Starting phenix.real_space_refine on Wed Jul 1 21:02:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dm2_27524/07_2026/8dm2_27524.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm2_27524/07_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_27524/07_2026/8dm2_27524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm2_27524/07_2026/8dm2_27524.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm2_27524/07_2026/8dm2_27524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm2_27524/07_2026/8dm2_27524.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dm2_27524/07_2026/8dm2_27524.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dm2_27524/07_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-6108/lib/python3.11/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 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 chiralities: 4 Time building chain proxies: 0.54, per 1000 atoms: 0.26 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: 0.23 Conformation dependent library (CDL) restraints added in 56.8 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: 0.04 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: 0.19 Time building geometry restraints manager: 0.30 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: 1100 16.84 - 33.68: 86 33.68 - 50.53: 16 50.53 - 67.37: 3 67.37 - 84.21: 2 Dihedral angle restraints: 1207 sinusoidal: 475 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 1204 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: 4.840 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.980 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:5.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 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 : 12.991 84.211 727 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/Z covalent geometry : bond 0.00744 / 0.34 ( 2157) covalent geometry : angle 1.02064 / 0.57 ( 2931) SS BOND : bond 0.00316 / 0.16 ( 2) SS BOND : angle 2.18502 / 1.15 ( 4) hydrogen bonds : bond 0.05975 / 3.91 ( 80) hydrogen bonds : angle 6.55212 / 4.73 ( 213) link_BETA1-4 : bond 0.01125 / 0.59 ( 1) link_BETA1-4 : angle 2.47550 / 1.31 ( 3) link_NAG-ASN : bond 0.00709 / 0.44 ( 5) link_NAG-ASN : angle 2.79250 / 1.92 ( 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 : 0.068 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: 0.2953 time to fit residues: 22.3580 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 : 0.046 ------------------------------------------------------------------------------- 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: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.130777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.104743 restraints weight = 3554.747| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.81 r_work: 0.3247 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 2165 Z= 0.194 Angle : 0.746 9.599 2953 Z= 0.387 Chirality : 0.049 0.161 343 Planarity : 0.005 0.052 364 Dihedral : 6.472 52.078 271 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.56 % Allowed : 17.78 % Favored : 78.67 % 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: -0.12 (0.52), residues: 239 helix: None (None), residues: 0 sheet: 1.03 (0.46), residues: 111 loop : -1.15 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 102 TYR 0.012 0.002 TYR A 266 PHE 0.015 0.002 PHE A 133 TRP 0.011 0.002 TRP A 64 HIS 0.008 0.002 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 ( 2157) covalent geometry : angle 0.73243 / 0.38 ( 2931) SS BOND : bond 0.00231 / 0.12 ( 2) SS BOND : angle 1.57998 / 0.86 ( 4) hydrogen bonds : bond 0.03429 / 2.14 ( 80) hydrogen bonds : angle 6.45988 / 4.70 ( 213) link_BETA1-4 : bond 0.00307 / 0.16 ( 1) link_BETA1-4 : angle 1.15821 / 0.59 ( 3) link_NAG-ASN : bond 0.00397 / 0.20 ( 5) link_NAG-ASN : angle 1.92329 / 1.31 ( 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 58 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.045 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8940 (mttm) cc_final: 0.7087 (tptt) REVERT: A 102 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7786 (mtt90) REVERT: A 119 ILE cc_start: 0.8540 (mt) cc_final: 0.8261 (mp) REVERT: A 153 MET cc_start: 0.6306 (OUTLIER) cc_final: 0.6018 (mtt) REVERT: A 157 PHE cc_start: 0.8243 (m-10) cc_final: 0.8011 (m-10) REVERT: A 205 SER cc_start: 0.9034 (p) cc_final: 0.8816 (p) REVERT: A 246 ARG cc_start: 0.5904 (mmt180) cc_final: 0.5598 (mmt180) REVERT: A 273 ARG cc_start: 0.7769 (mmt90) cc_final: 0.7523 (mtp85) outliers start: 8 outliers final: 1 residues processed: 54 average time/residue: 0.2729 time to fit residues: 15.1034 Evaluate side-chains 40 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.054 ------------------------------------------------------------------------------- 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: 