Starting phenix.real_space_refine on Thu Oct 22 17:13:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zlh_74403/10_2026/9zlh_74403.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zlh_74403/10_2026/9zlh_74403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zlh_74403/10_2026/9zlh_74403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zlh_74403/10_2026/9zlh_74403.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zlh_74403/10_2026/9zlh_74403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zlh_74403/10_2026/9zlh_74403.map" } resolution = 2.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.106 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 8 5.16 5 C 1066 2.51 5 N 313 2.21 5 O 356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1745 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1657 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 16, 'TRANS': 189} Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 88 Unusual residues: {'ADP': 1, 'U1C': 1} Classifications: {'undetermined': 2, 'water': 38} Link IDs: {None: 39} Time building chain proxies: 0.41, per 1000 atoms: 0.23 Number of scatterers: 1745 At special positions: 0 Unit cell: (61.42, 62.25, 47.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 P 2 15.00 O 356 8.00 N 313 7.00 C 1066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.10 Conformation dependent library (CDL) restraints added in 36.4 milliseconds 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 392 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 3 sheets defined 55.3% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing helix chain 'A' and resid 864 through 890 removed outlier: 5.133A pdb=" N ILE A 870 " --> pdb=" O HIS A 866 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LYS A 873 " --> pdb=" O ARG A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 935 Processing helix chain 'A' and resid 945 through 950 removed outlier: 3.953A pdb=" N ASN A 949 " --> pdb=" O LYS A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 960 Processing helix chain 'A' and resid 978 through 1004 Processing helix chain 'A' and resid 1023 through 1027 Processing helix chain 'A' and resid 1028 through 1049 Processing sheet with id=AA1, first strand: chain 'A' and resid 892 through 893 removed outlier: 6.175A pdb=" N THR A 892 " --> pdb=" O HIS A 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 938 through 940 Processing sheet with id=AA3, first strand: chain 'A' and resid 1006 through 1007 removed outlier: 6.442A pdb=" N SER A1006 " --> pdb=" O ASN A1018 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 88 hydrogen bonds defined for protein. 246 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: 0.15 Time building geometry restraints manager: 0.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 455 1.33 - 1.45: 307 1.45 - 1.57: 974 1.57 - 1.69: 3 1.69 - 1.81: 12 Bond restraints: 1751 Sorted by residual: bond pdb=" C3 U1C A7602 " pdb=" N2 U1C A7602 " ideal model delta sigma weight residual 1.444 1.376 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1 U1C A7602 " pdb=" N2 U1C A7602 " ideal model delta sigma weight residual 1.508 1.455 0.053 2.00e-02 2.50e+03 7.02e+00 bond pdb=" C2 U1C A7602 " pdb=" N1 U1C A7602 " ideal model delta sigma weight residual 1.418 1.365 0.053 2.00e-02 2.50e+03 6.94e+00 bond pdb=" C8 U1C A7602 " pdb=" O3 U1C A7602 " ideal model delta sigma weight residual 1.413 1.367 0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" C3 U1C A7602 " pdb=" N1 U1C A7602 " ideal model delta sigma weight residual 1.431 1.388 0.043 2.00e-02 2.50e+03 4.71e+00 ... (remaining 1746 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 2354 2.84 - 5.68: 29 5.68 - 8.51: 2 8.51 - 11.35: 1 11.35 - 14.19: 4 Bond angle restraints: 2390 Sorted by residual: angle pdb=" C1 U1C A7602 " pdb=" N2 U1C A7602 " pdb=" N3 U1C A7602 " ideal model delta sigma weight residual 113.55 127.74 -14.19 3.00e+00 1.11e-01 2.24e+01 angle pdb=" C5 U1C A7602 " pdb=" C4 U1C A7602 " pdb=" N3 U1C A7602 " ideal model delta sigma weight residual 133.11 119.19 13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" C3 U1C A7602 " pdb=" N2 U1C A7602 " pdb=" N3 U1C A7602 " ideal model delta sigma weight residual 131.42 119.72 11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" C4 U1C A7602 " pdb=" N3 U1C A7602 " pdb=" N2 U1C A7602 " ideal model delta sigma weight residual 128.26 116.64 11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CA LEU A 913 " pdb=" CB LEU A 913 " pdb=" CG