Starting phenix.real_space_refine on Thu Jul 2 20:32:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubb_42081/07_2026/8ubb_42081.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubb_42081/07_2026/8ubb_42081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ubb_42081/07_2026/8ubb_42081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubb_42081/07_2026/8ubb_42081.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ubb_42081/07_2026/8ubb_42081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubb_42081/07_2026/8ubb_42081.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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 148 5.49 5 S 36 5.16 5 C 6052 2.51 5 N 1862 2.21 5 O 2251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10349 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2690 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain: "B" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "C" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "D" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 868 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 876 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "F" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "G" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 289 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna3p': 12} Chain: "H" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'RNA': 13} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 8} Link IDs: {'rna3p': 12} Chain: "I" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2605 Classifications: {'RNA': 122} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 11, 'rna3p_pur': 51, 'rna3p_pyr': 48} Link IDs: {'rna2p': 23, 'rna3p': 98} Chain breaks: 2 Time building chain proxies: 2.02, per 1000 atoms: 0.20 Number of scatterers: 10349 At special positions: 0 Unit cell: (80, 99, 129, 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 36 16.00 P 148 15.00 O 2251 8.00 N 1862 7.00 C 6052 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: 0.94 Conformation dependent library (CDL) restraints added in 300.0 milliseconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1672 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 1 sheets defined 77.1% alpha, 1.9% beta 38 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.867A pdb=" N GLU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 80 through 91 Processing helix chain 'A' and resid 93 through 99 removed outlier: 3.783A pdb=" N ILE A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 183 through 203 removed outlier: 4.043A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 207 removed outlier: 4.397A pdb=" N GLN A 207 " --> pdb=" O GLU A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 207' Processing helix chain 'A' and resid 223 through 241 Processing helix chain 'A' and resid 259 through 263 removed outlier: 4.530A pdb=" N GLY A 262 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 289 Processing helix chain 'A' and resid 294 through 309 removed outlier: 3.893A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TRP A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.555A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 39 through 50 Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 64 through 88 Processing helix chain 'B' and resid 95 through 122 Processing helix chain 'C' and resid 12 through 34 removed outlier: 3.634A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 51 through 63 Processing helix chain 'C' and resid 64 through 88 Processing helix chain 'C' and resid 95 through 121 Processing helix chain 'D' and resid 14 through 34 Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 38 through 62 removed outlier: 3.756A pdb=" N VAL D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 Processing helix chain 'D' and resid 95 through 121 Processing helix chain 'E' and resid 13 through 32 removed outlier: 3.637A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 38 through 62 removed outlier: 4.083A pdb=" N GLY E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 86 removed outlier: 3.547A pdb=" N ASP E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 121 Processing helix chain 'F' and resid 14 through 34 removed outlier: 4.376A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Proline residue: F 29 - end of helix removed outlier: 3.534A pdb=" N ILE F 34 " --> pdb=" O ILE F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 64 through 87 Processing helix chain 'F' and resid 88 through 93 Proline