Starting phenix.real_space_refine on Wed Aug 5 14:04:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubb_42081/08_2026/8ubb_42081.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubb_42081/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ubb_42081/08_2026/8ubb_42081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubb_42081/08_2026/8ubb_42081.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubb_42081/08_2026/8ubb_42081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubb_42081/08_2026/8ubb_42081.cif" } 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-2.2rc3-6140/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: 1.82, per 1000 atoms: 0.18 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: 0.74 Conformation dependent library (CDL) restraints added in 286.9 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: 1.70 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: 2.04 Time building geometry restraints manager: 1.05 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=" P A I 81 " pdb=" O5' A I 81 " ideal model delta sigma weight residual 1.593 1.632 -0.039 1.00e-02 1.00e+04 1.49e+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 ... (remaining 10876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 14617 2.60 - 5.20: 685 5.20 - 7.80: 100 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 119.70 110.38 9.32 1.20e+00 6.94e-01 6.03e+01 angle pdb=" O5' U I 7 " pdb=" C5' U I 7 " pdb=" C4' U I 7 " ideal model delta sigma weight residual 109.40 115.18 -5.78 8.00e-01 1.56e+00 5.22e+01 angle pdb=" C3' U I 3 " pdb=" O3' U I 3 " pdb=" P G I 4 " ideal model delta sigma weight residual 119.70 111.15 8.55 1.20e+00 6.94e-01 5.07e+01 angle pdb=" C3' A I 119 " pdb=" O3' A I 119 " pdb=" P U I 120 " ideal model delta sigma weight residual 119.70 111.28 8.42 1.20e+00 6.94e-01 4.92e+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 ... (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: 1612 0.113 - 0.225: 201 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: 3.100 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.540 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.430 ------------------------------------------------------------------------------- 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= 0.482 Angle : 1.260 12.992 15424 Z= 0.815 Chirality : 0.074 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 0.01045 / 0.48 (10881) covalent geometry : angle 1.25963 / 0.82 (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 : 0.320 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: A 1 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6556 (ppp) REVERT: A 3 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6706 (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: 0.5072 (ptt180) REVERT: A 109 CYS cc_start: 0.8194 (m) cc_final: 0.7899 (t) REVERT: A 130 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7615 (mmm160) REVERT: A 154 MET cc_start: 0.8389 (mtt) cc_final: 0.8022 (mtt) REVERT: A 172 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7989 (tt) REVERT: A 200 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7766 (tt) REVERT: A 203 ASP cc_start: 0.8292 (m-30) cc_final: 0.8091 (m-30) REVERT: A 214 MET cc_start: 0.8472 (tpp) cc_final: 0.8245 (mmm) REVERT: A 226 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7335 (tm-30) REVERT: A 272 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7226 (mp) REVERT: B 14 MET cc_start: 0.8383 (mtt) cc_final: 0.7992 (mtp) REVERT: B 77 MET cc_start: 0.8611 (tpt) cc_final: 0.7986 (tpp) REVERT: B 108 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8127 (tm-30) 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: 0.8201 (mp) REVERT: D 18 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7519 (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: 0.8126 (tp40) REVERT: D 62 SER cc_start: 0.6289 (OUTLIER) cc_final: 0.6069 (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: 0.7930 (t0) REVERT: D 75 LEU cc_start: 0.8342 (mt) cc_final: 0.7995 (mt) REVERT: D 95 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7374 (p) 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: 0.6690 (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: 0.6092 (m-70) outliers start: 149 outliers final: 33 residues processed: 356 average time/residue: 0.1466 time to fit residues: 67.1584 Evaluate side-chains 270 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 215 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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 