Starting phenix.real_space_refine on Fri Dec 27 04:44:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm2_27524/12_2024/8dm2_27524.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm2_27524/12_2024/8dm2_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_27524/12_2024/8dm2_27524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm2_27524/12_2024/8dm2_27524.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm2_27524/12_2024/8dm2_27524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm2_27524/12_2024/8dm2_27524.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 3.63, per 1000 atoms: 1.73 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: 0.55 Conformation dependent library (CDL) restraints added in 270.5 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: 0.26 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: 0.68 Time building geometry restraints manager: 0.65 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: 3.600 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.300 Find NCS groups from input model: 0.020 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:14.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.760 ------------------------------------------------------------------------------- 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 2157 Z= 0.483 Angle : 1.021 7.202 2931 Z= 0.568 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (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 TRP 0.009 0.002 TRP A 64 HIS 0.005 0.002 HIS A 66 PHE 0.023 0.003 PHE A 175 TYR 0.019 0.003 TYR A 144 ARG 0.005 0.001 ARG A 190 *********************** 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 : 0.178 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.6920 (mttm) cc_final: 0.5331 (tptp) REVERT: A 266 TYR cc_start: 0.8088 (m-80) cc_final: 0.7716 (m-80) outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.9576 time to fit residues: 72.5319 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 : 0.241 ------------------------------------------------------------------------------- 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 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 23 optimal weight: 0.0970 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 2157 Z= 0.281 Angle : 0.733 9.998 2931 Z= 0.386 Chirality : 0.050 0.166 343 Planarity : 0.005 0.046 364 Dihedral : 9.546 58.548 397 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.00 % Allowed : 16.89 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.52), residues: 239 helix: None (None), residues: 0 sheet: 1.07 (0.46), residues: 111 loop : -1.18 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.004 0.001 HIS A 69 PHE 0.015 0.002 PHE A 133 TYR 0.011 0.002 TYR A 279 ARG 0.008 0.001 ARG A 102 *********************** 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 59 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8891 (mttm) cc_final: 0.7061 (tptt) REVERT: A 91 TYR cc_start: 0.8606 (t80) cc_final: 0.8316 (t80) REVERT: A 119 ILE cc_start: 0.8467 (mt) cc_final: 0.8199 (mp) REVERT: A 153 MET cc_start: 0.6493 (OUTLIER) cc_final: 0.6162 (mtt) REVERT: A 157 PHE cc_start: 0.8223 (m-10) cc_final: 0.7970 (m-10) REVERT: A 191 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: A 205 SER cc_start: 0.9053 (p) cc_final: 0.8818 (p) REVERT: A 246 ARG cc_start: 0.5782 (mmt180) cc_final: 0.5494 (mmt180) REVERT: A 273 ARG cc_start: 0.7693 (mmt90) cc_final: 0.7456 (mtp85) outliers start: 9 outliers final: 1 residues processed: 55 average time/residue: 1.0058 time to fit residues: 56.7693 Evaluate side-chains 41 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.6634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 2157 Z= 0.341 Angle : 0.751 10.732 2931 Z= 0.380 Chirality : 0.050 0.163 343 Planarity : 0.004 0.030 364 Dihedral : 8.745 56.702 395 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.78 % Allowed : 21.78 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.53), residues: 239 helix: None (None), residues: 0 sheet: 0.78 (0.47), residues: 108 loop : -1.28 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.009 0.002 HIS A 69 PHE 0.014 0.002 PHE A 133 TYR 0.015 0.002 TYR A 279 ARG 0.004 0.001 ARG A 158 *********************** 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: 13 poor density : 38 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9228 (mttm) cc_final: 0.7335 (tptt) REVERT: A 91 TYR cc_start: 0.8716 (t80) cc_final: 0.8447 (t80) REVERT: A 153 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6371 (mtt) REVERT: A 157 PHE cc_start: 0.8230 (m-10) cc_final: 0.8008 (m-10) REVERT: A 205 SER cc_start: 0.9022 (p) cc_final: 0.8713 (p) REVERT: A 246 ARG cc_start: 0.6209 (mmt180) cc_final: 0.5936 (mmt90) outliers start: 13 outliers final: 3 residues processed: 47 average time/residue: 0.9042 time to fit residues: 43.7277 Evaluate side-chains 31 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 0.2980 chunk 19 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.7000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2157 Z= 0.211 Angle : 0.615 8.454 2931 Z= 0.314 Chirality : 0.049 0.207 343 Planarity : 0.004 0.030 364 Dihedral : 7.554 50.166 395 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.44 % Allowed : 25.33 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.54), residues: 