residue: F 91 - end of helix No H-bonds generated for 'chain 'F' and resid 88 through 93' Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.211A pdb=" N LEU F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 213 removed outlier: 3.844A pdb=" N HIS A 133 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS A 248 " --> pdb=" O ASP A 138 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1685 1.33 - 1.45: 3592 1.45 - 1.57: 5249 1.57 - 1.69: 294 1.69 - 1.81: 61 Bond restraints: 10881 Sorted by residual: bond pdb=" C2 U I 94 " pdb=" N3 U I 94 " ideal model delta sigma weight residual 1.373 1.346 0.027 7.00e-03 2.04e+04 1.53e+01 bond pdb=" CB ARG B 122 " pdb=" CG ARG B 122 " ideal model delta sigma weight residual 1.520 1.412 0.108 3.00e-02 1.11e+03 1.29e+01 bond pdb=" CG1 ILE C 24 " pdb=" CD1 ILE C 24 " ideal model delta sigma weight residual 1.513 1.374 0.139 3.90e-02 6.57e+02 1.26e+01 bond pdb=" CG1 ILE F 24 " pdb=" CD1 ILE F 24 " ideal model delta sigma weight residual 1.513 1.378 0.135 3.90e-02 6.57e+02 1.21e+01 bond pdb=" CG1 ILE D 88 " pdb=" CD1 ILE D 88 " ideal model delta sigma weight residual 1.513 1.379 0.134 3.90e-02 6.57e+02 1.18e+01 ... (remaining 10876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 14711 2.60 - 5.20: 592 5.20 - 7.80: 99 7.80 - 10.39: 18 10.39 - 12.99: 4 Bond angle restraints: 15424 Sorted by residual: angle pdb=" C3' C I 104 " pdb=" O3' C I 104 " pdb=" P G I 105 " ideal model delta sigma weight residual 120.20 110.38 9.82 1.50e+00 4.44e-01 4.28e+01 angle pdb=" N GLN E 32 " pdb=" CA GLN E 32 " pdb=" C GLN E 32 " ideal model delta sigma weight residual 113.38 105.47 7.91 1.23e+00 6.61e-01 4.14e+01 angle pdb=" C ALA A 153 " pdb=" N MET A 154 " pdb=" CA MET A 154 " ideal model delta sigma weight residual 120.58 131.13 -10.55 1.71e+00 3.42e-01 3.81e+01 angle pdb=" C3' U I 3 " pdb=" O3' U I 3 " pdb=" P G I 4 " ideal model delta sigma weight residual 120.20 111.15 9.05 1.50e+00 4.44e-01 3.64e+01 angle pdb=" C3' A I 119 " pdb=" O3' A I 119 " pdb=" P U I 120 " ideal model delta sigma weight residual 120.20 111.28 8.92 1.50e+00 4.44e-01 3.54e+01 ... (remaining 15419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 5887 35.55 - 71.10: 771 71.10 - 106.65: 78 106.65 - 142.20: 4 142.20 - 177.75: 5 Dihedral angle restraints: 6745 sinusoidal: 4152 harmonic: 2593 Sorted by residual: dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual -128.00 46.57 -174.57 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C I 82 " pdb=" C1' C I 82 " pdb=" N1 C I 82 " pdb=" C2 C I 82 " ideal model delta sinusoidal sigma weight residual 232.00 76.28 155.72 1 1.70e+01 3.46e-03 6.35e+01 dihedral pdb=" C5' C I 20 " pdb=" C4' C I 20 " pdb=" C3' C I 20 " pdb=" O3' C I 20 " ideal model delta sinusoidal sigma weight residual 147.00 108.63 38.37 1 8.00e+00 1.56e-02 3.24e+01 ... (remaining 6742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1718 0.113 - 0.225: 95 0.225 - 0.338: 13 0.338 - 0.450: 4 0.450 - 0.563: 2 Chirality restraints: 1832 Sorted by residual: chirality pdb=" P U I 3 " pdb=" OP1 U I 3 " pdb=" OP2 U I 3 " pdb=" O5' U I 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.93e+00 chirality pdb=" P A I 81 " pdb=" OP1 A I 81 " pdb=" OP2 A I 81 " pdb=" O5' A I 81 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" P U I 120 " pdb=" OP1 U I 120 " pdb=" OP2 U I 120 " pdb=" O5' U I 120 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.91e+00 ... (remaining 1829 not shown) Planarity restraints: 1399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 90 " -0.087 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PRO C 91 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 70 " -0.064 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A 71 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 231 " -0.038 2.00e-02 2.50e+03 2.59e-02 1.18e+01 pdb=" CG PHE A 231 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 231 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 231 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 231 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 231 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 231 " -0.010 2.00e-02 2.50e+03 ... (remaining 1396 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1413 2.74 - 3.28: 11235 3.28 - 3.82: 23299 3.82 - 4.36: 28718 4.36 - 4.90: 40236 Nonbonded interactions: 104901 Sorted by model distance: nonbonded pdb=" OH TYR F 26 " pdb=" OG1 THR F 101 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR A 193 " pdb=" O LEU A 242 " model vdw 2.210 