Starting phenix.real_space_refine on Tue Mar 3 10:50:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm2_27524/03_2026/8dm2_27524.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm2_27524/03_2026/8dm2_27524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dm2_27524/03_2026/8dm2_27524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm2_27524/03_2026/8dm2_27524.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm2_27524/03_2026/8dm2_27524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm2_27524/03_2026/8dm2_27524.cif" } resolution = 2.91 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 1360 2.51 5 N 337 2.21 5 O 400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2104 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2020 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 11, 'TRANS': 237} Chain breaks: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 0.73, per 1000 atoms: 0.35 Number of scatterers: 2104 At special positions: 0 Unit cell: (52, 64, 69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 7 16.00 O 400 8.00 N 337 7.00 C 1360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 0.22 Conformation dependent library (CDL) restraints added in 75.8 milliseconds 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 474 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 51.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 30 removed outlier: 7.712A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.983A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.723A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 213 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: 0.29 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 631 1.34 - 1.45: 479 1.45 - 1.57: 1038 1.57 - 1.69: 0 1.69 - 1.80: 9 Bond restraints: 2157 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.77e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.37e+00 ... (remaining 2152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 2560 1.44 - 2.88: 301 2.88 - 4.32: 55 4.32 - 5.76: 12 5.76 - 7.20: 3 Bond angle restraints: 2931 Sorted by residual: angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 122.46 129.45 -6.99 1.41e+00 5.03e-01 2.46e+01 angle pdb=" C ALA A 292 " pdb=" N LEU A 293 " pdb=" CA LEU A 293 " ideal model delta sigma weight residual 121.70 128.33 -6.63 1.80e+00 3.09e-01 1.36e+01 angle pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " pdb=" CG ASP A 198 " ideal model delta sigma weight residual 112.60 116.03 -3.43 1.00e+00 1.00e+00 1.18e+01 angle pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 114.40 121.60 -7.20 2.30e+00 1.89e-01 9.80e+00 angle pdb=" CA TYR A 144 " pdb=" CB TYR A 144 " pdb=" CG TYR A 144 " ideal model delta sigma weight residual 113.90 118.71 -4.81 1.80e+00 3.09e-01 7.15e+00 ... (remaining 2926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 1215 16.84 - 33.68: 87 33.68 - 50.53: 21 50.53 - 67.37: 8 67.37 - 84.21: 2 Dihedral angle restraints: 1333 sinusoidal: 601 harmonic: 732 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -52.53 -33.47 1 1.00e+01 1.00e-02 1.59e+01 dihedral pdb=" C ASP A 198 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " ideal model delta harmonic sigma weight residual -122.60 -131.58 8.98 0 2.50e+00 1.60e-01 1.29e+01 dihedral pdb=" N ASP A 198 " pdb=" C ASP A 198 " pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " ideal model delta harmonic sigma weight residual 122.80 131.10 -8.30 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 1330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 236 0.062 - 0.124: 83 0.124 - 0.186: 19 0.186 - 0.248: 3 0.248 - 0.310: 2 Chirality restraints: 343 Sorted by residual: chirality pdb=" CG LEU A 249 " pdb=" CB LEU A 249 " pdb=" CD1 LEU A 249 " pdb=" CD2 LEU A 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA ASP A 198 " pdb=" N ASP A 198 " pdb=" C ASP A 198 " pdb=" CB ASP A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE A 233 " pdb=" CA ILE A 233 " pdb=" CG1 ILE A 233 " pdb=" CG2 ILE A 233 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 340 not shown) Planarity restraints: 369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 210 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C ILE A 210 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE A 210 