108 GLU 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 108 GLU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 18 GLU 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: 10.0000 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS 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 F 13 GLN F 97 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.175683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132951 restraints weight = 15250.334| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.58 r_work: 0.3507 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 10881 Z= 0.274 Angle : 0.888 12.737 15424 Z= 0.472 Chirality : 0.051 0.269 1832 Planarity : 0.009 0.132 1399 Dihedral : 25.182 179.902 3462 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 32.03 Ramachandran Plot: Outliers : 1.14 % Allowed : 7.96 % Favored : 90.90 % Rotamer: Outliers : 8.99 % Allowed : 18.79 % Favored : 72.21 % 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: -2.78 (0.25), residues: 879 helix: -1.07 (0.18), residues: 663 sheet: -3.37 (1.04), residues: 26 loop : -3.92 (0.37), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 31 TYR 0.025 0.003 TYR B 20 PHE 0.033 0.003 PHE A 231 TRP 0.021 0.003 TRP E 116 HIS 0.013 0.002 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.27 (10881) covalent geometry : angle 0.88829 / 0.47 (15424) hydrogen bonds : bond 0.09276 / 6.04 ( 589) hydrogen bonds : angle 5.97234 / 4.09 ( 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 302 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 235 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7781 (m-40) cc_final: 0.7112 (m-40) REVERT: A 107 TYR cc_start: 0.7233 (m-80) cc_final: 0.6972 (m-80) REVERT: A 165 ARG cc_start: 0.8427 (mtp85) cc_final: 0.8094 (mtt180) REVERT: A 208 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.5973 (mtt90) REVERT: A 226 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: A 270 LYS cc_start: 0.7889 (ttpt) cc_final: 0.7111 (ttpp) REVERT: A 272 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7251 (pp) REVERT: B 67 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8259 (mttp) REVERT: C 19 ARG cc_start: 0.6981 (mmt90) cc_final: 0.6720 (mmm-85) REVERT: D 52 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7552 (tp40) REVERT: D 115 SER cc_start: 0.8720 (m) cc_final: 0.8488 (m) REVERT: E 52 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.7043 (tm130) REVERT: F 14 MET cc_start: 0.7072 (mmp) cc_final: 0.6654 (ttm) REVERT: F 15 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6706 (pp) REVERT: F 47 LYS cc_start: 0.8474 (ttmm) cc_final: 0.8123 (mttm) outliers start: 67 outliers final: 25 residues processed: 275 average time/residue: 0.1078 time to fit residues: 38.9667 Evaluate side-chains 235 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 B residue 67 LYS Chi-restraints excluded: chain B residue 104 VAL 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 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 27 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: 0.6980 chunk 67 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN A 306 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 52 GLN F 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.174824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.131381 restraints weight = 15378.663| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.63 r_work: 0.3488 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 10881 Z= 0.258 Angle : 0.782 13.869 15424 Z= 0.421 Chirality : 0.045 0.318 1832 Planarity : 0.008 0.161 1399 Dihedral : 24.593 176.673 3373 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 28.47 Ramachandran Plot: Outliers : 0.91 % Allowed : 9.33 % Favored : 89.76 % Rotamer: Outliers : 6.44 % Allowed : 20.54 % 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: -2.10 (0.27), residues: 879 helix: -0.64 (0.19), residues: 663 sheet: -3.02 (1.02), residues: 26 loop : -3.46 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 19 TYR 0.026 0.003 TYR C 28 PHE 0.037 0.003 PHE A 231 TRP 0.012 0.002 TRP A 266 HIS 0.007 0.002 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.26 (10881) covalent geometry : angle 0.78194 / 0.42 (15424) hydrogen bonds : bond 0.07855 / 5.16 ( 589) hydrogen bonds : angle 5.61236 / 3.87 ( 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 266 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 TYR cc_start: 0.7032 (m-80) cc_final: 0.6685 (m-80) REVERT: A 165 ARG cc_start: 0.8306 (mtp85) cc_final: 