 (ptt180) cc_final: 0.6636 (ptt180) REVERT: C 295 LEU cc_start: 0.8553 (mt) cc_final: 0.7889 (tt) outliers start: 18 outliers final: 8 residues processed: 163 average time/residue: 0.0580 time to fit residues: 12.5669 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 : 0.110 ------------------------------------------------------------------------------- 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 B residue 211 THR Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 225 SER 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 36 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.180204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.159035 restraints weight = 11195.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.162971 restraints weight = 6956.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.165823 restraints weight = 4828.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.167857 restraints weight = 3605.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.169363 restraints weight = 2865.868| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5227 Z= 0.222 Angle : 0.762 11.034 7021 Z= 0.419 Chirality : 0.046 0.189 800 Planarity : 0.005 0.051 823 Dihedral : 11.142 59.161 699 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.50 % Allowed : 15.25 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.33), residues: 580 helix: 1.09 (0.25), residues: 379 sheet: -0.72 (1.01), residues: 32 loop : -1.62 (0.42), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 23 TYR 0.027 0.003 TYR A 186 PHE 0.028 0.002 PHE A 173 TRP 0.032 0.003 TRP A 174 HIS 0.006 0.002 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 ( 5223) covalent geometry : angle 0.76223 / 0.42 ( 7021) hydrogen bonds : bond 0.08284 / 5.37 ( 299) hydrogen bonds : angle 5.27785 / 3.79 ( 870) metal coordination : bond 0.00788 / 0.39 ( 4) *********************** 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 153 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 7 MET cc_start: 0.7344 (mmt) cc_final: 0.7078 (mtp) REVERT: B 22 PHE cc_start: 0.6909 (m-80) cc_final: 0.6630 (m-80) REVERT: B 162 ARG cc_start: 0.6347 (mtt180) cc_final: 0.5963 (ttm170) REVERT: B 203 TYR cc_start: 0.7192 (t80) cc_final: 0.6986 (t80) REVERT: B 240 ASP cc_start: 0.8567 (m-30) cc_final: 0.8184 (t0) REVERT: B 285 ASN cc_start: 0.6694 (m110) cc_final: 0.6283 (m-40) REVERT: A 122 LEU cc_start: 0.8532 (mt) cc_final: 0.8278 (tp) REVERT: A 141 ASN cc_start: 0.7699 (m-40) cc_final: 0.7299 (p0) REVERT: A 165 GLU cc_start: 0.6920 (pm20) cc_final: 0.6706 (pt0) REVERT: A 186 TYR cc_start: 0.7472 (m-10) cc_final: 0.7196 (m-80) REVERT: A 194 ARG cc_start: 0.7297 (ptt180) cc_final: 0.7021 (ptt180) REVERT: A 246 ASP cc_start: 0.7611 (m-30) cc_final: 0.7375 (t0) REVERT: C 295 LEU cc_start: 0.8617 (mt) cc_final: 0.7776 (tt) outliers start: 31 outliers final: 24 residues processed: 138 average time/residue: 0.0480 time to fit residues: 9.0121 Evaluate side-chains 136 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 SER 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 173 PHE 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 243 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 232 ILE 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 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 47 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.0020 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 144 ASN C 332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.181823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.160361 restraints weight = 10380.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.164605 restraints weight = 6560.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.167788 restraints weight = 4573.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.170038 restraints weight = 3386.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.171676 restraints weight = 2635.843| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.5466 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= 0.163 Angle : 0.638 8.888 7021 Z= 0.354 Chirality : 0.043 0.222 800 Planarity : 0.005 0.051 823 Dihedral : 10.261 59.142 699 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.26 % Allowed : 18.26 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.34), residues: 580 helix: 1.41 (0.26), residues: 371 sheet: -0.93 (0.98), residues: 36 loop : -1.65 (0.42), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 247 TYR 0.023 0.002 TYR A 175 PHE 0.016 0.002 PHE C 328 TRP 0.038 0.002 TRP A 174 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 ( 5223) covalent geometry : angle 0.63777 / 0.35 ( 7021) hydrogen bonds : bond 0.06798 / 4.41 ( 299) hydrogen bonds : angle 4.87165 / 3.47 ( 870) metal coordination : bond 0.00559 / 0.27 ( 4) *********************** 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 153 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 240 ASP cc_start: 0.8627 (m-30) cc_final: 0.8241 (t0) REVERT: B 285 ASN cc_start: 0.6854 (m110) cc_final: 0.6345 (m-40) REVERT: A 22 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7576 (t80) REVERT: A 122 LEU cc_start: 0.8482 (mt) cc_final: 0.8236 (tp) REVERT: A 141 ASN cc_start: 0.7366 (m-40) cc_final: 0.7156 (p0) REVERT: A 246 ASP cc_start: 0.7421 (m-30) cc_final: 0.7167 (t0) REVERT: C 325 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8405 (tm-30) outliers start: 24 outliers final: 17 residues processed: 142 average time/residue: 0.0439 time to fit residues: 8.5965 Evaluate side-chains 133 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 11 SER 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 195 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 244 GLU 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 31 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.185517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.164502 restraints weight = 10214.