3.040 nonbonded pdb=" NE2 GLN E 98 " pdb=" O3' C I 17 " model vdw 2.251 3.120 nonbonded pdb=" O ARG A 31 " pdb=" OH TYR B 11 " model vdw 2.252 3.040 nonbonded pdb=" NE2 HIS A 202 " pdb=" O2' G I 129 " model vdw 2.260 3.120 ... (remaining 104896 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = chain 'D' selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } 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=0.00 max=1.00 mean=0.99 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: 2.400 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.390 Find NCS groups from input model: 0.070 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 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 : 0.010 0.172 10881 Z= 0.460 Angle : 1.206 12.992 15424 Z= 0.733 Chirality : 0.064 0.563 1832 Planarity : 0.010 0.133 1399 Dihedral : 25.815 177.753 5073 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 41.97 Ramachandran Plot: Outliers : 3.64 % Allowed : 10.69 % Favored : 85.67 % Rotamer: Outliers : 20.00 % Allowed : 14.23 % Favored : 65.77 % Cbeta Deviations : 0.12 % 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: -4.10 (0.24), residues: 879 helix: -2.03 (0.17), residues: 643 sheet: -3.81 (1.05), residues: 26 loop : -4.23 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 42 TYR 0.026 0.004 TYR A 41 PHE 0.054 0.006 PHE A 231 TRP 0.024 0.005 TRP D 81 HIS 0.015 0.003 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.01040 / 0.46 (10881) covalent geometry : angle 1.20616 / 0.73 (15424) hydrogen bonds : bond 0.22640 / 14.32 ( 589) hydrogen bonds : angle 9.80307 / 6.66 ( 1616) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 265 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6566 (ppp) REVERT: A 3 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6702 (mttm) REVERT: A 33 TRP cc_start: 0.7820 (t-100) cc_final: 0.7283 (t60) REVERT: A 37 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8540 (tt0) REVERT: A 52 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: A 59 GLU cc_start: 0.8373 (mp0) cc_final: 0.8119 (pt0) REVERT: A 74 ARG cc_start: 0.5299 (OUTLIER) cc_final: 0.5073 (ptt180) REVERT: A 109 CYS cc_start: 0.8194 (m) cc_final: 0.7898 (t) REVERT: A 130 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7616 (mmm160) REVERT: A 154 MET cc_start: 0.8389 (mtt) cc_final: 0.8017 (mtt) REVERT: A 158 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8366 (mmmm) REVERT: A 172 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7987 (tt) REVERT: A 200 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7763 (tt) REVERT: A 203 ASP cc_start: 0.8292 (m-30) cc_final: 0.8089 (m-30) REVERT: A 214 MET cc_start: 0.8472 (tpp) cc_final: 0.8246 (mmm) REVERT: A 226 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: A 256 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7570 (mmm-85) REVERT: A 272 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7213 (mp) REVERT: B 14 MET cc_start: 0.8383 (mtt) cc_final: 0.7991 (mtp) REVERT: B 77 MET cc_start: 0.8611 (tpt) cc_final: 0.7986 (tpp) REVERT: C 14 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.6973 (ttp) REVERT: C 18 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8278 (tt0) REVERT: C 20 TYR cc_start: 0.8729 (t80) cc_final: 0.8526 (t80) REVERT: C 48 CYS cc_start: 0.8823 (t) cc_final: 0.8615 (t) REVERT: C 57 ILE cc_start: 0.8462 (mm) cc_final: 0.8200 (mp) REVERT: D 18 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7520 (tp30) REVERT: D 19 ARG cc_start: 0.8157 (mmt-90) cc_final: 0.7943 (mmt-90) REVERT: D 52 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8125 (tp40) REVERT: D 62 SER cc_start: 0.6289 (OUTLIER) cc_final: 0.6070 (p) REVERT: D 67 LYS cc_start: 0.8107 (mptt) cc_final: 0.7895 (mmmt) REVERT: D 72 ASP cc_start: 0.8153 (t0) cc_final: 0.7931 (t0) REVERT: D 75 LEU cc_start: 0.8342 (mt) cc_final: 0.7994 (mt) REVERT: D 95 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7374 (p) REVERT: D 103 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8288 (mm-40) REVERT: D 108 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6705 (mt-10) REVERT: E 18 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8156 (tp30) REVERT: E 43 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: E 52 GLN cc_start: 0.8192 (tm-30) cc_final: 0.6689 (tm-30) REVERT: E 69 TYR cc_start: 0.8132 (m-10) cc_final: 0.7925 (m-80) REVERT: E 111 ARG cc_start: 0.8426 (mtm110) cc_final: 0.8102 (ttp-110) REVERT: F 14 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.6751 (tmm) REVERT: F 