Starting phenix.real_space_refine on Sat Aug 23 06:03:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubb_42081/08_2025/8ubb_42081.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubb_42081/08_2025/8ubb_42081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ubb_42081/08_2025/8ubb_42081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubb_42081/08_2025/8ubb_42081.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ubb_42081/08_2025/8ubb_42081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubb_42081/08_2025/8ubb_42081.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 148 5.49 5 S 36 5.16 5 C 6052 2.51 5 N 1862 2.21 5 O 2251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10349 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2690 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain: "B" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "C" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "D" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 868 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 876 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "F" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "G" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 289 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna3p': 12} Chain: "H" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'RNA': 13} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 8} Link IDs: {'rna3p': 12} Chain: "I" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2605 Classifications: {'RNA': 122} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 11, 'rna3p_pur': 51, 'rna3p_pyr': 48} Link IDs: {'rna2p': 23, 'rna3p': 98} Chain breaks: 2 Time building chain proxies: 2.10, per 1000 atoms: 0.20 Number of scatterers: 10349 At special positions: 0 Unit cell: (80, 99, 129, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 148 15.00 O 2251 8.00 N 1862 7.00 C 6052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 165.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.867A pdb=" N GLU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 80 through 91 Processing helix chain 'A' and resid 93 through 99 removed outlier: 3.783A pdb=" N ILE A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 183 through 203 removed outlier: 4.043A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 207 removed outlier: 4.397A pdb=" N GLN A 207 " --> pdb=" O GLU A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 207' Processing helix chain 'A' and resid 223 through 241 Processing helix chain 'A' and resid 259 through 263 removed outlier: 4.530A pdb=" N GLY A 262 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 289 Processing helix chain 'A' and resid 294 through 309 removed outlier: 3.893A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TRP A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.555A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 39 through 50 Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 64 through 88 Processing helix chain 'B' and resid 95 through 122 Processing helix chain 'C' and resid 12 through 34 removed outlier: 3.634A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 51 through 63 Processing helix chain 'C' and resid 64 through 88 Processing helix chain 'C' and resid 95 through 121 Processing helix chain 'D' and resid 14 through 34 Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 38 through 62 removed outlier: 3.756A pdb=" N VAL D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 Processing helix chain 'D' and resid 95 through 121 Processing helix chain 'E' and resid 13 through 32 removed outlier: 3.637A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 38 through 62 removed outlier: 4.083A pdb=" N GLY E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 86 removed outlier: 3.547A pdb=" N ASP E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 121 Processing helix chain 'F' and resid 14 through 34 removed outlier: 4.376A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Proline residue: F 29 - end of helix removed outlier: 3.534A pdb=" N ILE F 34 " --> pdb=" O ILE F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 64 through 87 Processing helix chain 'F' and resid 88 through 93 Proline residue: F 91 - end of helix No H-bonds generated for 'chain 'F' and resid 88 through 93' Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.211A pdb=" N LEU F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 213 removed outlier: 3.844A pdb=" N HIS A 133 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS A 248 " --> pdb=" O ASP A 138 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 0.87 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=" CB ARG B 122 " pdb=" CG ARG B 122 " ideal model delta sigma weight residual 1.520 1.412 0.108 3.00e-02 1.11e+03 1.29e+01 bond pdb=" CG1 ILE C 24 " pdb=" CD1 ILE C 24 " ideal model delta sigma weight residual 1.513 1.374 0.139 3.90e-02 6.57e+02 1.26e+01 