0.7871 (mtt180) REVERT: A 187 GLN cc_start: 0.8694 (mm110) cc_final: 0.8479 (mm110) REVERT: A 226 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: A 263 TYR cc_start: 0.6642 (m-80) cc_final: 0.6432 (m-80) REVERT: A 270 LYS cc_start: 0.7553 (ttpt) cc_final: 0.7195 (ttpp) REVERT: A 272 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7047 (pp) REVERT: B 69 TYR cc_start: 0.8126 (m-80) cc_final: 0.7912 (m-80) REVERT: C 22 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7530 (mtt180) REVERT: C 98 GLN cc_start: 0.8302 (mt0) cc_final: 0.7965 (mt0) REVERT: D 26 TYR cc_start: 0.8663 (t80) cc_final: 0.8420 (t80) REVERT: D 54 GLU cc_start: 0.8034 (tp30) cc_final: 0.7709 (tp30) REVERT: D 115 SER cc_start: 0.8599 (m) cc_final: 0.8395 (m) REVERT: E 77 MET cc_start: 0.8454 (tpt) cc_final: 0.7859 (tpt) REVERT: F 47 LYS cc_start: 0.8442 (ttmm) cc_final: 0.8103 (mttm) REVERT: F 108 GLU cc_start: 0.7664 (tp30) cc_final: 0.7405 (tp30) outliers start: 48 outliers final: 31 residues processed: 247 average time/residue: 0.1063 time to fit residues: 35.0101 Evaluate side-chains 238 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 226 GLU Chi-restraints excluded: chain A residue 230 VAL 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 53 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 100 GLU 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 44 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 94 optimal weight: 40.0000 chunk 87 optimal weight: 50.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 121 ASN ** D 38 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.175750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.132545 restraints weight = 15465.889| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.64 r_work: 0.3515 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 10881 Z= 0.218 Angle : 0.725 10.621 15424 Z= 0.385 Chirality : 0.043 0.310 1832 Planarity : 0.008 0.138 1399 Dihedral : 24.344 176.184 3367 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 26.85 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.74 % Favored : 91.35 % Rotamer: Outliers : 5.23 % Allowed : 20.81 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.27), residues: 879 helix: -0.39 (0.19), residues: 667 sheet: -2.67 (1.04), residues: 26 loop : -3.27 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 111 TYR 0.028 0.002 TYR C 28 PHE 0.032 0.003 PHE A 231 TRP 0.009 0.002 TRP A 15 HIS 0.009 0.002 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (10881) covalent geometry : angle 0.72482 / 0.39 (15424) hydrogen bonds : bond 0.06910 / 4.53 ( 589) hydrogen bonds : angle 5.37603 / 3.71 ( 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 263 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7421 (m-40) cc_final: 0.6808 (m-40) REVERT: A 107 TYR cc_start: 0.7243 (m-80) cc_final: 0.7005 (m-80) REVERT: A 165 ARG cc_start: 0.8303 (mtp85) cc_final: 0.7816 (mtt180) REVERT: A 187 GLN cc_start: 0.8648 (mm110) cc_final: 0.8350 (mm-40) REVERT: A 272 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7190 (pp) REVERT: B 69 TYR cc_start: 0.7931 (m-80) cc_final: 0.7676 (m-80) REVERT: B 103 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7921 (mm-40) REVERT: F 19 ARG cc_start: 0.7842 (mtp85) cc_final: 0.7330 (mtp85) REVERT: F 47 LYS cc_start: 0.8418 (ttmm) cc_final: 0.8046 (mttm) REVERT: F 108 GLU cc_start: 0.7454 (tp30) cc_final: 0.7046 (tp30) outliers start: 39 outliers final: 26 residues processed: 250 average time/residue: 0.1053 time to fit residues: 35.3410 Evaluate side-chains 239 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 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 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 25 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 104 VAL 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 F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU 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: 30.0000 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 20 optimal weight: 0.1980 chunk 75 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 79 optimal weight: 0.0870 chunk 19 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.176317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.134272 restraints weight = 15503.803| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.64 r_work: 0.3538 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4702 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= 0.197 Angle : 0.698 15.347 15424 Z= 0.371 Chirality : 0.042 