19 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7857 (mmm160) REVERT: F 20 TYR cc_start: 0.8393 (t80) cc_final: 0.7979 (t80) REVERT: F 25 SER cc_start: 0.9279 (t) cc_final: 0.8998 (p) REVERT: F 54 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: F 55 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7197 (mp) REVERT: F 92 HIS cc_start: 0.6308 (m-70) cc_final: 0.6085 (m-70) outliers start: 149 outliers final: 33 residues processed: 356 average time/residue: 0.1309 time to fit residues: 59.6632 Evaluate side-chains 272 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 36 ARG Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.0970 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS A 259 ASN A 290 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN D 13 GLN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN F 97 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.175797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132901 restraints weight = 15219.662| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.60 r_work: 0.3506 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 10881 Z= 0.278 Angle : 0.875 12.826 15424 Z= 0.474 Chirality : 0.048 0.258 1832 Planarity : 0.009 0.132 1399 Dihedral : 25.300 179.651 3470 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 32.19 Ramachandran Plot: Outliers : 1.02 % Allowed : 7.96 % Favored : 91.01 % Rotamer: Outliers : 9.13 % Allowed : 19.33 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.71 (0.26), residues: 879 helix: -1.06 (0.18), residues: 661 sheet: -3.37 (1.03), residues: 26 loop : -3.74 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 19 TYR 0.023 0.003 TYR B 20 PHE 0.033 0.004 PHE A 231 TRP 0.020 0.003 TRP E 116 HIS 0.019 0.003 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.28 (10881) covalent geometry : angle 0.87455 / 0.47 (15424) hydrogen bonds : bond 0.08982 / 5.86 ( 589) hydrogen bonds : angle 5.97721 / 4.11 ( 1616) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 237 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7795 (m-40) cc_final: 0.7277 (m-40) REVERT: A 107 TYR cc_start: 0.7204 (m-80) cc_final: 0.6939 (m-80) REVERT: A 165 ARG cc_start: 0.8411 (mtp85) cc_final: 0.8036 (mtt180) REVERT: A 208 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.5962 (mtt90) REVERT: A 226 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: A 270 LYS cc_start: 0.7857 (ttpt) cc_final: 0.7034 (ttpp) REVERT: A 272 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7210 (pp) REVERT: C 19 ARG cc_start: 0.6933 (mmt90) cc_final: 0.6698 (mmm-85) REVERT: D 52 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7584 (tp40) REVERT: D 115 SER cc_start: 0.8799 (m) cc_final: 0.8570 (m) REVERT: E 52 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7048 (tm130) REVERT: F 14 MET cc_start: 0.7057 (mmp) cc_final: 0.6666 (ttm) REVERT: F 15 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6697 (pp) REVERT: F 47 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8117 (mttm) REVERT: F 55 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8172 (mp) outliers start: 68 outliers final: 26 residues processed: 278 average time/residue: 0.1062 time to fit residues: 39.0936 Evaluate side-chains 236 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 108 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 62 optimal weight: 0.4980 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 0.0470 chunk 77 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN A 259 ASN A 306 HIS ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 52 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.175908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.132636 restraints weight = 15395.592| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.66 r_work: 0.3507 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 10881 Z= 0.238 Angle : 0.764 15.248 15424 Z= 0.412 Chirality : 0.045 0.278 1832 Planarity : 0.008 0.166 1399 Dihedral : 24.723 176.048 3376 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 28.73 Ramachandran Plot: Outliers : 0.91 % Allowed : 9.22 % Favored : 89.87 % Rotamer: Outliers : 6.71 % Allowed : 20.67 % Favored : 72.62 % 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: -2.10 (0.27), residues: 879 helix: -0.67 (0.19), residues: 663 sheet: -3.03 (1.02), residues: 26 loop : -3.35 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 111 TYR 0.025 0.003 TYR C 28 PHE 0.036 0.003 PHE A 231 TRP 0.011 0.002 TRP A 15 HIS 0.014 0.002 