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.168838 restraints weight = 6295.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.172062 restraints weight = 4319.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.174413 restraints weight = 3144.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.175999 restraints weight = 2401.713| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.6060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5227 Z= 0.142 Angle : 0.620 8.635 7021 Z= 0.337 Chirality : 0.042 0.214 800 Planarity : 0.004 0.048 823 Dihedral : 9.379 59.179 699 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.08 % Allowed : 20.21 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.34), residues: 580 helix: 1.66 (0.26), residues: 371 sheet: -0.98 (0.97), residues: 36 loop : -1.52 (0.42), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 247 TYR 0.021 0.002 TYR A 175 PHE 0.023 0.001 PHE C 328 TRP 0.042 0.003 TRP A 174 HIS 0.003 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 5223) covalent geometry : angle 0.62006 / 0.34 ( 7021) hydrogen bonds : bond 0.05781 / 3.73 ( 299) hydrogen bonds : angle 4.58632 / 3.24 ( 870) metal coordination : bond 0.00297 / 0.15 ( 4) *********************** 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 151 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.113 Fit side-chains REVERT: B 162 ARG cc_start: 0.6180 (mtt180) cc_final: 0.5661 (ttt90) REVERT: B 203 TYR cc_start: 0.7047 (t80) cc_final: 0.6628 (t80) REVERT: B 240 ASP cc_start: 0.8630 (m-30) cc_final: 0.8308 (t0) REVERT: B 266 MET cc_start: 0.6782 (tpt) cc_final: 0.6579 (tpt) REVERT: B 285 ASN cc_start: 0.6798 (m110) cc_final: 0.6210 (m-40) REVERT: A 22 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7354 (t80) REVERT: A 122 LEU cc_start: 0.8472 (mt) cc_final: 0.8268 (tp) REVERT: A 123 LYS cc_start: 0.7958 (tttt) cc_final: 0.7615 (pttm) REVERT: A 246 ASP cc_start: 0.7304 (m-30) cc_final: 0.7001 (t0) outliers start: 23 outliers final: 15 residues processed: 144 average time/residue: 0.0481 time to fit residues: 9.2684 Evaluate side-chains 129 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET 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 195 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain A residue 22 PHE 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 220 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.186509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.165298 restraints weight = 10641.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.169883 restraints weight = 6606.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.173038 restraints weight = 4518.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.175278 restraints weight = 3316.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.176835 restraints weight = 2559.339| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.6458 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= 0.136 Angle : 0.625 11.257 7021 Z= 0.330 Chirality : 0.042 0.201 800 Planarity : 0.004 0.049 823 Dihedral : 8.863 59.101 699 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.72 % Allowed : 21.10 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.35), residues: 580 helix: 1.72 (0.26), residues: 368 sheet: -1.01 (0.96), residues: 36 loop : -1.36 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 23 TYR 0.018 0.002 TYR A 175 PHE 0.023 0.001 PHE C 328 TRP 0.031 0.002 TRP A 174 HIS 0.002 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 ( 5223) covalent geometry : angle 0.62502 / 0.33 ( 7021) hydrogen bonds : bond 0.05404 / 3.49 ( 299) hydrogen bonds : angle 4.51864 / 3.16 ( 870) metal coordination : bond 0.00299 / 0.15 ( 4) *********************** 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 137 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: B 240 ASP cc_start: 0.8691 (m-30) cc_final: 0.8328 (t0) REVERT: B 266 MET cc_start: 0.6819 (tpt) cc_final: 0.6602 (tpt) REVERT: B 285 ASN cc_start: 0.6612 (m110) cc_final: 0.6023 (m-40) REVERT: A 122 LEU cc_start: 0.8516 (mt) cc_final: 0.8279 (tp) REVERT: A 142 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7334 (mt-10) REVERT: A 246 ASP cc_start: 0.7342 (m-30) cc_final: 0.6999 (t0) outliers start: 21 outliers final: 15 residues processed: 127 average time/residue: 0.0514 time to fit residues: 8.9212 Evaluate side-chains 127 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 11 SER 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 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 173 PHE 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 309 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4296 r_free = 0.4296 target = 0.187230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.166549 restraints weight = 10356.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.170939 restraints weight = 6463.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.174016 restraints weight = 4451.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.176237 restraints weight = 3271.