239 helix: None (None), residues: 0 sheet: 0.78 (0.48), residues: 107 loop : -1.43 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 64 HIS 0.004 0.001 HIS A 69 PHE 0.013 0.001 PHE A 133 TYR 0.008 0.001 TYR A 279 ARG 0.004 0.001 ARG A 273 *********************** 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 42 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9246 (mttm) cc_final: 0.7286 (tptt) REVERT: A 153 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6531 (mtt) REVERT: A 157 PHE cc_start: 0.8168 (m-10) cc_final: 0.7933 (m-10) REVERT: A 205 SER cc_start: 0.8960 (p) cc_final: 0.8602 (p) REVERT: A 246 ARG cc_start: 0.6024 (mmt180) cc_final: 0.5659 (mmt180) outliers start: 10 outliers final: 3 residues processed: 36 average time/residue: 1.0259 time to fit residues: 37.9939 Evaluate side-chains 33 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 197 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.0470 chunk 22 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.7921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2157 Z= 0.311 Angle : 0.687 8.608 2931 Z= 0.343 Chirality : 0.049 0.184 343 Planarity : 0.004 0.034 364 Dihedral : 6.826 44.514 395 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.56 % Allowed : 26.67 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.65 (0.49), residues: 107 loop : -1.45 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 258 HIS 0.006 0.002 HIS A 69 PHE 0.014 0.002 PHE A 175 TYR 0.012 0.002 TYR A 279 ARG 0.004 0.001 ARG A 158 *********************** 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 38 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.232 Fit side-chains REVERT: A 41 LYS cc_start: 0.9264 (mttm) cc_final: 0.7285 (tptt) REVERT: A 153 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6617 (mtt) REVERT: A 157 PHE cc_start: 0.8213 (m-10) cc_final: 0.7999 (m-10) REVERT: A 205 SER cc_start: 0.8890 (p) cc_final: 0.8530 (p) REVERT: A 246 ARG cc_start: 0.6258 (mmt180) cc_final: 0.5866 (mmt180) outliers start: 8 outliers final: 4 residues processed: 34 average time/residue: 1.0793 time to fit residues: 37.8080 Evaluate side-chains 29 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 4 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.8110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2157 Z= 0.245 Angle : 0.618 7.455 2931 Z= 0.310 Chirality : 0.048 0.196 343 Planarity : 0.004 0.034 364 Dihedral : 6.172 45.302 395 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.00 % Allowed : 28.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.68 (0.50), residues: 106 loop : -1.48 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.004 0.001 HIS A 69 PHE 0.011 0.001 PHE A 133 TYR 0.009 0.001 TYR A 279 ARG 0.006 0.001 ARG A 102 *********************** 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 36 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.256 Fit side-chains REVERT: A 41 LYS cc_start: 0.9256 (mttm) cc_final: 0.7296 (tptt) REVERT: A 52 GLN cc_start: 0.8671 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 96 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6935 (tp30) REVERT: A 153 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6798 (mtt) REVERT: A 157 PHE cc_start: 0.8196 (m-10) cc_final: 0.7973 (m-10) REVERT: A 205 SER cc_start: 0.8823 (p) cc_final: 0.8461 (p) outliers start: 9 outliers final: 4 residues processed: 32 average time/residue: 1.2213 time to fit residues: 40.0312 Evaluate side-chains 28 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 96 GLU 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 4 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.8284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2157 Z= 0.237 Angle : 0.637 9.896 2931 Z= 0.314 Chirality : 0.048 0.190 343 Planarity : 0.003 0.034 364 Dihedral : 5.969 46.009 395 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.00 % Allowed : 29.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.66 (0.50), residues: 106 loop : -1.40 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.004 0.001 HIS A 69 PHE 0.011 0.001 PHE A 175 TYR 0.008 0.001 TYR A 279 ARG 0.003 0.000 ARG A 158 *********************** 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 33 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.228 Fit side-chains REVERT: A 33 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.9076 (m) REVERT: A 41 LYS cc_start: 0.9253 (mttm) cc_final: 0.7302 (tptt) REVERT: A 52 GLN cc_start: 0.8662 (tm-30) cc_final: 0.7955 (tm-30) REVERT: A 153 MET cc_start: 0.6901 (mtp) cc_final: 0.6699 (mtt) REVERT: A 157 PHE cc_start: 0.8191 (m-10) cc_final: 0.7966 (m-10) REVERT: A 190 ARG cc_start: 0.8721 (ttm110) cc_final: 0.7953 (ttm-80) REVERT: A 205 SER cc_start: 0.8815 (p) cc_final: 0.8451 (p) REVERT: A 246 ARG cc_start: 0.6152 (mmt180) cc_final: 0.5925 (mmt180) outliers start: 9 outliers final: 5 residues processed: 31 average time/residue: 1.2677 time to fit residues: 40.2419 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 : 0.311 ------------------------------------------------------------------------------- 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 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 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 14 optimal weight: 0.0370 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.8394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2157 Z= 0.187 Angle : 0.610 9.045 2931 Z= 0.303 Chirality : 0.047 0.187 343 Planarity : 0.003 0.034 364 Dihedral : 5.808 46.789 395 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.11 % Allowed : 30.