0.311 1832 Planarity : 0.008 0.163 1399 Dihedral : 24.068 175.422 3361 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.74 % Favored : 91.35 % Rotamer: Outliers : 5.10 % Allowed : 23.36 % Favored : 71.54 % 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: -1.34 (0.27), residues: 879 helix: -0.17 (0.19), residues: 664 sheet: -2.14 (1.09), residues: 26 loop : -2.96 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 19 TYR 0.023 0.002 TYR C 28 PHE 0.031 0.002 PHE A 231 TRP 0.009 0.002 TRP A 266 HIS 0.011 0.002 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (10881) covalent geometry : angle 0.69781 / 0.37 (15424) hydrogen bonds : bond 0.06415 / 4.21 ( 589) hydrogen bonds : angle 5.20718 / 3.56 ( 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: 38 poor density : 224 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.7228 (m-80) cc_final: 0.6960 (m-80) REVERT: A 165 ARG cc_start: 0.8286 (mtp85) cc_final: 0.7808 (mtt180) REVERT: A 224 PRO cc_start: 0.7003 (Cg_exo) cc_final: 0.6781 (Cg_endo) REVERT: A 263 TYR cc_start: 0.6394 (m-80) cc_final: 0.5558 (t80) REVERT: A 272 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7197 (pp) REVERT: B 69 TYR cc_start: 0.7855 (m-80) cc_final: 0.7654 (m-80) REVERT: B 98 GLN cc_start: 0.7967 (mt0) cc_final: 0.7671 (tt0) REVERT: B 103 GLN cc_start: 0.8227 (mm-40) cc_final: 0.8024 (mm-40) REVERT: B 119 ARG cc_start: 0.7784 (ptm-80) cc_final: 0.7556 (ptm-80) REVERT: C 98 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8007 (mt0) REVERT: D 37 LYS cc_start: 0.8117 (mtpp) cc_final: 0.7329 (mmmt) REVERT: D 42 ARG cc_start: 0.8498 (ttm170) cc_final: 0.8039 (ttm170) REVERT: F 47 LYS cc_start: 0.8387 (ttmm) cc_final: 0.8110 (mttm) outliers start: 38 outliers final: 28 residues processed: 247 average time/residue: 0.1148 time to fit residues: 37.3838 Evaluate side-chains 244 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 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 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 B residue 122 ARG 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 50 LEU Chi-restraints excluded: chain E residue 75 LEU 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 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: 8.9990 chunk 87 optimal weight: 50.0000 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 93 optimal weight: 40.0000 chunk 83 optimal weight: 0.5980 chunk 88 optimal weight: 30.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.174784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132192 restraints weight = 15668.268| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.63 r_work: 0.3508 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 10881 Z= 0.238 Angle : 0.699 8.981 15424 Z= 0.372 Chirality : 0.042 0.232 1832 Planarity : 0.007 0.137 1399 Dihedral : 23.908 174.974 3354 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 26.74 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.51 % Favored : 91.58 % Rotamer: Outliers : 5.10 % Allowed : 24.03 % Favored : 70.87 % 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: -1.17 (0.28), residues: 879 helix: -0.07 (0.19), residues: 667 sheet: -1.75 (1.17), residues: 26 loop : -2.94 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 111 TYR 0.027 0.003 TYR C 20 PHE 0.029 0.003 PHE A 231 TRP 0.011 0.002 TRP A 266 HIS 0.007 0.001 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 (10881) covalent geometry : angle 0.69865 / 0.37 (15424) hydrogen bonds : bond 0.06449 / 4.24 ( 589) hydrogen bonds : angle 5.23461 / 3.58 ( 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 260 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7491 (m-40) cc_final: 0.6933 (m-40) REVERT: A 165 ARG cc_start: 0.8321 (mtp85) cc_final: 0.7831 (mtt180) REVERT: A 212 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8166 (ttp80) REVERT: A 263 TYR cc_start: 0.6491 (m-80) cc_final: 0.5633 (t80) REVERT: A 270 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7225 (ttpt) REVERT: A 272 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7395 (pp) REVERT: B 103 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7992 (mm-40) REVERT: D 37 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7323 (mmmt) REVERT: E 69 TYR cc_start: 0.8052 (m-80) cc_final: 0.7822 (m-10) REVERT: F 47 LYS cc_start: 0.8355 (ttmm) cc_final: 0.8078 (mttm) outliers start: 38 outliers final: 24 residues processed: 245 average time/residue: 0.1216 time to fit residues: 38.7411 Evaluate side-chains 241 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 