LEU A 913 " ideal model delta sigma weight residual 116.30 126.08 -9.78 3.50e+00 8.16e-02 7.80e+00 ... (remaining 2385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.77: 970 25.77 - 51.54: 74 51.54 - 77.31: 11 77.31 - 103.08: 1 103.08 - 128.85: 1 Dihedral angle restraints: 1057 sinusoidal: 452 harmonic: 605 Sorted by residual: dihedral pdb=" O2A ADP A7601 " pdb=" O3A ADP A7601 " pdb=" PA ADP A7601 " pdb=" PB ADP A7601 " ideal model delta sinusoidal sigma weight residual 300.00 171.15 128.85 1 2.00e+01 2.50e-03 3.91e+01 dihedral pdb=" CA GLY A1048 " pdb=" C GLY A1048 " pdb=" N TYR A1049 " pdb=" CA TYR A1049 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CG ARG A 987 " pdb=" CD ARG A 987 " pdb=" NE ARG A 987 " pdb=" CZ ARG A 987 " ideal model delta sinusoidal sigma weight residual 90.00 133.13 -43.13 2 1.50e+01 4.44e-03 9.97e+00 ... (remaining 1054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 154 0.028 - 0.056: 63 0.056 - 0.084: 24 0.084 - 0.111: 15 0.111 - 0.139: 2 Chirality restraints: 258 Sorted by residual: chirality pdb=" CA VAL A1022 " pdb=" N VAL A1022 " pdb=" C VAL A1022 " pdb=" CB VAL A1022 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA VAL A 852 " pdb=" N VAL A 852 " pdb=" C VAL A 852 " pdb=" CB VAL A 852 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE A1053 " pdb=" N ILE A1053 " pdb=" C ILE A1053 " pdb=" CB ILE A1053 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.08e-01 ... (remaining 255 not shown) Planarity restraints: 309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 U1C A7602 " -0.039 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C5 U1C A7602 " 0.037 2.00e-02 2.50e+03 pdb=" N2 U1C A7602 " 0.038 2.00e-02 2.50e+03 pdb=" N3 U1C A7602 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 904 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 905 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 905 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 905 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1018 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A1019 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A1019 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1019 " 0.023 5.00e-02 4.00e+02 ... (remaining 306 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 792 2.96 - 3.44: 1771 3.44 - 3.93: 3143 3.93 - 4.41: 3644 4.41 - 4.90: 5479 Nonbonded interactions: 14829 Sorted by model distance: nonbonded pdb=" O2' ADP A7601 " pdb=" O3' ADP A7601 " model vdw 2.471 2.432 nonbonded pdb=" O4' ADP A7601 " pdb=" O5' ADP A7601 " model vdw 2.538 2.432 nonbonded pdb=" O ASN A1052 " pdb=" OD1 ASN A1052 " model vdw 2.552 3.040 nonbonded pdb=" N VAL A1022 " pdb=" O VAL A1022 " model vdw 2.631 2.496 nonbonded pdb=" N THR A 958 " pdb=" OG1 THR A 958 " model vdw 2.642 2.496 ... (remaining 14824 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.430 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 : 0.005 0.068 1751 Z= 0.222 Angle : 0.879 14.188 2390 Z= 0.360 Chirality : 0.041 0.139 258 Planarity : 0.007 0.046 309 Dihedral : 18.647 128.849 665 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.65 % Allowed : 27.47 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.58), residues: 204 helix: 1.94 (0.51), residues: 104 sheet: 0.12 (1.95), residues: 9 loop : 0.22 (0.64), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 998 TYR 0.012 0.002 TYR A 893 PHE 0.007 0.002 PHE A 851 TRP 0.002 0.001 TRP A 891 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 ( 1751) covalent geometry : angle 0.87942 / 0.36 ( 2390) hydrogen bonds : bond 0.05803 / 4.30 ( 88) hydrogen bonds : angle 3.83679 / 2.89 ( 246) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.043 Fit side-chains REVERT: A 915 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6904 (mt-10) REVERT: A 924 MET cc_start: 0.8905 (mmm) cc_final: 0.8630 (mmm) REVERT: A 927 GLU cc_start: 0.8160 (tp30) cc_final: 0.7284 (tm-30) REVERT: A 941 MET cc_start: 0.5697 (tpt) cc_final: 0.5452 (tpp) REVERT: A 973 SER cc_start: 0.8197 (p) cc_final: 0.7884 (m) REVERT: A 1025 ARG cc_start: 0.7593 (ptt-90) cc_final: 0.6773 (ptp90) outliers start: 3 outliers final: 0 residues processed: 51 average time/residue: 0.4359 time to fit residues: 22.5735 Evaluate side-chains 39 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [12, 13, 1, 8, 16, 15, 9, 11, 18, 6, 4] chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 963 ASN A1035 ASN A1052 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.155195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128947 