Starting phenix.real_space_refine on Sun Mar 10 14:33:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm2_27524/03_2024/8dm2_27524.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm2_27524/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm2_27524/03_2024/8dm2_27524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm2_27524/03_2024/8dm2_27524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm2_27524/03_2024/8dm2_27524.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm2_27524/03_2024/8dm2_27524.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 1.66, per 1000 atoms: 0.79 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 - 3.50 Amino acid : False - 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: 0.84 Conformation dependent library (CDL) restraints added in 348.0 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: 0.23 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: 0.56 Time building geometry restraints manager: 0.89 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: 100.61 - 107.27: 88 107.27 - 113.93: 1170 113.93 - 120.60: 825 120.60 - 127.26: 823 127.26 - 133.92: 25 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 2.440 nonbonded pdb=" NH1 ARG A 102 " pdb=" OE2 GLU A 154 " model vdw 2.407 2.520 nonbonded pdb=" O HIS A 245 " pdb=" N THR A 259 " model vdw 2.408 2.520 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 ========== 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: 2.670 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: 0.010 Extract box with map and model: 12.660 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.090 Find NCS groups from input model: 0.060 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:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.630 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.241 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: 0.9129 time to fit residues: 69.2242 Evaluate side-chains 42 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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: 0.1980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 23 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2157 Z= 0.275 Angle : 0.693 9.755 2931 Z= 0.361 Chirality : 0.049 0.170 343 Planarity : 0.005 0.049 364 Dihedral : 8.905 58.175 397 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.00 % Allowed : 16.44 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.13 (0.52), residues: 239 helix: None (None), residues: 0 sheet: 0.88 (0.45), residues: 114 loop : -1.05 (0.54), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.001 0.001 HIS A 66 PHE 0.017 0.002 PHE A 133 TYR 0.010 0.001 TYR A 266 ARG 0.009 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 fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8701 (mttm) cc_final: 0.6857 (tmtt) REVERT: A 91 TYR cc_start: 0.8484 (t80) cc_final: 0.8263 (t80) REVERT: A 102 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7691 (mtt90) REVERT: A 153 MET cc_start: 0.6085 (OUTLIER) cc_final: 0.5808 (mtt) REVERT: A 157 PHE cc_start: 0.8221 (m-10) cc_final: 0.7963 (m-10) REVERT: A 205 SER cc_start: 0.9052 (p) cc_final: 0.8819 (p) outliers start: 9 outliers final: 1 residues processed: 55 average time/residue: 0.8962 time to fit residues: 50.5775 Evaluate side-chains 35 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 19 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.6485 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= 0.331 Angle : 0.725 9.965 2931 Z= 0.369 Chirality : 0.050 0.179 343 Planarity : 0.004 0.025 364 Dihedral : 7.970 55.196 395 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.00 % Allowed : 21.78 % Favored : 74.22 % 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: -0.34 (0.53), residues: 239 helix: None (None), residues: 0 sheet: 0.99 (0.47), residues: 106 loop : -1.32 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 104 HIS 0.012 0.002 HIS A 69 PHE 0.015 0.002 PHE A 133 TYR 0.016 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 46 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9222 (mttm) cc_final: 0.7271 (tptt) REVERT: A 153 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.6278 (mtt) REVERT: A 157 PHE cc_start: 0.8215 (m-10) cc_final: 0.8007 (m-10) REVERT: A 205 SER cc_start: 0.9044 (p) cc_final: 0.8756 (p) REVERT: A 246 ARG cc_start: 0.6269 (mmt180) cc_final: 0.6008 (mmt180) outliers start: 9 outliers final: 2 residues processed: 42 average time/residue: 0.8349 time to fit residues: 36.1208 Evaluate side-chains 29 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.7438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2157 Z= 0.255 Angle : 0.598 8.142 2931 Z= 0.307 Chirality : 0.048 0.182 343 Planarity : 0.004 0.034 364 Dihedral : 6.958 45.739 395 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.33 % Allowed : 24.44 % 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: -0.44 (0.54), residues: 239 helix: None (None), residues: 0 sheet: 0.93 (0.49), residues: 106 loop : -1.41 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.007 0.002 HIS A 69 PHE 0.013 0.001 PHE A 133 TYR 0.009 0.001 TYR A 279 ARG 0.006 0.001 ARG A 102 *********************** 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 fitting. rotamer outliers: 12 poor density : 30 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9169 (mttm) cc_final: 