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN A 211 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 197 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C ILE A 197 " -0.033 2.00e-02 2.50e+03 pdb=" O ILE A 197 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP A 198 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 273 " -0.168 9.50e-02 1.11e+02 7.54e-02 3.54e+00 pdb=" NE ARG A 273 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 273 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 273 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 273 " -0.008 2.00e-02 2.50e+03 ... (remaining 366 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 747 2.87 - 3.38: 1629 3.38 - 3.88: 3434 3.88 - 4.39: 3985 4.39 - 4.90: 6978 Nonbonded interactions: 16773 Sorted by model distance: nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.362 3.040 nonbonded pdb=" NH1 ARG A 102 " pdb=" OE2 GLU A 154 " model vdw 2.407 3.120 nonbonded pdb=" O HIS A 245 " pdb=" N THR A 259 " model vdw 2.408 3.120 nonbonded pdb=" O5 NAG A1302 " pdb=" O6 NAG A1302 " model vdw 2.447 2.432 nonbonded pdb=" O5 NAG A1301 " pdb=" O6 NAG A1301 " model vdw 2.474 2.432 ... (remaining 16768 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.050 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.470 Find NCS groups from input model: 0.010 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 2165 Z= 0.339 Angle : 1.042 7.202 2953 Z= 0.571 Chirality : 0.069 0.310 343 Planarity : 0.007 0.075 364 Dihedral : 13.368 84.211 853 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.44 % Allowed : 3.11 % Favored : 96.44 % 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: -0.51 (0.50), residues: 239 helix: None (None), residues: 0 sheet: 0.70 (0.44), residues: 112 loop : -1.37 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 190 TYR 0.019 0.003 TYR A 144 PHE 0.023 0.003 PHE A 175 TRP 0.009 0.002 TRP A 64 HIS 0.005 0.002 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00744 ( 2157) covalent geometry : angle 1.02064 ( 2931) SS BOND : bond 0.00316 ( 2) SS BOND : angle 2.18502 ( 4) hydrogen bonds : bond 0.05975 ( 80) hydrogen bonds : angle 6.55212 ( 213) link_BETA1-4 : bond 0.01125 ( 1) link_BETA1-4 : angle 2.47550 ( 3) link_NAG-ASN : bond 0.00709 ( 5) link_NAG-ASN : angle 2.79250 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.6919 (mttm) cc_final: 0.5330 (tptp) REVERT: A 266 TYR cc_start: 0.8089 (m-80) cc_final: 0.7717 (m-80) outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.4698 time to fit residues: 35.5279 Evaluate side-chains 42 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 6 optimal weight: 0.4980 chunk 4 optimal weight: 0.4980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.131484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.105329 restraints weight = 3572.597| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.88 r_work: 0.3261 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 2165 Z= 0.197 Angle : 0.752 9.810 2953 Z= 0.388 Chirality : 0.050 0.169 343 Planarity : 0.006 0.064 364 Dihedral : 9.255 57.870 397 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.11 % Allowed : 19.11 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.52), residues: 239 helix: None (None), residues: 0 sheet: 1.04 (0.46), residues: 111 loop : -1.13 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 102 TYR 0.014 0.002 TYR A 266 PHE 0.018 0.002 PHE A 133 TRP 0.009 0.002 TRP A 64 HIS 0.009 0.002 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 2157) covalent geometry : angle 0.73637 ( 2931) SS BOND : bond 0.00389 ( 2) SS BOND : angle 1.53431 ( 4) hydrogen bonds : bond 0.03310 ( 80) hydrogen bonds : angle 6.49649 ( 213) link_BETA1-4 : bond 0.00000 ( 1) link_BETA1-4 : angle 1.56934 ( 3) link_NAG-ASN : bond 0.00425 ( 5) link_NAG-ASN : angle 2.03684 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9001 (mttm) cc_final: 0.7156 (tptt) REVERT: A 102 ARG cc_start: 0.8105 (ttm-80) cc_final: 0.7787 (mtt90) REVERT: A 119 ILE cc_start: 0.8556 (mt) cc_final: 0.8284 (mp) REVERT: A 153 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.6105 (mtt) REVERT: A 157 PHE cc_start: 0.8223 (m-10) cc_final: 0.7992 (m-10) REVERT: A 205 SER cc_start: 0.9025 (p) cc_final: 0.8808 (p) REVERT: A 246 ARG cc_start: 0.5883 (mmt180) cc_final: 0.5561 (mmt180) REVERT: A 273 ARG cc_start: 0.7758 (mmt90) cc_final: 0.7538 (mtp85) outliers start: 7 outliers final: 1 residues processed: 58 average time/residue: 0.4298 time to fit residues: 25.5392 Evaluate side-chains 37 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 153 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 188 ASN A 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.128405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.102785 restraints weight = 3772.300| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.92 r_work: 0.3233 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 2165 Z= 0.200 Angle : 0.709 8.646 2953 Z= 0.366 Chirality : 0.049 0.168 343 Planarity : 0.004 0.029 364 Dihedral : 8.214 54.990 395 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 7.11 % Allowed : 20.89 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.36 (0.54), residues: 239 helix: None (None), residues: 0 sheet: 0.80 (0.47), residues: 108 loop : -1.19 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 158 TYR 0.013 0.002 TYR A 144 PHE 0.013 0.002 PHE A 133 TRP 0.004 0.001 TRP A 64 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 2157) covalent geometry : angle 0.69250 ( 2931) SS BOND : bond 0.00885 ( 2) SS BOND : angle 2.04270 ( 4) hydrogen bonds : bond 0.03553 ( 80) hydrogen bonds : angle 6.13838 ( 213) link_BETA1-4 : bond 0.00086 ( 1) link_BETA1-4 : angle 1.33471 ( 3) link_NAG-ASN : bond 0.00305 ( 5) link_NAG-ASN : angle 1.94452 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9168 (mttm) cc_final: 0.7220 (tptt) REVERT: A 102 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7870 (mmt90) REVERT: A 153 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6575 (mtt) REVERT: A 157 PHE cc_start: 0.8289 (m-10) cc_final: 0.8055 (m-10) REVERT: A 191 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7816 (mt-10) REVERT: A 205 SER cc_start: 0.9049 (p) cc_final: 0.8780 (p) REVERT: A 240 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.8806 (t) REVERT: A 246 ARG cc_start: 0.6220 (mmt180) cc_final: 0.5740 (mmt90) REVERT: A 273 ARG cc_start: 0.7861 (mmt90) cc_final: 0.7652 (mtp85) outliers start: 16 outliers final: 3 residues processed: 47 average time/residue: 0.4763 time to fit residues: 22.9115 Evaluate side-chains 31 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 17 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.127330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.101454 restraints weight = 3656.363| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.88 r_work: 0.3215 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.7435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2165 Z= 0.181 Angle : 0.655 8.217 2953 Z= 0.333 Chirality : 0.048 0.186 343 Planarity : 0.004 0.029 364 Dihedral : 7.113 46.806 395 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.89 % Allowed : 27.11 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.53 (0.54), residues: 239 helix: None (None), residues: 0 sheet: 0.76 (0.48), residues: 107 loop : -1.37 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 158 TYR 0.011 0.002 TYR A 279 PHE 0.013 0.001 PHE A 133 TRP 0.004 0.001 TRP A 258 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 2157) covalent geometry : angle 0.64101 ( 2931) SS BOND : bond 0.00662 ( 2) SS BOND : angle 1.59167 ( 4) hydrogen bonds : bond 0.03280 ( 80) hydrogen bonds : angle 6.01808 ( 213) link_BETA1-4 : bond 0.00075 ( 1) link_BETA1-4 : angle 0.95753 ( 3) link_NAG-ASN : bond 0.00292 ( 5) link_NAG-ASN : angle 1.84765 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9199 (mttm) cc_final: 0.7254 (tptt) REVERT: A 153 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6649 (mtt) REVERT: A 157 PHE cc_start: 0.8259 (m-10) cc_final: 0.8045 (m-10) REVERT: A 205 SER cc_start: 0.8948 (p) cc_final: 0.8642 (p) REVERT: A 240 THR cc_start: 0.9361 (OUTLIER) cc_final: 0.9026 (t) REVERT: A 246 ARG cc_start: 0.6303 (mmt180) cc_final: 0.5934 (mmt180) outliers start: 11 outliers final: 4 residues processed: 37 average time/residue: 0.5873 time to fit residues: 22.1765 Evaluate side-chains 32 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 1 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.126918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.100883 restraints weight = 