restraints weight = 1713.835| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.74 r_work: 0.3434 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1751 Z= 0.146 Angle : 0.665 8.760 2390 Z= 0.295 Chirality : 0.040 0.128 258 Planarity : 0.006 0.041 309 Dihedral : 12.305 127.824 245 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 6.04 % Allowed : 21.43 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.58), residues: 204 helix: 1.95 (0.50), residues: 104 sheet: 0.27 (1.88), residues: 9 loop : 0.26 (0.63), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 871 TYR 0.009 0.002 TYR A 920 PHE 0.006 0.002 PHE A 851 TRP 0.003 0.001 TRP A 891 HIS 0.006 0.001 HIS A 879 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 1751) covalent geometry : angle 0.66509 / 0.30 ( 2390) hydrogen bonds : bond 0.05262 / 3.67 ( 88) hydrogen bonds : angle 3.83190 / 2.92 ( 246) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.087 Fit side-chains REVERT: A 872 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7823 (tp30) REVERT: A 915 GLU cc_start: 0.6809 (tm-30) cc_final: 0.6423 (mt-10) REVERT: A 924 MET cc_start: 0.8737 (mmm) cc_final: 0.8501 (mmm) REVERT: A 944 GLU cc_start: 0.7814 (tt0) cc_final: 0.7598 (tt0) REVERT: A 1025 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6248 (ptp90) REVERT: A 1029 GLU cc_start: 0.6573 (mm-30) cc_final: 0.6328 (mm-30) outliers start: 11 outliers final: 2 residues processed: 48 average time/residue: 0.5325 time to fit residues: 26.0328 Evaluate side-chains 46 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain A residue 1025 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [4, 0, 10, 19, 6, 1, 13, 9, 12, 5, 11] chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 0.0050 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 963 ASN A1011 GLN A1035 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.154612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129987 restraints weight = 1719.866| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.59 r_work: 0.3423 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1751 Z= 0.133 Angle : 0.641 7.925 2390 Z= 0.282 Chirality : 0.040 0.126 258 Planarity : 0.005 0.040 309 Dihedral : 12.194 126.219 245 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.40 % Allowed : 23.08 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.58), residues: 204 helix: 2.01 (0.50), residues: 104 sheet: 0.37 (1.91), residues: 9 loop : 0.19 (0.63), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1036 TYR 0.010 0.001 TYR A 893 PHE 0.006 0.002 PHE A 851 TRP 0.002 0.001 TRP A1005 HIS 0.004 0.001 HIS A 879 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 1751) covalent geometry : angle 0.64085 / 0.28 ( 2390) hydrogen bonds : bond 0.05009 / 3.48 ( 88) hydrogen bonds : angle 3.76586 / 2.87 ( 246) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.062 Fit side-chains REVERT: A 915 GLU cc_start: 0.6623 (tm-30) cc_final: 0.6155 (mt-10) REVERT: A 917 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: A 924 MET cc_start: 0.8547 (mmm) cc_final: 0.8315 (mmm) REVERT: A 947 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6975 (mt-10) REVERT: A 963 ASN cc_start: 0.6479 (OUTLIER) cc_final: 0.6107 (m-40) REVERT: A 1025 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6003 (ptp90) REVERT: A 1029 GLU cc_start: 0.6319 (mm-30) cc_final: 0.6098 (mm-30) outliers start: 8 outliers final: 0 residues processed: 44 average time/residue: 0.4757 time to fit residues: 21.3117 Evaluate side-chains 44 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain A residue 1025 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [12, 17, 4, 18, 1, 9, 19, 14, 16, 13, 6] chunk 12 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 963 ASN A1011 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.155645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.131317 restraints weight = 1712.498| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.56 r_work: 0.3440 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1751 Z= 0.121 Angle : 0.626 7.138 2390 Z= 0.274 Chirality : 0.039 0.124 258 Planarity : 0.005 0.040 309 Dihedral : 12.115 124.224 245 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.40 % Allowed : 21.98 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.58), residues: 204 helix: 2.12 (0.50), residues: 104 sheet: 0.37 (1.94), residues: 9 loop : 0.16 (0.64), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1020 