0.7150 (tptt) REVERT: A 153 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6605 (mtt) REVERT: A 157 PHE cc_start: 0.8192 (m-10) cc_final: 0.7971 (m-10) REVERT: A 205 SER cc_start: 0.8883 (p) cc_final: 0.8537 (p) REVERT: A 246 ARG cc_start: 0.6340 (mmt180) cc_final: 0.6115 (mmt180) outliers start: 12 outliers final: 3 residues processed: 36 average time/residue: 0.9651 time to fit residues: 35.7376 Evaluate side-chains 30 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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: 0.8980 chunk 4 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.7989 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= 0.282 Angle : 0.629 8.678 2931 Z= 0.320 Chirality : 0.048 0.170 343 Planarity : 0.004 0.029 364 Dihedral : 6.523 45.341 395 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.33 % Allowed : 25.33 % 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 (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: -0.49 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.92 (0.50), residues: 106 loop : -1.47 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.006 0.002 HIS A 69 PHE 0.011 0.002 PHE A 133 TYR 0.014 0.002 TYR A 279 ARG 0.005 0.001 ARG A 102 *********************** 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 37 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 25 time to evaluate : 0.209 Fit side-chains REVERT: A 41 LYS cc_start: 0.9163 (mttm) cc_final: 0.7107 (tptt) REVERT: A 153 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6778 (mtt) REVERT: A 157 PHE cc_start: 0.8204 (m-10) cc_final: 0.7968 (m-10) REVERT: A 177 MET cc_start: 0.7254 (pmm) cc_final: 0.6809 (mpp) REVERT: A 190 ARG cc_start: 0.8803 (ttm110) cc_final: 0.7975 (ttm-80) REVERT: A 205 SER cc_start: 0.8823 (p) cc_final: 0.8469 (p) outliers start: 12 outliers final: 6 residues processed: 33 average time/residue: 1.1589 time to fit residues: 39.1690 Evaluate side-chains 32 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 70 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.0970 chunk 6 optimal weight: 0.2980 chunk 4 optimal weight: 0.5980 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 17 ASN ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.8144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2157 Z= 0.213 Angle : 0.584 9.551 2931 Z= 0.296 Chirality : 0.046 0.167 343 Planarity : 0.003 0.025 364 Dihedral : 6.185 45.659 395 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.44 % Allowed : 28.00 % 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 (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: -0.58 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.80 (0.50), residues: 106 loop : -1.47 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 258 HIS 0.005 0.001 HIS A 69 PHE 0.009 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 38 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 28 time to evaluate : 0.241 Fit side-chains REVERT: A 33 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9118 (m) REVERT: A 41 LYS cc_start: 0.9144 (mttm) cc_final: 0.7095 (tptt) REVERT: A 52 GLN cc_start: 0.8673 (tm-30) cc_final: 0.7991 (tm-30) REVERT: A 153 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6898 (mtt) REVERT: A 157 PHE cc_start: 0.8196 (m-10) cc_final: 0.7975 (m-10) REVERT: A 177 MET cc_start: 0.7137 (pmm) cc_final: 0.6683 (mpp) REVERT: A 190 ARG cc_start: 0.8797 (ttm110) cc_final: 0.7997 (ttm-80) REVERT: A 205 SER cc_start: 0.8753 (p) cc_final: 0.8405 (p) REVERT: A 239 GLN cc_start: 0.8380 (mt0) cc_final: 0.8072 (mt0) outliers start: 10 outliers final: 5 residues processed: 35 average time/residue: 1.0623 time to fit residues: 38.1606 Evaluate side-chains 31 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL 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 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: 0.0670 chunk 15 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 overall best weight: 0.2718 ------------------------------------------------------------------------------- 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: 0.7240 moved from start: 0.8281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2157 Z= 0.174 Angle : 0.603 11.855 2931 Z= 0.295 Chirality : 0.046 0.161 343 Planarity : 0.003 0.025 364 Dihedral : 5.880 47.064 395 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.44 % Allowed : 29.33 % 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: -0.58 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.69 (0.49), residues: 106 loop : -1.35 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 258 HIS 0.007 0.002 HIS A 69 PHE 0.009 0.001 PHE A 133 TYR 0.006 0.001 TYR A 279 ARG 0.002 0.000 ARG A 102 *********************** 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 45 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9114 (m) REVERT: A 41 LYS cc_start: 0.9128 (mttm) cc_final: 0.7115 (tptt) REVERT: A 52 GLN cc_start: 0.8672 (tm-30) cc_final: 0.7989 (tm-30) REVERT: A 153 MET cc_start: 0.7142 (mtp) cc_final: 0.6930 (mtt) REVERT: A 157 PHE cc_start: 0.8155 (m-10) cc_final: 0.7948 (m-10) REVERT: A 205 SER cc_start: 0.8653 (p) cc_final: 0.8307 (p) outliers start: 10 outliers final: 5 residues processed: 41 average time/residue: 1.0149 time to fit residues: 42.7176 Evaluate side-chains 31 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 