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.24 (10881) covalent geometry : angle 0.76356 / 0.41 (15424) hydrogen bonds : bond 0.07635 / 5.03 ( 589) hydrogen bonds : angle 5.58391 / 3.84 ( 1616) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 TYR cc_start: 0.6977 (m-80) cc_final: 0.6655 (m-80) REVERT: A 165 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7855 (mtt180) REVERT: A 226 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: A 263 TYR cc_start: 0.6653 (m-80) cc_final: 0.6425 (m-80) REVERT: A 272 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7005 (pp) REVERT: C 98 GLN cc_start: 0.8311 (mt0) cc_final: 0.8053 (tt0) REVERT: D 26 TYR cc_start: 0.8663 (t80) cc_final: 0.8419 (t80) REVERT: D 115 SER cc_start: 0.8567 (m) cc_final: 0.8358 (m) REVERT: E 69 TYR cc_start: 0.8198 (m-80) cc_final: 0.7995 (m-10) REVERT: E 77 MET cc_start: 0.8397 (tpt) cc_final: 0.7898 (tpt) REVERT: F 47 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8072 (mttm) REVERT: F 108 GLU cc_start: 0.7690 (tp30) cc_final: 0.7447 (tp30) outliers start: 50 outliers final: 32 residues processed: 250 average time/residue: 0.1091 time to fit residues: 36.0140 Evaluate side-chains 240 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 44 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 68 optimal weight: 0.0980 chunk 94 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 308 GLN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 121 ASN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.176746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.133979 restraints weight = 15491.291| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.68 r_work: 0.3530 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 10881 Z= 0.211 Angle : 0.717 10.442 15424 Z= 0.387 Chirality : 0.043 0.323 1832 Planarity : 0.008 0.139 1399 Dihedral : 24.472 177.604 3367 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 28.26 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.74 % Favored : 91.35 % Rotamer: Outliers : 5.50 % Allowed : 21.48 % Favored : 73.02 % 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: -1.69 (0.27), residues: 879 helix: -0.40 (0.19), residues: 669 sheet: -2.66 (1.04), residues: 26 loop : -3.19 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 22 TYR 0.024 0.002 TYR C 28 PHE 0.031 0.003 PHE A 231 TRP 0.010 0.002 TRP A 303 HIS 0.008 0.002 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 (10881) covalent geometry : angle 0.71686 / 0.39 (15424) hydrogen bonds : bond 0.06764 / 4.41 ( 589) hydrogen bonds : angle 5.37761 / 3.72 ( 1616) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.7078 (m-80) cc_final: 0.6819 (m-80) REVERT: A 165 ARG cc_start: 0.8256 (mtp85) cc_final: 0.7802 (mtt180) REVERT: A 187 GLN cc_start: 0.8893 (mm110) cc_final: 0.8608 (mm110) REVERT: A 208 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.5184 (mtt90) REVERT: A 272 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7391 (pp) REVERT: B 103 GLN cc_start: 0.8227 (mm-40) cc_final: 0.8007 (mm-40) REVERT: C 42 ARG cc_start: 0.8204 (ttp80) cc_final: 0.7857 (ttp-170) REVERT: D 22 ARG cc_start: 0.8537 (mtm180) cc_final: 0.8322 (mtm180) REVERT: F 47 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8080 (mttm) outliers start: 41 outliers final: 24 residues processed: 249 average time/residue: 0.1020 time to fit residues: 34.0653 Evaluate side-chains 238 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 95 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.175766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133096 restraints weight = 15515.306| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.70 r_work: 0.3519 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 10881 Z= 0.226 Angle : 0.709 15.086 15424 Z= 0.378 Chirality : 0.042 0.313 1832 Planarity : 0.008 0.162 1399 Dihedral : 24.173 176.226 3358 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 27.32 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.28 % Favored : 91.81 % Rotamer: Outliers : 4.97 % Allowed : 24.43 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.42 (0.27), residues: 879 helix: -0.24 (0.19), residues: 668 sheet: -2.23 (1.08), residues: 26 loop : -3.01 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 111 TYR 0.026 0.003 TYR C 28 PHE 0.031 0.003 PHE A 231 TRP 0.010 0.002 TRP F 116 HIS 0.010 0.001 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 (10881) covalent geometry : angle 0.70891 / 0.38 (15424) hydrogen bonds : bond 0.06443 / 4.21 ( 589) hydrogen bonds : angle 5.25257 / 3.60 ( 1616) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 225 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3825 (OUTLIER) cc_final: 0.3266 (tmm) REVERT: A 107 TYR cc_start: 0.7262 (m-80) cc_final: 0.6985 (m-80) REVERT: A 165 ARG cc_start: 0.8257 (mtp85) cc_final: 0.7856 (mtt180) REVERT: A 224 PRO cc_start: 0.7097 (Cg_exo) cc_final: 0.6864 (Cg_endo) REVERT: A 263 TYR cc_start: 0.6648 (m-80) cc_final: 0.5584 (t80) REVERT: B 82 LEU cc_start: 0.8731 (mt) cc_final: 0.8521 (mp) REVERT: B 119 ARG cc_start: 0.7846 (ptm-80) cc_final: 0.7580 (ptm-80) REVERT: C 98 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7991 (mt0) REVERT: D 22 ARG cc_start: 0.8501 (mtm180) cc_final: 0.8288 (mtm180) REVERT: E 69 TYR cc_start: 0.8176 (m-10) cc_final: 0.7959 (m-10) REVERT: F 19 ARG cc_start: 0.7950 (mtp85) cc_final: 0.7414 (mtp85) REVERT: F 47 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8141 (mttm) REVERT: F 108 GLU cc_start: 0.7614 (tp30) cc_final: 0.7092 (tt0) outliers start: 37 outliers final: 26 residues processed: 246 average time/residue: 0.1064 time to fit residues: 34.1909 Evaluate side-chains 246 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 87 optimal weight: 30.0000 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 93 optimal weight: 40.0000 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.172920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.129445 restraints weight = 15713.234| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.69 r_work: 0.3464 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 10881 Z= 0.305 Angle : 0.733 10.032 15424 Z= 0.388 Chirality : 0.043 0.242 1832 Planarity : 0.007 0.141 1399 Dihedral : 24.028 177.158 3356 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 28.94 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.96 % Favored : 91.13 % Rotamer: Outliers : 4.97 % Allowed : 24.43 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.41 (0.27), residues: 879 helix: -0.28 (0.19), residues: 663 sheet: -1.92 (1.14), residues: 26 loop : -2.77 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 111 TYR 0.031 0.003 TYR C 28 PHE 0.031 0.003 PHE A 231 TRP 0.010 0.002 TRP A 249 HIS 0.014 0.002 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.31 (10881) covalent geometry : angle 0.73325 / 0.39 (15424) hydrogen bonds : bond 0.06712 / 4.39 ( 589) hydrogen bonds : angle 5.29699 / 3.63 ( 1616) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 PHE cc_start: 0.8130 (t80) cc_final: 0.7916 (t80) REVERT: A 263 TYR cc_start: 0.6713 (m-80) cc_final: 0.5655 (t80) REVERT: B 82 LEU cc_start: 0.8737 (mt) cc_final: 0.8536 (mp) REVERT: C 98 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8061 (mt0) REVERT: C 111 ARG cc_start: 0.7702 (ttp80) cc_final: 0.7408 (mtm110) REVERT: D 22 ARG cc_start: 0.8513 (mtm180) cc_final: 0.8304 (mtm180) REVERT: D 37 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7434 (mmmt) REVERT: D 79 ARG cc_start: 0.7988 (mtm-85) cc_final: 0.7735 (mtt-85) REVERT: F 47 LYS cc_start: 0.8494 (ttmm) cc_final: 0.8225 (mttm) outliers start: 37 outliers final: 25 residues processed: 237 average time/residue: 0.1163 time to fit residues: 36.0028 Evaluate side-chains 231 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 22 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 30 optimal weight: 0.0970 chunk 62 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.176607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.134667 restraints weight = 15503.079| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.63 r_work: 0.3545 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10881 Z= 0.195 Angle : 0.708 9.090 15424 Z= 0.376 Chirality : 0.041 0.196 1832 Planarity : 0.007 0.128 1399 Dihedral : 23.921 174.910 3354 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 26.64 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.74 % Favored : 91.47 % Rotamer: Outliers : 5.10 % Allowed : 24.83 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.27 (0.27), residues: 879 helix: -0.22 (0.19), residues: 664 sheet: -1.64 (1.19), residues: 26 loop : -2.57 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 22 TYR 0.028 0.003 TYR A 107 PHE 0.028 0.003 PHE A 231 TRP 0.015 0.002 TRP F 116 HIS 0.008 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (10881) covalent geometry : angle 0.70779 / 0.38 (15424) hydrogen bonds : bond 0.06039 / 3.96 ( 589) hydrogen bonds : angle 5.14148 / 3.53 ( 1616) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7474 (m-40) cc_final: 0.6885 (m-40) REVERT: A 263 TYR cc_start: 0.6549 (m-80) cc_final: 0.5618 (t80) REVERT: C 98 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8055 (mt0) REVERT: C 111 ARG cc_start: 0.7576 (ttp80) cc_final: 0.7252 (mtm110) REVERT: D 22 ARG cc_start: 0.8467 (mtm180) cc_final: 0.8247 (mtm180) REVERT: D 37 LYS cc_start: 0.8006 (mtpp) cc_final: 0.7313 (mmmt) REVERT: D 47 LYS cc_start: 0.8422 (mttm) cc_final: 0.8100 (mmtt) REVERT: F 47 LYS cc_start: 0.8418 (ttmm) cc_final: 0.8113 (mttm) outliers start: 38 outliers final: 26 residues processed: 257 average time/residue: 0.1085 time to fit residues: 37.0613 Evaluate side-chains 243 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 66 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 94 optimal weight: 30.0000 chunk 66 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 87 optimal weight: 30.0000 chunk 59 optimal weight: 0.5980 chunk 99 optimal weight: 9.9990 chunk 11 optimal weight: 0.3980 chunk 10 optimal weight: 0.0970 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS E 13 GLN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.178363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.137710 restraints weight = 15479.604| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.62 r_work: 0.3570 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10881 Z= 0.190 Angle : 0.690 9.786 15424 Z= 0.368 Chirality : 0.041 0.192 1832 Planarity : 0.007 0.122 1399 Dihedral : 23.767 176.434 3351 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 27.11 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.62 % Favored : 91.47 % Rotamer: Outliers : 3.36 % Allowed : 26.44 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.13 (0.27), residues: 879 helix: -0.13 (0.19), residues: 666 sheet: -1.45 (1.22), residues: 26 loop : -2.52 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 19 TYR 0.026 0.002 TYR F 20 PHE 0.026 0.002 PHE A 231 TRP 0.018 0.002 TRP F 116 HIS 0.008 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (10881) covalent geometry : angle 0.69029 / 0.37 (15424) hydrogen bonds : bond 0.05889 / 3.87 ( 589) hydrogen bonds : angle 5.10830 / 3.54 ( 1616) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.7404 (m-80) cc_final: 0.7065 (m-80) REVERT: A 187 GLN cc_start: 0.8654 (mm110) cc_final: 0.8405 (mm-40) REVERT: A 263 TYR cc_start: 0.6528 (m-80) cc_final: 0.5702 (t80) REVERT: C 98 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: D 19 ARG cc_start: 0.7743 (mmt-90) cc_final: 0.7535 (mmp80) REVERT: D 22 ARG cc_start: 0.8500 (mtm180) cc_final: 0.8250 (mtm180) REVERT: D 26 TYR cc_start: 0.8450 (t80) cc_final: 0.8208 (t80) REVERT: D 37 LYS cc_start: 0.7958 (mtpp) cc_final: 0.7314 (mmmt) REVERT: D 47 LYS cc_start: 0.8435 (mttm) cc_final: 0.8149 (mmtt) REVERT: D 79 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.7599 (mtt-85) REVERT: E 19 ARG cc_start: 0.7772 (mtp180) cc_final: 0.7520 (mtp180) REVERT: F 20 TYR cc_start: 0.8352 (t80) cc_final: 0.8106 (t80) REVERT: F 47 LYS cc_start: 0.8366 (ttmm) cc_final: 0.8100 (mttm) outliers start: 25 outliers final: 20 residues processed: 234 average time/residue: 0.1117 time to fit residues: 34.3108 Evaluate side-chains 228 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 66 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 95 optimal weight: 30.0000 chunk 89 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 10 optimal weight: 0.0030 chunk 50 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 chunk 44 optimal weight: 0.0370 overall best weight: 0.3468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.178887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138896 restraints weight = 15535.295| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.59 r_work: 0.3592 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10881 Z= 0.181 Angle : 0.693 12.358 15424 Z= 0.367 Chirality : 0.040 0.190 1832 Planarity : 0.007 0.134 1399 Dihedral : 23.681 178.031 3346 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 26.59 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.17 % Favored : 91.92 % Rotamer: Outliers : 3.49 % Allowed : 27.52 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.03 (0.28), residues: 879 helix: -0.10 (0.19), residues: 664 sheet: -1.18 (1.28), residues: 26 loop : -2.35 (0.46), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 208 TYR 0.029 0.003 TYR D 20 PHE 0.025 0.002 PHE A 231 TRP 0.020 0.002 TRP F 116 HIS 0.007 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (10881) covalent geometry : angle 0.69321 / 0.37 (15424) hydrogen