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.177745 restraints weight = 2535.381| |-----------------------------------------------------------------------------| r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.6689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5227 Z= 0.129 Angle : 0.611 10.947 7021 Z= 0.318 Chirality : 0.041 0.178 800 Planarity : 0.004 0.050 823 Dihedral : 8.526 59.348 699 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.26 % Allowed : 21.10 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.35), residues: 580 helix: 1.74 (0.26), residues: 369 sheet: -1.03 (0.96), residues: 36 loop : -1.65 (0.43), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 23 TYR 0.016 0.002 TYR A 261 PHE 0.020 0.001 PHE C 328 TRP 0.026 0.002 TRP A 174 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 ( 5223) covalent geometry : angle 0.61121 / 0.32 ( 7021) hydrogen bonds : bond 0.05076 / 3.27 ( 299) hydrogen bonds : angle 4.39845 / 3.08 ( 870) metal coordination : bond 0.00305 / 0.15 ( 4) *********************** 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 142 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: B 240 ASP cc_start: 0.8699 (m-30) cc_final: 0.8367 (t0) REVERT: B 266 MET cc_start: 0.6761 (tpt) cc_final: 0.6534 (tpt) REVERT: B 285 ASN cc_start: 0.6551 (m110) cc_final: 0.6155 (m-40) REVERT: A 22 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7263 (t80) REVERT: A 106 CYS cc_start: 0.7243 (m) cc_final: 0.6901 (m) REVERT: A 122 LEU cc_start: 0.8518 (mt) cc_final: 0.8272 (tp) REVERT: A 168 GLN cc_start: 0.6269 (pm20) cc_final: 0.6050 (pp30) REVERT: A 246 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6932 (t0) outliers start: 24 outliers final: 18 residues processed: 132 average time/residue: 0.0611 time to fit residues: 10.8023 Evaluate side-chains 134 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 11 SER 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 225 SER Chi-restraints excluded: chain A residue 22 PHE 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 173 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.185060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.164483 restraints weight = 10345.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.168828 restraints weight = 6359.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.171858 restraints weight = 4343.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.174019 restraints weight = 3182.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.175600 restraints weight = 2466.878| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.6757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5227 Z= 0.143 Angle : 0.641 10.529 7021 Z= 0.341 Chirality : 0.043 0.171 800 Planarity : 0.005 0.052 823 Dihedral : 8.419 59.115 699 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.26 % Allowed : 21.45 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.35), residues: 580 helix: 1.56 (0.26), residues: 370 sheet: -1.29 (0.94), residues: 36 loop : -1.89 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 23 TYR 0.017 0.002 TYR A 261 PHE 0.018 0.002 PHE B 14 TRP 0.022 0.002 TRP A 174 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 5223) covalent geometry : angle 0.64072 / 0.34 ( 7021) hydrogen bonds : bond 0.05319 / 3.40 ( 299) hydrogen bonds : angle 4.47997 / 3.15 ( 870) metal coordination : bond 0.00479 / 0.24 ( 4) *********************** 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 142 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 162 ARG cc_start: 0.6246 (ttt180) cc_final: 0.5535 (ttt90) REVERT: B 240 ASP cc_start: 0.8742 (m-30) cc_final: 0.8391 (t0) REVERT: B 255 LYS cc_start: 0.8548 (mttt) cc_final: 0.8033 (mmtt) REVERT: B 285 ASN cc_start: 0.6633 (m110) cc_final: 0.6241 (m-40) REVERT: A 22 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7295 (t80) REVERT: A 122 LEU cc_start: 0.8594 (mt) cc_final: 0.8321 (tp) REVERT: A 168 GLN cc_start: 0.6366 (pm20) cc_final: 0.6036 (pp30) REVERT: A 246 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7101 (t0) outliers start: 24 outliers final: 16 residues processed: 135 average time/residue: 0.0666 time to fit residues: 12.0271 Evaluate side-chains 132 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 11 SER 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 211 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain C residue 309 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 44 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 43 optimal weight: 0.0770 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN C 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.190191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.168870 restraints weight = 11079.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.173188 restraints weight = 6777.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.176235 restraints weight = 4655.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.178446 restraints weight = 3448.