3653.268| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.89 r_work: 0.3196 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.8063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2165 Z= 0.189 Angle : 0.671 8.099 2953 Z= 0.342 Chirality : 0.048 0.190 343 Planarity : 0.004 0.031 364 Dihedral : 6.461 45.920 395 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.33 % Allowed : 27.56 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.61 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.71 (0.49), residues: 107 loop : -1.44 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 273 TYR 0.011 0.001 TYR A 279 PHE 0.011 0.001 PHE A 133 TRP 0.004 0.001 TRP A 258 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 2157) covalent geometry : angle 0.65988 ( 2931) SS BOND : bond 0.00636 ( 2) SS BOND : angle 1.44802 ( 4) hydrogen bonds : bond 0.03419 ( 80) hydrogen bonds : angle 5.89348 ( 213) link_BETA1-4 : bond 0.00331 ( 1) link_BETA1-4 : angle 0.80970 ( 3) link_NAG-ASN : bond 0.00258 ( 5) link_NAG-ASN : angle 1.72807 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.080 Fit side-chains REVERT: A 33 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9091 (m) REVERT: A 41 LYS cc_start: 0.9192 (mttm) cc_final: 0.7210 (tptt) REVERT: A 153 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6947 (mtt) REVERT: A 177 MET cc_start: 0.7200 (mpp) cc_final: 0.6889 (pmm) REVERT: A 190 ARG cc_start: 0.8957 (ttm110) cc_final: 0.7969 (ttm-80) REVERT: A 205 SER cc_start: 0.8895 (p) cc_final: 0.8580 (p) outliers start: 12 outliers final: 5 residues processed: 32 average time/residue: 0.5741 time to fit residues: 18.7773 Evaluate side-chains 26 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 197 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.126531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.100532 restraints weight = 3660.253| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.94 r_work: 0.3192 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.8311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2165 Z= 0.189 Angle : 0.649 9.374 2953 Z= 0.328 Chirality : 0.048 0.185 343 Planarity : 0.004 0.029 364 Dihedral : 6.153 45.431 395 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.89 % Allowed : 27.56 % Favored : 67.56 % 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: -0.56 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.71 (0.50), residues: 106 loop : -1.35 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 158 TYR 0.011 0.001 TYR A 279 PHE 0.017 0.002 PHE A 157 TRP 0.004 0.001 TRP A 258 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 2157) covalent geometry : angle 0.63769 ( 2931) SS BOND : bond 0.00709 ( 2) SS BOND : angle 1.29067 ( 4) hydrogen bonds : bond 0.03321 ( 80) hydrogen bonds : angle 5.82176 ( 213) link_BETA1-4 : bond 0.00212 ( 1) link_BETA1-4 : angle 0.87899 ( 3) link_NAG-ASN : bond 0.00262 ( 5) link_NAG-ASN : angle 1.70426 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 0.096 Fit side-chains REVERT: A 33 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9097 (m) REVERT: A 41 LYS cc_start: 0.9190 (mttm) cc_final: 0.7149 (tptt) REVERT: A 153 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6913 (mtt) REVERT: A 177 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6952 (pmm) REVERT: A 190 ARG cc_start: 0.8740 (ttm110) cc_final: 0.8056 (ttm-80) REVERT: A 205 SER cc_start: 0.8878 (p) cc_final: 0.8558 (p) outliers start: 11 outliers final: 6 residues processed: 29 average time/residue: 0.5779 time to fit residues: 17.1247 Evaluate side-chains 31 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 197 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.0970 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.0970 overall best weight: 0.3176 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.128367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.102368 restraints weight = 3653.974| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.98 r_work: 0.3220 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.8369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2165 Z= 0.122 Angle : 0.590 8.217 2953 Z= 0.302 Chirality : 0.046 0.188 343 Planarity : 0.003 0.031 364 Dihedral : 5.809 46.926 395 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.33 % Allowed : 28.00 % Favored : 66.67 % 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: -0.58 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.50 (0.50), residues: 110 loop : -1.21 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.007 0.001 TYR A 144 PHE 0.010 0.001 PHE A 133 TRP 0.003 0.001 TRP A 64 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 2157) covalent geometry : angle 0.57787 ( 2931) SS BOND : bond 0.00507 ( 2) SS BOND : angle 1.31727 ( 4) hydrogen bonds : bond 0.02894 ( 80) hydrogen bonds : angle 5.70019 ( 213) link_BETA1-4 : bond 0.00266 ( 1) link_BETA1-4 : angle 0.94661 ( 3) link_NAG-ASN : bond 0.00098 ( 5) link_NAG-ASN : angle 1.64183 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.082 Fit side-chains REVERT: A 33 THR cc_start: 0.9310 (OUTLIER) cc_final: 0.9077 (m) REVERT: A 41 LYS cc_start: 0.9163 (mttm) cc_final: 0.7158 (tptt) REVERT: A 52 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8074 (tm-30) REVERT: A 153 MET cc_start: 0.7094 (mtp) cc_final: 0.6893 (mtt) REVERT: A 177 MET cc_start: 0.7062 (mpp) cc_final: 0.6697 (pmm) REVERT: A 190 ARG cc_start: 0.8687 (ttm110) cc_final: 0.7955 (ttm-80) REVERT: A 205 SER cc_start: 0.8794 (p) cc_final: 0.8476 (p) REVERT: A 246 ARG cc_start: 0.6246 (mmt180) cc_final: 0.6037 (mmt180) outliers start: 12 outliers final: 6 residues processed: 37 average time/residue: 0.4944 time to fit residues: 18.7038 Evaluate side-chains 32 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 197 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 18 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.126371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.100385 restraints weight = 3679.519| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.93 r_work: 0.3186 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.8560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2165 Z= 0.205 Angle : 0.673 8.200 2953 Z= 0.344 Chirality : 0.048 0.188 343 Planarity : 0.004 0.030 364 Dihedral : 6.091 47.076 395 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.33 % Allowed : 28.89 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.57), residues: 239 helix: None (None), residues: 0 sheet: 0.63 (0.52), residues: 106 loop : -1.33 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 102 TYR 0.012 0.001 TYR A 279 PHE 0.015 0.002 PHE A 157 TRP 0.004 0.001 TRP A 258 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 2157) covalent geometry : angle 0.66145 ( 2931) SS BOND : bond 0.00741 ( 2) SS BOND : angle 1.28154 ( 4) hydrogen bonds : bond 0.03364 ( 80) hydrogen bonds : angle 5.70214 ( 213) link_BETA1-4 : bond 0.00174 ( 1) link_BETA1-4 : angle 1.09069 ( 3) link_NAG-ASN : bond 0.00314 ( 5) link_NAG-ASN : angle 1.72133 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.056 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.9086 (m) REVERT: A 41 LYS cc_start: 0.9182 (mttm) cc_final: 0.7146 (tptt) REVERT: A 52 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8102 (tm-30) REVERT: A 153 MET cc_start: 0.7091 (mtp) cc_final: 0.6879 (mtt) REVERT: A 205 SER cc_start: 0.8874 (p) cc_final: 0.8530 (p) REVERT: A 246 ARG cc_start: 0.6448 (mmt180) cc_final: 0.6194 (mmt90) outliers start: 12 outliers final: 6 residues processed: 35 average time/residue: 0.5590 time to fit residues: 19.9198 Evaluate side-chains 31 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 128 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.0370 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.127990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.101718 restraints weight = 3686.455| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.96 r_work: 0.3211 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.8605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2165 Z= 0.145 Angle : 0.650 9.248 2953 Z= 0.331 Chirality : 0.047 0.187 343 Planarity : 0.004 0.032 364 Dihedral : 5.892 46.432 395 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.33 % Allowed : 29.78 % Favored : 64.89 % 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: -0.64 (0.57), residues: 239 helix: None (None), residues: 0 sheet: 0.59 (0.52), residues: 106 loop : -1.34 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.007 0.001 TYR A 279 PHE 0.013 0.001 PHE A 175 TRP 0.003 0.001 TRP A 64 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 