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.61 (0.50), residues: 106 loop : -1.40 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 64 HIS 0.003 0.001 HIS A 69 PHE 0.010 0.001 PHE A 133 TYR 0.006 0.001 TYR A 144 ARG 0.002 0.000 ARG A 273 *********************** 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 31 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.251 Fit side-chains REVERT: A 33 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.9093 (m) REVERT: A 41 LYS cc_start: 0.9259 (mttm) cc_final: 0.7257 (tmtt) REVERT: A 52 GLN cc_start: 0.8646 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 153 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6861 (mtt) REVERT: A 157 PHE cc_start: 0.8151 (m-10) cc_final: 0.7913 (m-10) REVERT: A 177 MET cc_start: 0.6614 (pmm) cc_final: 0.5210 (tpp) REVERT: A 190 ARG cc_start: 0.8755 (ttm110) cc_final: 0.7980 (ttm-80) REVERT: A 205 SER cc_start: 0.8773 (p) cc_final: 0.8422 (p) REVERT: A 246 ARG cc_start: 0.6057 (mmt180) cc_final: 0.5815 (mmt180) outliers start: 7 outliers final: 3 residues processed: 29 average time/residue: 1.2664 time to fit residues: 37.6595 Evaluate side-chains 29 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR 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 22 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 2 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.8464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2157 Z= 0.217 Angle : 0.623 8.901 2931 Z= 0.310 Chirality : 0.047 0.187 343 Planarity : 0.003 0.033 364 Dihedral : 5.779 47.386 395 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.67 % Allowed : 31.11 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.58 (0.50), residues: 106 loop : -1.42 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 258 HIS 0.003 0.001 HIS A 69 PHE 0.010 0.001 PHE A 133 TYR 0.008 0.001 TYR A 279 ARG 0.005 0.000 ARG A 102 *********************** 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: 6 poor density : 25 time to evaluate : 0.234 Fit side-chains REVERT: A 33 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9080 (m) REVERT: A 41 LYS cc_start: 0.9279 (mttm) cc_final: 0.7273 (tmtt) REVERT: A 52 GLN cc_start: 0.8659 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 157 PHE cc_start: 0.8144 (m-10) cc_final: 0.7911 (m-10) REVERT: A 190 ARG cc_start: 0.8763 (ttm110) cc_final: 0.7964 (ttm-80) REVERT: A 205 SER cc_start: 0.8784 (p) cc_final: 0.8415 (p) outliers start: 6 outliers final: 3 residues processed: 29 average time/residue: 1.2945 time to fit residues: 38.4666 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 : 0.245 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.8604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2157 Z= 0.317 Angle : 0.671 9.613 2931 Z= 0.332 Chirality : 0.049 0.192 343 Planarity : 0.003 0.029 364 Dihedral : 6.085 46.932 395 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.11 % Allowed : 31.56 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.56), residues: 239 helix: None (None), residues: 0 sheet: 0.52 (0.50), residues: 106 loop : -1.51 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 258 HIS 0.004 0.002 HIS A 69 PHE 0.015 0.001 PHE A 175 TYR 0.012 0.002 TYR A 279 ARG 0.003 0.000 ARG A 158 ********************** 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 28 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.261 Fit side-chains REVERT: A 33 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.9044 (m) REVERT: A 41 LYS cc_start: 0.9293 (mttm) cc_final: 0.7302 (tmtt) REVERT: A 52 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8011 (tm-30) REVERT: A 157 PHE cc_start: 0.8100 (m-10) cc_final: 0.7857 (m-10) REVERT: A 190 ARG cc_start: 0.8801 (ttm110) cc_final: 0.8024 (ttm-80) REVERT: A 205 SER cc_start: 0.8868 (p) cc_final: 0.8489 (p) outliers start: 7 outliers final: 4 residues processed: 26 average time/residue: 1.3856 time to fit residues: 36.8758 Evaluate side-chains 26 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 197 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.128393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.102228 restraints weight = 3646.425| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.97 r_work: 0.3227 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.8666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2157 Z= 0.192 Angle : 0.613 8.619 2931 Z= 0.305 Chirality : 0.047 0.184 343 Planarity : 0.003 0.034 364 Dihedral : 5.753 47.060 395 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.22 % Allowed : 31.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.52 (0.50), residues: 106 loop : -1.49 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 64 HIS 0.003 0.001 HIS A 207 PHE 0.010 0.001 PHE A 175 TYR 0.007 0.001 TYR A 144 ARG 0.002 0.000 ARG A 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1578.98 seconds wall clock time: 29 minutes 24.36 seconds (1764.36 seconds total)