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.180082 restraints weight = 2693.239| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.7115 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= 0.128 Angle : 0.632 11.408 7021 Z= 0.331 Chirality : 0.042 0.162 800 Planarity : 0.004 0.050 823 Dihedral : 8.029 58.750 699 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.37 % Allowed : 21.99 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.35), residues: 580 helix: 1.61 (0.27), residues: 370 sheet: -1.06 (1.00), residues: 36 loop : -1.75 (0.43), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 23 TYR 0.018 0.001 TYR B 175 PHE 0.025 0.001 PHE B 151 TRP 0.025 0.002 TRP A 174 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 ( 5223) covalent geometry : angle 0.63246 / 0.33 ( 7021) hydrogen bonds : bond 0.04794 / 3.05 ( 299) hydrogen bonds : angle 4.49633 / 3.12 ( 870) metal coordination : bond 0.00202 / 0.10 ( 4) *********************** 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 146 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 186 TYR cc_start: 0.7389 (m-80) cc_final: 0.7180 (m-80) REVERT: B 240 ASP cc_start: 0.8651 (m-30) cc_final: 0.8345 (t0) REVERT: B 255 LYS cc_start: 0.8487 (mttt) cc_final: 0.8197 (mmtt) REVERT: A 10 VAL cc_start: 0.8753 (m) cc_final: 0.8512 (p) REVERT: A 22 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7327 (t80) REVERT: A 106 CYS cc_start: 0.7393 (m) cc_final: 0.7044 (m) REVERT: A 122 LEU cc_start: 0.8567 (mt) cc_final: 0.8323 (tp) REVERT: A 211 THR cc_start: 0.8337 (p) cc_final: 0.8025 (p) REVERT: A 246 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6856 (t0) outliers start: 19 outliers final: 14 residues processed: 138 average time/residue: 0.0637 time to fit residues: 11.7546 Evaluate side-chains 140 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 11 SER 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 A residue 22 PHE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain C residue 325 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.0470 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 45 optimal weight: 0.0070 chunk 8 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.191037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.169093 restraints weight = 11324.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.173499 restraints weight = 6992.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.176717 restraints weight = 4833.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.178859 restraints weight = 3597.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.180520 restraints weight = 2849.720| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.7319 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= 0.136 Angle : 0.667 11.550 7021 Z= 0.348 Chirality : 0.042 0.167 800 Planarity : 0.004 0.050 823 Dihedral : 7.894 59.060 699 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.01 % Allowed : 23.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.35), residues: 580 helix: 1.71 (0.27), residues: 370 sheet: -0.96 (1.01), residues: 36 loop : -1.82 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 23 TYR 0.016 0.001 TYR B 175 PHE 0.025 0.001 PHE B 151 TRP 0.023 0.002 TRP A 174 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 ( 5223) covalent geometry : angle 0.66746 / 0.35 ( 7021) hydrogen bonds : bond 0.04767 / 3.03 ( 299) hydrogen bonds : angle 4.44900 / 3.08 ( 870) metal coordination : bond 0.00206 / 0.10 ( 4) ********************** 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 145 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 186 TYR cc_start: 0.7480 (m-80) cc_final: 0.7264 (m-80) REVERT: B 240 ASP cc_start: 0.8634 (m-30) cc_final: 0.8355 (t0) REVERT: B 266 MET cc_start: 0.6682 (tpt) cc_final: 0.6454 (tpt) REVERT: B 300 GLU cc_start: 0.6529 (mm-30) cc_final: 0.6026 (pp20) REVERT: A 22 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7340 (t80) REVERT: A 106 CYS cc_start: 0.7363 (m) cc_final: 0.7025 (m) REVERT: A 122 LEU cc_start: 0.8565 (mt) cc_final: 0.8331 (tp) REVERT: A 211 THR cc_start: 0.8361 (p) cc_final: 0.8038 (p) REVERT: A 246 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6861 (t0) REVERT: A 266 MET cc_start: 0.5754 (ttm) cc_final: 0.5514 (ttm) outliers start: 17 outliers final: 14 residues processed: 135 average time/residue: 0.0602 time to fit residues: 10.8512 Evaluate side-chains 139 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 11 SER 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 280 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 173 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 246 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 43 optimal weight: 0.0010 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.191317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.169180 restraints weight = 11152.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.173602 restraints weight = 6818.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.176713 restraints weight = 4694.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.178918 restraints weight = 3501.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.180467 restraints weight = 2759.906| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.7509 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= 0.131 Angle : 0.647 10.856 7021 Z= 0.338 Chirality : 0.042 0.169 800 Planarity : 0.004 0.051 823 Dihedral : 7.670 58.485 699 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.84 % Allowed : 23.94 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.35), residues: 580 helix: 1.67 (0.27), residues: 375 sheet: -0.69 (1.05), residues: 36 loop : -1.87 (0.43), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 23 TYR 0.018 0.001 TYR A 261 PHE 0.024 0.001 PHE B 151 TRP 0.022 0.002 TRP A 174 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 5223) covalent geometry : angle 0.64747 / 0.34 ( 7021) hydrogen bonds : bond 0.04795 / 2.99 ( 299) hydrogen bonds : angle 4.43127 / 3.07 ( 870) metal coordination : bond 0.00227 / 0.11 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 951.80 seconds wall clock time: 17 minutes 8.66 seconds (1028.66 seconds total)