101 ILE 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: 0.7980 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.8480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 2157 Z= 0.360 Angle : 0.701 11.731 2931 Z= 0.341 Chirality : 0.050 0.182 343 Planarity : 0.003 0.022 364 Dihedral : 6.497 46.648 395 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 6.67 % Allowed : 29.33 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.65 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.65 (0.50), residues: 106 loop : -1.41 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 258 HIS 0.004 0.001 HIS A 69 PHE 0.014 0.002 PHE A 168 TYR 0.013 0.002 TYR A 279 ARG 0.004 0.001 ARG A 158 *********************** 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 41 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 26 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.9078 (m) REVERT: A 41 LYS cc_start: 0.9158 (mttm) cc_final: 0.7053 (tmtt) REVERT: A 157 PHE cc_start: 0.8176 (m-10) cc_final: 0.7970 (m-10) REVERT: A 205 SER cc_start: 0.8792 (p) cc_final: 0.8437 (p) outliers start: 15 outliers final: 9 residues processed: 38 average time/residue: 0.9947 time to fit residues: 38.8355 Evaluate side-chains 34 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 24 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 ILE 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 83 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 177 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: 0.6980 chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.0870 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.8593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2157 Z= 0.251 Angle : 0.642 11.827 2931 Z= 0.316 Chirality : 0.048 0.166 343 Planarity : 0.003 0.024 364 Dihedral : 6.195 46.509 395 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.11 % Allowed : 32.89 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.69 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.55 (0.49), residues: 106 loop : -1.36 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 258 HIS 0.005 0.001 HIS A 69 PHE 0.009 0.001 PHE A 175 TYR 0.009 0.001 TYR A 279 ARG 0.003 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 34 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9082 (m) REVERT: A 41 LYS cc_start: 0.9141 (mttm) cc_final: 0.7045 (tmtt) REVERT: A 52 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8014 (tm-30) REVERT: A 157 PHE cc_start: 0.8121 (m-10) cc_final: 0.7899 (m-10) REVERT: A 205 SER cc_start: 0.8716 (p) cc_final: 0.8356 (p) outliers start: 7 outliers final: 5 residues processed: 33 average time/residue: 1.0877 time to fit residues: 36.8146 Evaluate side-chains 33 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL 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 19 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.0070 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.8723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2157 Z= 0.260 Angle : 0.655 11.899 2931 Z= 0.322 Chirality : 0.048 0.169 343 Planarity : 0.003 0.034 364 Dihedral : 6.175 47.074 395 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.00 % Allowed : 32.44 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.76 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.45 (0.49), residues: 106 loop : -1.36 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 258 HIS 0.005 0.001 HIS A 69 PHE 0.014 0.001 PHE A 175 TYR 0.010 0.001 TYR A 279 ARG 0.007 0.001 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 478 Ramachandran restraints generated. 239 Oldfield, 0 Emsley, 239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.9305 (OUTLIER) cc_final: 0.9080 (m) REVERT: A 41 LYS cc_start: 0.9139 (mttm) cc_final: 0.7065 (tmtt) REVERT: A 52 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8022 (tm-30) REVERT: A 157 PHE cc_start: 0.8130 (m-10) cc_final: 0.7902 (m-10) REVERT: A 205 SER cc_start: 0.8766 (p) cc_final: 0.8405 (p) outliers start: 9 outliers final: 6 residues processed: 33 average time/residue: 1.0748 time to fit residues: 36.3780 Evaluate side-chains 31 residues out of total 225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL 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 83 VAL 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: 0.0050 chunk 9 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.128381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.102258 restraints weight = 3674.999| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.94 r_work: 0.3223 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.8785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2157 Z= 0.193 Angle : 0.626 11.927 2931 Z= 0.308 Chirality : 0.047 0.158 343 Planarity : 0.003 0.030 364 Dihedral : 5.816 47.973 395 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.00 % Allowed : 32.00 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.76 (0.55), residues: 239 helix: None (None), residues: 0 sheet: 0.42 (0.49), residues: 106 loop : -1.34 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 258 HIS 0.005 0.001 HIS A 69 PHE 0.011 0.001 PHE A 175 TYR 0.007 0.001 TYR A 279 ARG 0.007 0.001 ARG A 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1547.65 seconds wall clock time: 28 minutes 2.17 seconds (1682.17 seconds total)