0.3980 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 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 = 0.3675 r_free = 0.3675 target = 0.126277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.100289 restraints weight = 3802.655| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.92 r_work: 0.3198 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.7286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 2165 Z= 0.249 Angle : 0.779 9.141 2953 Z= 0.394 Chirality : 0.052 0.193 343 Planarity : 0.005 0.029 364 Dihedral : 5.752 23.345 269 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.44 % Allowed : 22.67 % Favored : 72.89 % 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: -0.57 (0.53), residues: 239 helix: None (None), residues: 0 sheet: 0.68 (0.47), residues: 108 loop : -1.36 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 158 TYR 0.017 0.002 TYR A 279 PHE 0.014 0.002 PHE A 133 TRP 0.003 0.001 TRP A 258 HIS 0.004 0.002 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.25 ( 2157) covalent geometry : angle 0.76100 / 0.39 ( 2931) SS BOND : bond 0.00275 / 0.14 ( 2) SS BOND : angle 2.66288 / 1.46 ( 4) hydrogen bonds : bond 0.03813 / 2.34 ( 80) hydrogen bonds : angle 6.19391 / 4.48 ( 213) link_BETA1-4 : bond 0.00388 / 0.20 ( 1) link_BETA1-4 : angle 1.18722 / 0.60 ( 3) link_NAG-ASN : bond 0.00502 / 0.30 ( 5) link_NAG-ASN : angle 2.01912 / 1.33 ( 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 46 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.048 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9294 (mttm) cc_final: 0.7394 (tptt) REVERT: A 102 ARG cc_start: 0.8149 (ttm-80) cc_final: 0.7880 (mmt90) REVERT: A 153 MET cc_start: 0.6753 (mtp) cc_final: 0.6447 (mtt) REVERT: A 157 PHE cc_start: 0.8284 (m-10) cc_final: 0.8071 (m-10) REVERT: A 177 MET cc_start: 0.7329 (mpp) cc_final: 0.6867 (mpp) REVERT: A 190 ARG cc_start: 0.8891 (ttm110) cc_final: 0.7818 (ttm-80) REVERT: A 205 SER cc_start: 0.9004 (p) cc_final: 0.8721 (p) REVERT: A 240 THR cc_start: 0.9331 (OUTLIER) cc_final: 0.8943 (t) outliers start: 10 outliers final: 3 residues processed: 42 average time/residue: 0.2837 time to fit residues: 12.2232 Evaluate side-chains 27 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.045 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 17 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.126304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.100006 restraints weight = 3664.557| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.90 r_work: 0.3194 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.7714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2165 Z= 0.200 Angle : 0.655 8.073 2953 Z= 0.334 Chirality : 0.049 0.197 343 Planarity : 0.004 0.030 364 Dihedral : 5.380 20.297 269 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.00 % Allowed : 27.11 % Favored : 68.89 % 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: -0.68 (0.54), residues: 239 helix: None (None), residues: 0 sheet: 0.65 (0.48), residues: 107 loop : -1.46 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 158 TYR 0.011 0.002 TYR A 279 PHE 0.012 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/Z covalent geometry : bond 0.00474 / 0.20 ( 2157) covalent geometry : angle 0.63919 / 0.33 ( 2931) SS BOND : bond 0.00796 / 0.38 ( 2) SS BOND : angle 1.67269 / 0.89 ( 4) hydrogen bonds : bond 0.03408 / 2.01 ( 80) hydrogen bonds : angle 6.02062 / 4.34 ( 213) link_BETA1-4 : bond 0.00306 / 0.16 ( 1) link_BETA1-4 : angle 0.90289 / 0.46 ( 3) link_NAG-ASN : bond 0.00315 / 0.17 ( 5) link_NAG-ASN : angle 1.90157 / 1.29 ( 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 34 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.046 Fit side-chains REVERT: A 41 LYS cc_start: 0.9185 (mttm) cc_final: 0.7196 (tptt) REVERT: A 153 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6914 (mtt) REVERT: A 157 PHE cc_start: 0.8275 (m-10) cc_final: 0.8068 (m-10) REVERT: A 177 MET cc_start: 0.7373 (mpp) cc_final: 0.6972 (mpp) REVERT: A 190 ARG cc_start: 0.8692 (ttm110) cc_final: 0.7985 (ttm-80) REVERT: A 205 SER cc_start: 0.8957 (p) cc_final: 0.8631 (p) REVERT: A 246 ARG cc_start: 0.6443 (mmt180) cc_final: 0.6098 (mmt180) outliers start: 9 outliers final: 4 residues processed: 31 average time/residue: 0.4293 time to fit residues: 13.5947 Evaluate side-chains 28 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.076 ------------------------------------------------------------------------------- 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 128 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 197 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.126215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.100234 restraints weight = 3653.583| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.90 