TYR 0.008 0.001 TYR A 893 PHE 0.005 0.001 PHE A 851 TRP 0.002 0.001 TRP A1005 HIS 0.003 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 1751) covalent geometry : angle 0.62616 / 0.27 ( 2390) hydrogen bonds : bond 0.04740 / 3.30 ( 88) hydrogen bonds : angle 3.68546 / 2.81 ( 246) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.074 Fit side-chains REVERT: A 915 GLU cc_start: 0.6636 (tm-30) cc_final: 0.6154 (mt-10) REVERT: A 917 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: A 924 MET cc_start: 0.8530 (mmm) cc_final: 0.8317 (mmm) REVERT: A 947 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: A 1025 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6035 (ptp90) REVERT: A 1029 GLU cc_start: 0.6311 (mm-30) cc_final: 0.6064 (mm-30) outliers start: 8 outliers final: 1 residues processed: 44 average time/residue: 0.4941 time to fit residues: 22.1278 Evaluate side-chains 43 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 1025 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [8, 13, 1, 7, 18, 6, 10, 3, 15, 11, 9] chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1011 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.155163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130922 restraints weight = 1760.462| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.57 r_work: 0.3432 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1751 Z= 0.125 Angle : 0.629 7.154 2390 Z= 0.274 Chirality : 0.039 0.126 258 Planarity : 0.005 0.039 309 Dihedral : 12.029 122.025 245 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.40 % Allowed : 23.63 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.58), residues: 204 helix: 2.12 (0.50), residues: 104 sheet: 0.56 (1.99), residues: 9 loop : 0.21 (0.64), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 918 TYR 0.008 0.001 TYR A 920 PHE 0.005 0.001 PHE A 851 TRP 0.002 0.001 TRP A1005 HIS 0.004 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 1751) covalent geometry : angle 0.62905 / 0.27 ( 2390) hydrogen bonds : bond 0.04806 / 3.34 ( 88) hydrogen bonds : angle 3.66734 / 2.81 ( 246) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.083 Fit side-chains REVERT: A 915 GLU cc_start: 0.6660 (tm-30) cc_final: 0.6170 (mt-10) REVERT: A 917 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: A 924 MET cc_start: 0.8512 (mmm) cc_final: 0.8237 (mmm) REVERT: A 947 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6973 (mt-10) REVERT: A 1025 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.5985 (ptp90) REVERT: A 1029 GLU cc_start: 0.6366 (mm-30) cc_final: 0.6134 (mm-30) REVERT: A 1034 SER cc_start: 0.6801 (m) cc_final: 0.6443 (p) outliers start: 8 outliers final: 0 residues processed: 44 average time/residue: 0.4984 time to fit residues: 22.3288 Evaluate side-chains 42 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 947 GLU Chi-restraints excluded: chain A residue 1025 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [14, 6, 11, 19, 10, 0, 13, 3, 12, 7, 4] chunk 14 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1011 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.151478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127013 restraints weight = 1753.725| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.57 r_work: 0.3381 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 1751 Z= 0.176 Angle : 0.689 8.318 2390 Z= 0.305 Chirality : 0.042 0.131 258 Planarity : 0.006 0.039 309 Dihedral : 12.156 123.279 245 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.40 % Allowed : 22.53 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.57), residues: 204 helix: 1.91 (0.50), residues: 104 sheet: 0.47 (2.03), residues: 9 loop : 0.15 (0.62), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 886 TYR 0.009 0.002 TYR A 920 PHE 0.007 0.002 PHE A 851 TRP 0.004 0.001 TRP A1005 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 1751) covalent geometry : angle 0.68884 / 0.30 ( 2390) hydrogen bonds : bond 0.05848 / 4.03 ( 88) hydrogen bonds : angle 3.87740 / 2.96 ( 246) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.048 Fit side-chains REVERT: A 872 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7564 (tp30) REVERT: A 915 GLU cc_start: 0.6702 (tm-30) cc_final: 0.6213 (mt-10) REVERT: A 917 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: A 1025 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.5936 (ptp90) REVERT: A 1029 GLU cc_start: 0.6552 (mm-30) cc_final: 0.6317 (mm-30) REVERT: A 1034 SER cc_start: 0.6858 (m) cc_final: 