272 LEU 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 B residue 122 ARG 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 75 LEU 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 Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR 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: 0.4980 chunk 60 optimal weight: 2.9990 chunk 72 optimal weight: 0.0670 chunk 45 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** E 52 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.176995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.134946 restraints weight = 15526.837| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.67 r_work: 0.3548 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5141 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= 0.193 Angle : 0.697 9.912 15424 Z= 0.371 Chirality : 0.041 0.213 1832 Planarity : 0.007 0.136 1399 Dihedral : 23.824 174.424 3354 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 26.06 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.51 % Favored : 91.70 % Rotamer: Outliers : 4.56 % Allowed : 25.50 % Favored : 69.93 % 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: -1.12 (0.27), residues: 879 helix: -0.08 (0.19), residues: 669 sheet: -1.56 (1.20), residues: 26 loop : -2.74 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 19 TYR 0.039 0.003 TYR A 107 PHE 0.028 0.002 PHE A 231 TRP 0.014 0.002 TRP F 116 HIS 0.012 0.001 HIS F 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (10881) covalent geometry : angle 0.69740 / 0.37 (15424) hydrogen bonds : bond 0.06062 / 3.99 ( 589) hydrogen bonds : angle 5.16095 / 3.54 ( 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 259 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7451 (m-40) cc_final: 0.6861 (m-40) REVERT: A 125 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.7027 (mm-30) REVERT: A 165 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7770 (mtt180) REVERT: A 272 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7385 (pp) REVERT: B 11 TYR cc_start: 0.7435 (t80) cc_final: 0.7191 (t80) REVERT: B 103 GLN cc_start: 0.8226 (mm-40) cc_final: 0.8007 (mm-40) REVERT: C 98 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: D 19 ARG cc_start: 0.7903 (mmt-90) cc_final: 0.7599 (mmp80) REVERT: D 37 LYS cc_start: 0.7984 (mtpp) cc_final: 0.7283 (mmmt) REVERT: F 47 LYS cc_start: 0.8359 (ttmm) cc_final: 0.8102 (mttm) outliers start: 34 outliers final: 22 residues processed: 248 average time/residue: 0.1258 time to fit residues: 40.7491 Evaluate side-chains 237 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 125 GLU 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 230 VAL Chi-restraints excluded: chain A residue 272 LEU 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 B residue 122 ARG 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 75 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.0010 chunk 94 optimal weight: 40.0000 chunk 66 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 87 optimal weight: 40.0000 chunk 59 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 11 optimal weight: 0.3980 chunk 10 optimal weight: 0.2980 overall best weight: 0.3986 ------------------------------------------------------------------------------- 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 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 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 = 0.4285 r_free = 0.4285 target = 0.178341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.137658 restraints weight = 15518.470| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.62 r_work: 0.3574 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5406 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= 0.182 Angle : 0.677 9.822 15424 Z= 0.361 Chirality : 0.040 0.220 1832 Planarity : 0.007 0.125 1399 Dihedral : 23.698 174.565 3351 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 26.01 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.17 % Favored : 92.04 % Rotamer: Outliers : 3.49 % Allowed : 26.98 % Favored : 69.53 % 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: -1.07 (0.28), residues: 879 helix: -0.10 (0.19), residues: 662 sheet: -1.23 (1.24), residues: 26 loop : -2.45 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 19 TYR 0.029 0.003 TYR A 107 PHE 0.026 0.002 PHE A 231 TRP 0.015 0.002 TRP F 116 HIS 0.010 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (10881) covalent geometry : angle 0.67746 / 0.36 (15424) hydrogen bonds : bond 0.05878 / 3.88 ( 