bonds : bond 0.05713 / 3.76 ( 589) hydrogen bonds : angle 5.06196 / 3.48 ( 1616) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7308 (m-40) cc_final: 0.6754 (m-40) REVERT: A 187 GLN cc_start: 0.8586 (mm110) cc_final: 0.8327 (mm-40) REVERT: A 263 TYR cc_start: 0.6512 (m-80) cc_final: 0.5697 (t80) REVERT: A 270 LYS cc_start: 0.8047 (ttpt) cc_final: 0.7397 (mtpt) REVERT: A 273 ARG cc_start: 0.6982 (tmm-80) cc_final: 0.6746 (ttt90) REVERT: B 11 TYR cc_start: 0.7210 (t80) cc_final: 0.6907 (t80) REVERT: B 98 GLN cc_start: 0.8137 (tt0) cc_final: 0.7844 (tt0) REVERT: C 77 MET cc_start: 0.8477 (tpt) cc_final: 0.7955 (tpt) REVERT: C 90 LYS cc_start: 0.5692 (tptt) cc_final: 0.5461 (ttmm) REVERT: D 37 LYS cc_start: 0.7887 (mtpp) cc_final: 0.7281 (mmmt) REVERT: D 47 LYS cc_start: 0.8390 (mttm) cc_final: 0.8085 (mmtt) REVERT: E 67 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8443 (mtmm) REVERT: F 20 TYR cc_start: 0.8420 (t80) cc_final: 0.8110 (t80) REVERT: F 47 LYS cc_start: 0.8345 (ttmm) cc_final: 0.8114 (mttm) outliers start: 26 outliers final: 21 residues processed: 231 average time/residue: 0.1085 time to fit residues: 33.5523 Evaluate side-chains 222 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 74 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 88 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 87 optimal weight: 40.0000 chunk 64 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.177968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.137716 restraints weight = 15410.634| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.58 r_work: 0.3573 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 10881 Z= 0.206 Angle : 0.700 11.652 15424 Z= 0.369 Chirality : 0.041 0.230 1832 Planarity : 0.007 0.127 1399 Dihedral : 23.598 179.029 3346 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 27.06 Ramachandran Plot: Outliers : 0.91 % Allowed : 6.83 % Favored : 92.26 % Rotamer: Outliers : 2.95 % Allowed : 27.65 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.28), residues: 879 helix: -0.05 (0.19), residues: 663 sheet: -1.16 (1.27), residues: 26 loop : -2.26 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 19 TYR 0.026 0.003 TYR D 20 PHE 0.027 0.002 PHE A 231 TRP 0.017 0.002 TRP F 116 HIS 0.008 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (10881) covalent geometry : angle 0.70018 / 0.37 (15424) hydrogen bonds : bond 0.05775 / 3.78 ( 589) hydrogen bonds : angle 5.05493 / 3.47 ( 1616) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LYS cc_start: 0.8066 (ttpt) cc_final: 0.7847 (ttpp) REVERT: A 273 ARG cc_start: 0.7019 (tmm-80) cc_final: 0.6780 (ttt90) REVERT: B 11 TYR cc_start: 0.7302 (t80) cc_final: 0.7071 (t80) REVERT: B 98 GLN cc_start: 0.8173 (tt0) cc_final: 0.7775 (tt0) REVERT: D 37 LYS cc_start: 0.7786 (mtpp) cc_final: 0.7319 (mmmt) REVERT: D 47 LYS cc_start: 0.8432 (mttm) cc_final: 0.8092 (mmtt) REVERT: F 20 TYR cc_start: 0.8400 (t80) cc_final: 0.8131 (t80) REVERT: F 47 LYS cc_start: 0.8370 (ttmm) cc_final: 0.8115 (mttm) outliers start: 22 outliers final: 21 residues processed: 221 average time/residue: 0.1088 time to fit residues: 31.9764 Evaluate side-chains 223 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.0870 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 87 optimal weight: 40.0000 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.178494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.138230 restraints weight = 15630.829| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.61 r_work: 0.3578 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 10881 Z= 0.197 Angle : 0.708 15.332 15424 Z= 0.369 Chirality : 0.040 0.192 1832 Planarity : 0.007 0.127 1399 Dihedral : 23.551 179.945 3346 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 26.64 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.05 % Favored : 92.04 % Rotamer: Outliers : 3.22 % Allowed : 26.71 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.28), residues: 879 helix: -0.06 (0.19), residues: 660 sheet: -1.05 (1.27), residues: 26 loop : -2.19 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 19 TYR 0.029 0.003 TYR D 20 PHE 0.027 0.002 PHE A 231 TRP 0.019 0.002 TRP A 15 HIS 0.010 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (10881) covalent geometry : angle 0.70814 / 0.37 (15424) hydrogen bonds : bond 0.05734 / 3.76 ( 589) hydrogen bonds : angle 5.04997 / 3.47 ( 1616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2128.14 seconds wall clock time: 37 minutes 30.93 seconds (2250.93 seconds total)