r_work: 0.3192 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.8081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2165 Z= 0.169 Angle : 0.634 8.305 2953 Z= 0.322 Chirality : 0.047 0.163 343 Planarity : 0.004 0.032 364 Dihedral : 5.150 18.910 269 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.89 % Allowed : 25.78 % Favored : 69.33 % 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 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.70 (0.49), residues: 106 loop : -1.47 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 273 TYR 0.010 0.001 TYR A 279 PHE 0.011 0.001 PHE A 133 TRP 0.003 0.001 TRP A 258 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 2157) covalent geometry : angle 0.62194 / 0.32 ( 2931) SS BOND : bond 0.00621 / 0.30 ( 2) SS BOND : angle 1.44990 / 0.75 ( 4) hydrogen bonds : bond 0.03217 / 1.92 ( 80) hydrogen bonds : angle 5.86156 / 4.22 ( 213) link_BETA1-4 : bond 0.00338 / 0.18 ( 1) link_BETA1-4 : angle 0.88673 / 0.45 ( 3) link_NAG-ASN : bond 0.00239 / 0.14 ( 5) link_NAG-ASN : angle 1.67428 / 1.15 ( 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 33 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 0.080 Fit side-chains REVERT: A 41 LYS cc_start: 0.9174 (mttm) cc_final: 0.7176 (tptt) REVERT: A 153 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6780 (mtt) REVERT: A 157 PHE cc_start: 0.8284 (m-10) cc_final: 0.8070 (m-10) REVERT: A 177 MET cc_start: 0.7402 (mpp) cc_final: 0.7058 (pmm) REVERT: A 190 ARG cc_start: 0.8752 (ttm110) cc_final: 0.8073 (ttm-80) REVERT: A 205 SER cc_start: 0.8876 (p) cc_final: 0.8554 (p) outliers start: 11 outliers final: 3 residues processed: 30 average time/residue: 0.3935 time to fit residues: 12.1049 Evaluate side-chains 26 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.048 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.124811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.098776 restraints weight = 3700.857| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.94 r_work: 0.3168 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.8344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2165 Z= 0.222 Angle : 0.681 10.891 2953 Z= 0.342 Chirality : 0.049 0.179 343 Planarity : 0.004 0.030 364 Dihedral : 5.277 18.836 269 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 5.33 % Allowed : 25.78 % Favored : 68.89 % 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: -0.67 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.66 (0.51), residues: 106 loop : -1.45 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 158 TYR 0.013 0.002 TYR A 279 PHE 0.014 0.002 PHE A 175 TRP 0.005 0.001 TRP A 258 HIS 0.004 0.002 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 ( 2157) covalent geometry : angle 0.66875 / 0.34 ( 2931) SS BOND : bond 0.00784 / 0.38 ( 2) SS BOND : angle 1.38535 / 0.72 ( 4) hydrogen bonds : bond 0.03511 / 2.09 ( 80) hydrogen bonds : angle 5.83707 / 4.17 ( 213) link_BETA1-4 : bond 0.00315 / 0.17 ( 1) link_BETA1-4 : angle 0.95514 / 0.48 ( 3) link_NAG-ASN : bond 0.00393 / 0.23 ( 5) link_NAG-ASN : angle 1.76726 / 1.20 ( 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 32 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 20 time to evaluate : 0.078 Fit side-chains REVERT: A 41 LYS cc_start: 0.9172 (mttm) cc_final: 0.7166 (tptt) REVERT: A 153 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6698 (mtt) REVERT: A 157 PHE cc_start: 0.8301 (m-10) cc_final: 0.8101 (m-10) REVERT: A 177 MET cc_start: 0.7289 (mpp) cc_final: 0.6927 (pmm) REVERT: A 190 ARG cc_start: 0.8745 (ttm110) cc_final: 0.7936 (ttm-80) REVERT: A 205 SER cc_start: 0.8888 (p) cc_final: 0.8555 (p) outliers start: 12 outliers final: 3 residues processed: 28 average time/residue: 0.5893 time to fit residues: 16.8133 Evaluate side-chains 22 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.048 ------------------------------------------------------------------------------- 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 153 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: 0.6980 chunk 13 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.127471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.101242 restraints weight = 3676.696| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.97 r_work: 0.3201 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.8508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2165 Z= 0.133 Angle : 0.615 10.432 2953 Z= 0.307 Chirality : 0.046 0.166 343 Planarity : 0.004 0.033 364 Dihedral : 4.902 16.463 269 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.56 % Allowed : 28.00 % Favored : 68.44 % 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: -0.62 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.68 (0.51), residues: 106 loop : -1.40 