2157) covalent geometry : angle 0.63881 ( 2931) SS BOND : bond 0.00558 ( 2) SS BOND : angle 1.30732 ( 4) hydrogen bonds : bond 0.03070 ( 80) hydrogen bonds : angle 5.67871 ( 213) link_BETA1-4 : bond 0.00247 ( 1) link_BETA1-4 : angle 1.02738 ( 3) link_NAG-ASN : bond 0.00151 ( 5) link_NAG-ASN : angle 1.69660 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 0.048 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9063 (m) REVERT: A 41 LYS cc_start: 0.9167 (mttm) cc_final: 0.7163 (tptt) REVERT: A 52 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8019 (tm-30) REVERT: A 153 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6940 (mtt) REVERT: A 177 MET cc_start: 0.6703 (pmm) cc_final: 0.5702 (tpp) REVERT: A 205 SER cc_start: 0.8805 (p) cc_final: 0.8479 (p) REVERT: A 246 ARG cc_start: 0.6277 (mmt180) cc_final: 0.6013 (mmt90) outliers start: 12 outliers final: 6 residues processed: 34 average time/residue: 0.5287 time to fit residues: 18.2840 Evaluate side-chains 32 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 153 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.125517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.099846 restraints weight = 3681.385| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.87 r_work: 0.3160 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.8806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 2165 Z= 0.228 Angle : 0.700 9.820 2953 Z= 0.353 Chirality : 0.049 0.187 343 Planarity : 0.004 0.029 364 Dihedral : 6.186 46.765 395 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.44 % Allowed : 31.11 % Favored : 64.44 % 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 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.51 (0.52), residues: 106 loop : -1.46 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 102 TYR 0.013 0.002 TYR A 279 PHE 0.016 0.002 PHE A 175 TRP 0.004 0.001 TRP A 258 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00536 ( 2157) covalent geometry : angle 0.68926 ( 2931) SS BOND : bond 0.00726 ( 2) SS BOND : angle 1.33368 ( 4) hydrogen bonds : bond 0.03493 ( 80) hydrogen bonds : angle 5.79972 ( 213) link_BETA1-4 : bond 0.00209 ( 1) link_BETA1-4 : angle 1.15728 ( 3) link_NAG-ASN : bond 0.00360 ( 5) link_NAG-ASN : angle 1.68200 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.046 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.9066 (m) REVERT: A 41 LYS cc_start: 0.9180 (mttm) cc_final: 0.7118 (tmtt) REVERT: A 52 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8091 (tm-30) REVERT: A 177 MET cc_start: 0.6911 (pmm) cc_final: 0.5960 (tpp) REVERT: A 205 SER cc_start: 0.8896 (p) cc_final: 0.8556 (p) REVERT: A 246 ARG cc_start: 0.6483 (mmt180) cc_final: 0.6210 (mmt90) outliers start: 10 outliers final: 7 residues processed: 31 average time/residue: 0.4576 time to fit residues: 14.4688 Evaluate side-chains 32 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 231 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.0570 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.127108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.100948 restraints weight = 3705.419| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.96 r_work: 0.3192 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.8844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2165 Z= 0.156 Angle : 0.649 9.210 2953 Z= 0.330 Chirality : 0.047 0.186 343 Planarity : 0.003 0.032 364 Dihedral : 5.924 46.918 395 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.33 % Allowed : 30.22 % Favored : 64.44 % 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: -0.81 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.46 (0.51), residues: 106 loop : -1.43 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.008 0.001 TYR A 144 PHE 0.012 0.001 PHE A 175 TRP 0.002 0.001 TRP A 258 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 2157) covalent geometry : angle 0.63725 ( 2931) SS BOND : bond 0.00581 ( 2) SS BOND : angle 1.34167 ( 4) hydrogen bonds : bond 0.03123 ( 80) hydrogen bonds : angle 5.71605 ( 213) link_BETA1-4 : bond 0.00261 ( 1) link_BETA1-4 : angle 1.03683 ( 3) link_NAG-ASN : bond 0.00178 ( 5) link_NAG-ASN : angle 1.69717 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1065.38 seconds wall clock time: 18 minutes 47.08 seconds (1127.08 seconds total)