589) hydrogen bonds : angle 5.07960 / 3.48 ( 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 245 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7341 (m-40) cc_final: 0.6788 (m-40) REVERT: A 165 ARG cc_start: 0.8198 (mtp85) cc_final: 0.7774 (mtt180) REVERT: A 198 ASP cc_start: 0.7938 (m-30) cc_final: 0.7696 (m-30) REVERT: A 263 TYR cc_start: 0.6246 (m-80) cc_final: 0.5570 (t80) REVERT: A 272 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7307 (pp) REVERT: B 82 LEU cc_start: 0.8620 (mt) cc_final: 0.8378 (mp) REVERT: C 42 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7856 (ttp-170) REVERT: C 97 HIS cc_start: 0.7690 (t-90) cc_final: 0.7447 (t-90) REVERT: D 19 ARG cc_start: 0.7740 (mmt-90) cc_final: 0.7508 (mmp80) REVERT: D 37 LYS cc_start: 0.7915 (mtpp) cc_final: 0.7285 (mmmt) REVERT: E 69 TYR cc_start: 0.8000 (m-10) cc_final: 0.7794 (m-10) REVERT: F 20 TYR cc_start: 0.8332 (t80) cc_final: 0.8129 (t80) REVERT: F 47 LYS cc_start: 0.8347 (ttmm) cc_final: 0.8087 (mttm) outliers start: 26 outliers final: 22 residues processed: 235 average time/residue: 0.1195 time to fit residues: 37.4002 Evaluate side-chains 233 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 272 LEU 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 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 75 LEU 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 54 GLU 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: 40.0000 chunk 89 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 10 optimal weight: 0.0000 chunk 50 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 0.0770 chunk 44 optimal weight: 0.0670 overall best weight: 0.2680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 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 = 0.4304 r_free = 0.4304 target = 0.179970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.140441 restraints weight = 15502.753| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.59 r_work: 0.3616 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.5709 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= 0.172 Angle : 0.678 11.068 15424 Z= 0.361 Chirality : 0.039 0.223 1832 Planarity : 0.007 0.123 1399 Dihedral : 23.592 175.906 3349 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 25.70 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.17 % Favored : 92.15 % Rotamer: Outliers : 4.03 % Allowed : 27.38 % Favored : 68.59 % 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: -1.02 (0.28), residues: 879 helix: -0.09 (0.19), residues: 661 sheet: -0.98 (1.30), residues: 26 loop : -2.36 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 42 TYR 0.027 0.003 TYR F 20 PHE 0.025 0.002 PHE A 231 TRP 0.015 0.002 TRP A 266 HIS 0.007 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (10881) covalent geometry : angle 0.67767 / 0.36 (15424) hydrogen bonds : bond 0.05715 / 3.76 ( 589) hydrogen bonds : angle 5.04141 / 3.46 ( 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 255 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7401 (m-40) cc_final: 0.6841 (m-40) REVERT: A 31 ARG cc_start: 0.7690 (ttt-90) cc_final: 0.7480 (ttm-80) REVERT: A 165 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7787 (mtt180) REVERT: A 224 PRO cc_start: 0.6598 (Cg_exo) cc_final: 0.6317 (Cg_endo) REVERT: A 263 TYR cc_start: 0.6181 (m-80) cc_final: 0.5461 (t80) REVERT: A 270 LYS cc_start: 0.7742 (ttpp) cc_final: 0.5720 (ttmt) REVERT: A 272 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7309 (pp) REVERT: B 11 TYR cc_start: 0.7160 (t80) cc_final: 0.6845 (t80) REVERT: B 82 LEU cc_start: 0.8502 (mt) cc_final: 0.8293 (mp) REVERT: C 42 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7823 (ttp-170) REVERT: C 97 HIS cc_start: 0.7537 (t-90) cc_final: 0.7234 (t-90) REVERT: D 37 LYS cc_start: 0.7743 (mtpp) cc_final: 0.7232 (mmmt) REVERT: D 53 VAL cc_start: 0.8031 (m) cc_final: 0.7828 (t) REVERT: F 20 TYR cc_start: 0.8426 (t80) cc_final: 0.8118 (t80) REVERT: F 47 LYS cc_start: 0.8331 (ttmm) cc_final: 0.8068 (mttm) outliers start: 30 outliers final: 21 residues processed: 243 average time/residue: 0.1155 time to fit residues: 37.1817 Evaluate side-chains 231 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 272 LEU 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 97 HIS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain C residue 14 MET 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 D residue 121 ASN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE 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: 0.9990 