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 102 TYR 0.007 0.001 TYR A 144 PHE 0.011 0.001 PHE A 175 TRP 0.003 0.001 TRP A 64 HIS 0.002 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 2157) covalent geometry : angle 0.60380 / 0.30 ( 2931) SS BOND : bond 0.00576 / 0.28 ( 2) SS BOND : angle 1.31065 / 0.66 ( 4) hydrogen bonds : bond 0.02983 / 1.78 ( 80) hydrogen bonds : angle 5.73562 / 4.11 ( 213) link_BETA1-4 : bond 0.00276 / 0.15 ( 1) link_BETA1-4 : angle 0.80036 / 0.41 ( 3) link_NAG-ASN : bond 0.00170 / 0.09 ( 5) link_NAG-ASN : angle 1.65066 / 1.11 ( 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 34 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.072 Fit side-chains REVERT: A 41 LYS cc_start: 0.9148 (mttm) cc_final: 0.7183 (tptt) REVERT: A 52 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8088 (tm-30) REVERT: A 153 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6965 (mtt) REVERT: A 157 PHE cc_start: 0.8210 (m-10) cc_final: 0.7993 (m-10) REVERT: A 177 MET cc_start: 0.7255 (mpp) cc_final: 0.6962 (pmm) REVERT: A 190 ARG cc_start: 0.8741 (ttm110) cc_final: 0.8118 (ttm-80) REVERT: A 205 SER cc_start: 0.8832 (p) cc_final: 0.8501 (p) REVERT: A 246 ARG cc_start: 0.6372 (mmt180) cc_final: 0.6135 (mmt90) outliers start: 8 outliers final: 3 residues processed: 32 average time/residue: 0.5090 time to fit residues: 16.6446 Evaluate side-chains 27 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.095 ------------------------------------------------------------------------------- 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 153 MET 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: 0.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.125623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.099412 restraints weight = 3640.056| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.93 r_work: 0.3157 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.8629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 2165 Z= 0.214 Angle : 0.698 10.728 2953 Z= 0.347 Chirality : 0.049 0.170 343 Planarity : 0.004 0.030 364 Dihedral : 5.200 18.158 269 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.22 % Allowed : 30.22 % 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: -0.69 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.59 (0.51), residues: 106 loop : -1.40 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 102 TYR 0.012 0.002 TYR A 279 PHE 0.014 0.002 PHE A 220 TRP 0.004 0.001 TRP A 258 HIS 0.004 0.002 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 ( 2157) covalent geometry : angle 0.68500 / 0.34 ( 2931) SS BOND : bond 0.00731 / 0.35 ( 2) SS BOND : angle 1.35821 / 0.69 ( 4) hydrogen bonds : bond 0.03521 / 2.12 ( 80) hydrogen bonds : angle 5.74298 / 4.10 ( 213) link_BETA1-4 : bond 0.00245 / 0.13 ( 1) link_BETA1-4 : angle 0.92459 / 0.47 ( 3) link_NAG-ASN : bond 0.00405 / 0.24 ( 5) link_NAG-ASN : angle 1.86035 / 1.23 ( 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 27 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9162 (mttm) cc_final: 0.7247 (tptt) REVERT: A 52 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8137 (tm-30) REVERT: A 153 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6686 (mtt) REVERT: A 157 PHE cc_start: 0.8267 (m-10) cc_final: 0.8057 (m-10) REVERT: A 205 SER cc_start: 0.8859 (p) cc_final: 0.8518 (p) REVERT: A 220 PHE cc_start: 0.8250 (t80) cc_final: 0.7900 (m-80) REVERT: A 246 ARG cc_start: 0.6540 (mmt180) cc_final: 0.6270 (mmt90) outliers start: 5 outliers final: 3 residues processed: 26 average time/residue: 0.6672 time to fit residues: 17.6832 Evaluate side-chains 26 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.079 ------------------------------------------------------------------------------- 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 153 MET Chi-restraints excluded: chain A residue 197 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: 0.9980 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.126096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.099980 restraints weight = 3664.099| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.91 r_work: 0.3164 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.8714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 2165 Z= 0.198 Angle : 0.697 10.581 2953 Z= 0.347 Chirality : 0.048 0.168 343 Planarity : 0.004 0.031 364 Dihedral : 5.181 17.818 269 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.11 % Allowed : 28.89 % 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: -0.78 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.52 (0.51), residues: 106 loop : -1.46 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 102 TYR 0.010 0.001 TYR A 279 PHE 0.012 0.001 PHE A 175 TRP 0.004 0.001 TRP A 258 HIS 0.004 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 ( 2157) covalent geometry : angle 0.68598 / 0.34 ( 2931) SS BOND : bond 0.00680 / 0.33 ( 2) SS BOND : angle 1.28716 / 0.65 ( 4) hydrogen bonds : bond 0.03396 / 2.05 ( 80) hydrogen bonds : angle 5.73335 / 4.08 ( 213) link_BETA1-4 : bond 0.00295 / 0.16 ( 1) link_BETA1-4 : angle 0.89574 / 0.46 ( 3) link_NAG-ASN : bond 0.00328 / 0.20 ( 5) link_NAG-ASN : angle 1.78357 / 1.19 ( 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 31 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.049 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9142 (mttm) cc_final: 0.7175 (tptt) REVERT: A 52 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 96 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7417 (mt-10) REVERT: A 153 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6718 (mtt) REVERT: A 157 PHE cc_start: 0.8188 (m-10) cc_final: 0.7982 (m-10) REVERT: A 205 SER cc_start: 0.8856 (p) cc_final: 0.8511 (p) REVERT: A 246 ARG cc_start: 0.6492 (mmt180) cc_final: 0.6216 (mmt90) outliers start: 7 outliers final: 6 residues processed: 29 average time/residue: 0.5258 time to fit residues: 15.5355 Evaluate side-chains 30 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 22 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.0370 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 6 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.127404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101529 restraints weight = 3646.261| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.92 r_work: 0.3195 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.8781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2165 Z= 0.152 Angle : 0.674 9.975 2953 Z= 0.333 Chirality : 0.047 0.163 343 Planarity : 0.004 0.033 364 Dihedral : 4.957 16.343 269 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.67 % Allowed : 29.33 % 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: -0.77 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.50 (0.51), residues: 106 loop : -1.43 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 102 TYR 0.008 0.001 TYR A 144 PHE 0.011 0.001 PHE A 133 TRP 0.003 0.001 TRP A 64 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 2157) covalent geometry : angle 0.66301 / 0.33 ( 2931) SS BOND : bond 0.00569 / 0.27 ( 2) SS BOND : angle 1.29602 / 0.65 ( 4) hydrogen bonds : bond 0.03119 / 1.85 ( 80) hydrogen bonds : angle 5.67936 / 4.05 ( 213) link_BETA1-4 : bond 0.00310 / 0.16 ( 1) link_BETA1-4 : angle 0.86732 / 0.44 ( 3) link_NAG-ASN : bond 0.00222 / 0.13 ( 5) link_NAG-ASN : angle 1.71158 / 1.13 ( 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 30 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9120 (mttm) cc_final: 0.7164 (tptt) REVERT: A 52 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8129 (tm-30) REVERT: A 96 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7233 (mt-10) REVERT: A 157 PHE cc_start: 0.8170 (m-10) cc_final: 0.7951 (m-10) REVERT: A 177 MET cc_start: 0.6803 (pmm) cc_final: 0.5660 (tpp) REVERT: A 205 SER cc_start: 0.8836 (p) cc_final: 0.8477 (p) REVERT: A 246 ARG cc_start: 0.6343 (mmt180) cc_final: 0.6063 (mmt90) outliers start: 6 outliers final: 3 residues processed: 28 average time/residue: 0.5883 time to fit residues: 16.7788 Evaluate side-chains 25 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 197 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: 0.9990 chunk 11 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.127694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.101369 restraints weight = 3762.679| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 4.02 r_work: 0.3209 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.8826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2165 Z= 0.142 Angle : 0.668 9.939 2953 Z= 0.329 Chirality : 0.047 0.162 343 Planarity : 0.004 0.033 364 Dihedral : 4.855 16.396 269 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.22 % Allowed : 30.22 % 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: -0.77 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.49 (0.51), residues: 106 loop : -1.40 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 102 TYR 0.007 0.001 TYR A 170 PHE 0.011 0.001 PHE A 133 TRP 0.003 0.001 TRP A 64 HIS 0.003 0.001 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 2157) covalent geometry : angle 0.65663 / 0.33 ( 2931) SS BOND : bond 0.00538 / 0.26 ( 2) SS BOND : angle 1.29552 / 0.65 ( 4) hydrogen bonds : bond 0.03044 / 1.83 ( 80) hydrogen bonds : angle 5.59927 / 3.96 ( 213) link_BETA1-4 : bond 0.00288 / 0.15 ( 1) link_BETA1-4 : angle 0.99608 / 0.51 ( 3) link_NAG-ASN : bond 0.00191 / 0.11 ( 5) link_NAG-ASN : angle 1.69745 / 1.12 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 885.20 seconds wall clock time: 15 minutes 48.38 seconds (948.38 seconds total)