0.6505 (p) outliers start: 8 outliers final: 1 residues processed: 43 average time/residue: 0.4754 time to fit residues: 20.8168 Evaluate side-chains 42 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 1025 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [14, 18, 19, 12, 8, 3, 5, 9, 17, 4, 2] chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.152750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128376 restraints weight = 1705.334| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.54 r_work: 0.3401 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1751 Z= 0.149 Angle : 0.672 8.611 2390 Z= 0.295 Chirality : 0.041 0.129 258 Planarity : 0.005 0.040 309 Dihedral : 12.094 123.286 245 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.75 % Allowed : 24.18 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.57), residues: 204 helix: 1.95 (0.50), residues: 104 sheet: 0.56 (2.05), residues: 9 loop : 0.19 (0.62), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1025 TYR 0.008 0.001 TYR A 920 PHE 0.006 0.002 PHE A 851 TRP 0.003 0.001 TRP A 882 HIS 0.004 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 1751) covalent geometry : angle 0.67182 / 0.30 ( 2390) hydrogen bonds : bond 0.05387 / 3.72 ( 88) hydrogen bonds : angle 3.83345 / 2.93 ( 246) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.070 Fit side-chains REVERT: A 872 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7491 (tp30) REVERT: A 915 GLU cc_start: 0.6688 (tm-30) cc_final: 0.6203 (mt-10) REVERT: A 917 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: A 973 SER cc_start: 0.7917 (p) cc_final: 0.7646 (m) REVERT: A 1025 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.5933 (ptp90) REVERT: A 1029 GLU cc_start: 0.6503 (mm-30) cc_final: 0.6277 (mm-30) REVERT: A 1034 SER cc_start: 0.6866 (m) cc_final: 0.6515 (p) outliers start: 5 outliers final: 1 residues processed: 41 average time/residue: 0.4668 time to fit residues: 19.5243 Evaluate side-chains 43 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 1025 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [0, 19, 3, 7, 18, 2, 17, 4, 13, 9, 6] chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.151353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.127112 restraints weight = 1726.926| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.54 r_work: 0.3385 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1751 Z= 0.167 Angle : 0.695 9.262 2390 Z= 0.306 Chirality : 0.042 0.131 258 Planarity : 0.006 0.039 309 Dihedral : 12.160 123.590 245 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.75 % Allowed : 24.73 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.57), residues: 204 helix: 1.85 (0.50), residues: 104 sheet: 0.57 (2.04), residues: 9 loop : 0.17 (0.62), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1025 TYR 0.009 0.002 TYR A 920 PHE 0.006 0.002 PHE A 851 TRP 0.003 0.001 TRP A1005 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 1751) covalent geometry : angle 0.69485 / 0.31 ( 2390) hydrogen bonds : bond 0.05662 / 3.89 ( 88) hydrogen bonds : angle 3.89367 / 2.98 ( 246) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.071 Fit side-chains REVERT: A 872 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7481 (tp30) REVERT: A 915 GLU cc_start: 0.6712 (tm-30) cc_final: 0.6256 (mt-10) REVERT: A 917 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: A 973 SER cc_start: 0.7915 (p) cc_final: 0.7655 (m) REVERT: A 1025 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6029 (ptp90) REVERT: A 1029 GLU cc_start: 0.6484 (mm-30) cc_final: 0.6250 (mm-30) REVERT: A 1034 SER cc_start: 0.6887 (m) cc_final: 0.6533 (p) REVERT: A 1054 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7560 (mm-30) outliers start: 5 outliers final: 0 residues processed: 42 average time/residue: 0.4880 time to fit residues: 20.9122 Evaluate side-chains 44 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1054 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [14, 13, 12, 7, 17, 2, 10, 9, 15, 11, 1] chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126841 restraints weight = 1746.271| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.56 r_work: 0.3381 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 1751 Z= 0.170 Angle : 0.699 9.938 2390 Z= 0.309 Chirality : 0.042 0.131 258 Planarity : 0.006 0.039 309 Dihedral : 12.194 124.029 245 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.75 % Allowed : 24.73 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.57), residues: 