chunk 88 optimal weight: 30.0000 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 87 optimal weight: 50.0000 chunk 64 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 92 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 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 = 0.4296 r_free = 0.4296 target = 0.179485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.139844 restraints weight = 15379.651| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.58 r_work: 0.3606 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.179 10881 Z= 0.268 Angle : 0.928 59.197 15424 Z= 0.524 Chirality : 0.046 0.983 1832 Planarity : 0.007 0.122 1399 Dihedral : 23.593 175.919 3347 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 30.35 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.28 % Favored : 91.92 % Rotamer: Outliers : 2.95 % Allowed : 28.32 % Favored : 68.72 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.04 (0.28), residues: 879 helix: -0.10 (0.19), residues: 661 sheet: -0.96 (1.30), residues: 26 loop : -2.37 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 19 TYR 0.024 0.003 TYR F 20 PHE 0.024 0.002 PHE A 231 TRP 0.014 0.002 TRP A 266 HIS 0.008 0.002 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.27 (10881) covalent geometry : angle 0.92802 / 0.52 (15424) hydrogen bonds : bond 0.05784 / 3.79 ( 589) hydrogen bonds : angle 5.07450 / 3.51 ( 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 230 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7382 (m-40) cc_final: 0.6847 (m-40) REVERT: A 31 ARG cc_start: 0.7660 (ttt-90) cc_final: 0.7457 (ttm-80) REVERT: A 107 TYR cc_start: 0.7362 (m-80) cc_final: 0.7101 (m-80) REVERT: A 165 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7796 (mtt180) REVERT: A 224 PRO cc_start: 0.6566 (Cg_exo) cc_final: 0.6292 (Cg_endo) REVERT: A 263 TYR cc_start: 0.6178 (m-80) cc_final: 0.5469 (t80) REVERT: A 270 LYS cc_start: 0.7739 (ttpp) cc_final: 0.5750 (ttmt) REVERT: A 272 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7315 (pp) REVERT: B 11 TYR cc_start: 0.7163 (t80) cc_final: 0.6845 (t80) REVERT: C 42 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7838 (ttp-170) REVERT: C 97 HIS cc_start: 0.7526 (t-90) cc_final: 0.7208 (t-90) REVERT: D 37 LYS cc_start: 0.7783 (mtpp) cc_final: 0.7258 (mmmt) REVERT: D 53 VAL cc_start: 0.8124 (m) cc_final: 0.7905 (t) REVERT: F 20 TYR cc_start: 0.8440 (t80) cc_final: 0.8116 (t80) REVERT: F 47 LYS cc_start: 0.8315 (ttmm) cc_final: 0.8079 (mttm) outliers start: 22 outliers final: 21 residues processed: 222 average time/residue: 0.1145 time to fit residues: 33.5797 Evaluate side-chains 229 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 272 LEU 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 97 HIS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain C residue 14 MET 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 75 LEU 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: 0.6980 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 41 optimal weight: 0.0470 chunk 74 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 50.0000 chunk 33 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 89 GLN ** 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 52 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 = 0.4296 r_free = 0.4296 target = 0.179456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.139662 restraints weight = 15608.171| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.61 r_work: 0.3600 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.179 10881 Z= 0.268 Angle : 0.928 59.197 15424 Z= 0.524 Chirality : 0.046 0.983 1832 Planarity : 0.007 0.122 1399 Dihedral : 23.593 175.919 3347 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 30.88 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.28 % Favored : 91.92 % Rotamer: Outliers : 2.95 % Allowed : 28.05 % Favored : 68.99 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.04 (0.28), residues: 879 helix: -0.10 (0.19), residues: 661 sheet: -0.96 (1.30), residues: 26 loop : -2.37 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 19 TYR 0.024 0.003 TYR F 20 PHE 0.024 0.002 PHE A 231 TRP 0.014 0.002 TRP A 266 HIS 0.008 0.002 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.27 (10881) covalent geometry : angle 0.92802 / 0.52 (15424) hydrogen bonds : bond 0.05784 / 3.79 ( 589) hydrogen bonds : angle 5.07450 / 3.51 ( 1616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2235.03 seconds wall clock time: 39 minutes 19.24 seconds (2359.24 seconds total)