204 helix: 1.83 (0.49), residues: 104 sheet: 0.57 (2.03), residues: 9 loop : 0.09 (0.62), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 918 TYR 0.009 0.002 TYR A 920 PHE 0.006 0.002 PHE A 851 TRP 0.003 0.001 TRP A1005 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 1751) covalent geometry : angle 0.69872 / 0.31 ( 2390) hydrogen bonds : bond 0.05673 / 3.90 ( 88) hydrogen bonds : angle 3.90916 / 2.98 ( 246) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.049 Fit side-chains REVERT: A 872 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7526 (tp30) REVERT: A 915 GLU cc_start: 0.6750 (tm-30) cc_final: 0.6259 (mt-10) REVERT: A 973 SER cc_start: 0.7916 (p) cc_final: 0.7661 (m) REVERT: A 1025 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6058 (ptp90) REVERT: A 1029 GLU cc_start: 0.6488 (mm-30) cc_final: 0.6253 (mm-30) REVERT: A 1034 SER cc_start: 0.6903 (m) cc_final: 0.6551 (p) REVERT: A 1054 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7556 (mm-30) outliers start: 5 outliers final: 1 residues processed: 41 average time/residue: 0.4876 time to fit residues: 20.3440 Evaluate side-chains 43 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 1025 ARG Chi-restraints excluded: chain A residue 1054 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [9, 17, 11, 15, 12, 18, 0, 2, 19, 8, 13] chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.153047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.128808 restraints weight = 1702.963| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.54 r_work: 0.3406 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1751 Z= 0.136 Angle : 0.687 10.230 2390 Z= 0.297 Chirality : 0.040 0.128 258 Planarity : 0.005 0.041 309 Dihedral : 12.086 122.800 245 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.65 % Allowed : 26.37 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.58), residues: 204 helix: 1.98 (0.50), residues: 104 sheet: 0.66 (2.06), residues: 9 loop : 0.14 (0.63), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 871 TYR 0.009 0.001 TYR A 920 PHE 0.005 0.001 PHE A 851 TRP 0.002 0.001 TRP A 882 HIS 0.004 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 1751) covalent geometry : angle 0.68674 / 0.30 ( 2390) hydrogen bonds : bond 0.05082 / 3.51 ( 88) hydrogen bonds : angle 3.79190 / 2.89 ( 246) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 408 Ramachandran restraints generated. 204 Oldfield, 0 Emsley, 204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.075 Fit side-chains REVERT: A 872 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7542 (tp30) REVERT: A 915 GLU cc_start: 0.6731 (tm-30) cc_final: 0.6265 (mt-10) REVERT: A 927 GLU cc_start: 0.7334 (tp30) cc_final: 0.6564 (tp30) REVERT: A 973 SER cc_start: 0.7913 (p) cc_final: 0.7648 (m) REVERT: A 1025 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6034 (ptt90) REVERT: A 1029 GLU cc_start: 0.6428 (mm-30) cc_final: 0.6188 (mm-30) REVERT: A 1034 SER cc_start: 0.6876 (m) cc_final: 0.6525 (p) outliers start: 3 outliers final: 0 residues processed: 46 average time/residue: 0.6170 time to fit residues: 28.8358 Evaluate side-chains 39 residues out of total 182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 1025 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [17, 13, 15, 2, 18, 6, 8, 19, 3, 7, 14] chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.0470 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.154060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129822 restraints weight = 1739.606| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.58 r_work: 0.3417 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1751 Z= 0.130 Angle : 0.677 10.464 2390 Z= 0.293 Chirality : 0.040 0.126 258 Planarity : 0.005 0.041 309 Dihedral : 12.022 121.275 245 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.10 % Allowed : 26.92 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.58), residues: 204 helix: 2.03 (0.50), residues: 104 sheet: 0.79 (2.09), residues: 9 loop : 0.17 (0.63), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 871 TYR 0.009 0.001 TYR A 920 PHE 0.005 0.001 PHE A 851 TRP 0.002 0.001 TRP A 882 HIS 0.004 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 1751) covalent geometry : angle 0.67739 / 0.29 ( 2390) hydrogen bonds : bond 0.04883 / 3.38 ( 88) hydrogen bonds : angle 3.76129 / 2.85 ( 246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1076.42 seconds wall clock time: 19 minutes 19.70 seconds (1159.70 seconds total)