bond pdb=" CG1 ILE F 24 " pdb=" CD1 ILE F 24 " ideal model delta sigma weight residual 1.513 1.378 0.135 3.90e-02 6.57e+02 1.21e+01 bond pdb=" CG1 ILE D 88 " pdb=" CD1 ILE D 88 " ideal model delta sigma weight residual 1.513 1.379 0.134 3.90e-02 6.57e+02 1.18e+01 bond pdb=" CB PRO C 91 " pdb=" CG PRO C 91 " ideal model delta sigma weight residual 1.492 1.664 -0.172 5.00e-02 4.00e+02 1.18e+01 ... (remaining 10876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 14711 2.60 - 5.20: 592 5.20 - 7.80: 99 7.80 - 10.39: 18 10.39 - 12.99: 4 Bond angle restraints: 15424 Sorted by residual: angle pdb=" C3' C I 104 " pdb=" O3' C I 104 " pdb=" P G I 105 " ideal model delta sigma weight residual 120.20 110.38 9.82 1.50e+00 4.44e-01 4.28e+01 angle pdb=" N GLN E 32 " pdb=" CA GLN E 32 " pdb=" C GLN E 32 " ideal model delta sigma weight residual 113.38 105.47 7.91 1.23e+00 6.61e-01 4.14e+01 angle pdb=" C ALA A 153 " pdb=" N MET A 154 " pdb=" CA MET A 154 " ideal model delta sigma weight residual 120.58 131.13 -10.55 1.71e+00 3.42e-01 3.81e+01 angle pdb=" C3' U I 3 " pdb=" O3' U I 3 " pdb=" P G I 4 " ideal model delta sigma weight residual 120.20 111.15 9.05 1.50e+00 4.44e-01 3.64e+01 angle pdb=" C3' A I 119 " pdb=" O3' A I 119 " pdb=" P U I 120 " ideal model delta sigma weight residual 120.20 111.28 8.92 1.50e+00 4.44e-01 3.54e+01 ... (remaining 15419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 5887 35.55 - 71.10: 771 71.10 - 106.65: 78 106.65 - 142.20: 4 142.20 - 177.75: 5 Dihedral angle restraints: 6745 sinusoidal: 4152 harmonic: 2593 Sorted by residual: dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual -128.00 46.57 -174.57 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C I 82 " pdb=" C1' C I 82 " pdb=" N1 C I 82 " pdb=" C2 C I 82 " ideal model delta sinusoidal sigma weight residual 232.00 76.28 155.72 1 1.70e+01 3.46e-03 6.35e+01 dihedral pdb=" C5' C I 20 " pdb=" C4' C I 20 " pdb=" C3' C I 20 " pdb=" O3' C I 20 " ideal model delta sinusoidal sigma weight residual 147.00 108.63 38.37 1 8.00e+00 1.56e-02 3.24e+01 ... (remaining 6742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1718 0.113 - 0.225: 95 0.225 - 0.338: 13 0.338 - 0.450: 4 0.450 - 0.563: 2 Chirality restraints: 1832 Sorted by residual: chirality pdb=" P U I 3 " pdb=" OP1 U I 3 " pdb=" OP2 U I 3 " pdb=" O5' U I 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.93e+00 chirality pdb=" P A I 81 " pdb=" OP1 A I 81 " pdb=" OP2 A I 81 " pdb=" O5' A I 81 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" P U I 120 " pdb=" OP1 U I 120 " pdb=" OP2 U I 120 " pdb=" O5' U I 120 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.91e+00 ... (remaining 1829 not shown) Planarity restraints: 1399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 90 " -0.087 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PRO C 91 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 70 " -0.064 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A 71 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 231 " -0.038 2.00e-02 2.50e+03 2.59e-02 1.18e+01 pdb=" CG PHE A 231 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 231 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 231 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 231 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 231 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 231 " -0.010 2.00e-02 2.50e+03 ... (remaining 1396 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1413 2.74 - 3.28: 11235 3.28 - 3.82: 23299 3.82 - 4.36: 28718 4.36 - 4.90: 40236 Nonbonded interactions: 104901 Sorted by model distance: nonbonded pdb=" OH TYR F 26 " pdb=" OG1 THR F 101 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR A 193 " pdb=" O LEU A 242 " model vdw 2.210 3.040 nonbonded pdb=" NE2 GLN E 98 " pdb=" O3' C I 17 " model vdw 2.251 3.120 nonbonded pdb=" O ARG A 31 " pdb=" OH TYR B 11 " model vdw 2.252 3.040 nonbonded pdb=" NE2 HIS A 202 " pdb=" O2' G I 129 " model vdw 2.260 3.120 ... (remaining 104896 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = chain 'D' selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.120 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 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= 0.439 Angle : 1.206 12.992 15424 Z= 0.653 Chirality : 0.064 0.563 1832 Planarity : 0.010 0.133 1399 Dihedral : 25.815 177.753 5073 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 41.97 Ramachandran Plot: Outliers : 3.64 % Allowed : 10.69 % Favored : 85.67 % Rotamer: Outliers : 20.00 % Allowed : 14.23 % Favored : 65.77 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.01040 (10881) covalent geometry : angle 1.20614 (15424) hydrogen bonds : bond 0.22640 ( 589) hydrogen bonds : angle 9.80307 ( 1616) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 265 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6566 (ppp) REVERT: A 3 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6702 (mttm) REVERT: A 33 TRP cc_start: 0.7820 (t-100) cc_final: 0.7283 (t60) REVERT: A 37 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8540 (tt0) REVERT: A 52 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: A 59 GLU cc_start: 0.8373 (mp0) cc_final: 0.8119 (pt0) REVERT: A 74 ARG cc_start: 0.5299 (OUTLIER) cc_final: 0.5073 (ptt180) REVERT: A 109 CYS cc_start: 0.8194 (m) cc_final: 0.7898 (t) REVERT: A 130 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7616 (mmm160) REVERT: A 154 MET cc_start: 0.8389 (mtt) cc_final: 0.8017 (mtt) REVERT: A 158 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8366 (mmmm) REVERT: A 172 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7987 (tt) REVERT: A 200 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7763 (tt) REVERT: A 203 ASP cc_start: 0.8292 (m-30) cc_final: 0.8089 (m-30) REVERT: A 214 MET cc_start: 0.8472 (tpp) cc_final: 0.8246 (mmm) REVERT: A 226 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: A 256 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7570 (mmm-85) REVERT: A 272 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7213 (mp) REVERT: B 14 MET cc_start: 0.8383 (mtt) cc_final: 0.7991 (mtp) REVERT: B 77 MET cc_start: 0.8611 (tpt) cc_final: 0.7986 (tpp) REVERT: C 14 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.6973 (ttp) REVERT: C 18 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8278 (tt0) REVERT: C 20 TYR cc_start: 0.8729 (t80) cc_final: 0.8526 (t80) REVERT: C 48 CYS cc_start: 0.8823 (t) cc_final: 0.8615 (t) REVERT: C 57 ILE cc_start: 0.8462 (mm) cc_final: 0.8200 (mp) REVERT: D 18 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7520 (tp30) REVERT: D 19 ARG cc_start: 0.8157 (mmt-90) cc_final: 0.7943 (mmt-90) REVERT: D 52 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8125 (tp40) REVERT: D 62 SER cc_start: 0.6289 (OUTLIER) cc_final: 0.6070 (p) REVERT: D 67 LYS cc_start: 0.8107 (mptt) cc_final: 0.7895 (mmmt) REVERT: D 72 ASP cc_start: 0.8153 (t0) cc_final: 0.7931 (t0) REVERT: D 75 LEU cc_start: 0.8342 (mt) cc_final: 0.7994 (mt) REVERT: D 95 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7374 (p) REVERT: D 103 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8288 (mm-40) REVERT: D 108 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6705 (mt-10) REVERT: E 18 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8156 (tp30) REVERT: E 43 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: E 52 GLN cc_start: 0.8192 (tm-30) cc_final: 0.6689 (tm-30) REVERT: E 69 TYR cc_start: 0.8132 (m-10) cc_final: 0.7925 (m-80) REVERT: E 111 ARG cc_start: 0.8426 (mtm110) cc_final: 0.8102 (ttp-110) REVERT: F 14 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.6751 (tmm) REVERT: F 19 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7857 (mmm160) REVERT: F 20 TYR cc_start: 0.8393 (t80) cc_final: 0.7979 (t80) REVERT: F 25 SER cc_start: 0.9279 (t) cc_final: 0.8998 (p) REVERT: F 54 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: F 55 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7197 (mp) REVERT: F 92 HIS cc_start: 0.6308 (m-70) cc_final: 0.6085 (m-70) outliers start: 149 outliers final: 33 residues processed: 356 average time/residue: 0.1298 time to fit residues: 58.6330 Evaluate side-chains 272 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 36 ARG Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 116 HIS A 259 ASN A 290 HIS A 306 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN C 121 ASN D 13 GLN E 32 GLN E 52 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN F 97 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.176080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133971 restraints weight = 15335.302| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.60 r_work: 0.3529 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 10881 Z= 0.249 Angle : 0.832 10.157 15424 Z= 0.426 Chirality : 0.044 0.233 1832 Planarity : 0.008 0.121 1399 Dihedral : 25.078 176.961 3470 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 29.88 Ramachandran Plot: Outliers : 1.02 % Allowed : 8.42 % Favored : 90.56 % Rotamer: Outliers : 8.86 % Allowed : 19.46 % Favored : 71.68 % 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 aren not related in a simple way. whole: -2.29 (0.26), residues: 879 helix: -0.76 (0.19), residues: 661 sheet: -3.19 (1.05), residues: 26 loop : -3.54 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 111 TYR 0.023 0.002 TYR C 28 PHE 0.040 0.003 PHE A 231 TRP 0.015 0.002 TRP E 116 HIS 0.013 0.002 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00552 (10881) covalent geometry : angle 0.83153 (15424) hydrogen bonds : bond 0.07549 ( 589) hydrogen bonds : angle 5.71092 ( 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 307 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 241 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7429 (m-40) cc_final: 0.7120 (m-40) REVERT: A 165 ARG cc_start: 0.8296 (mtp85) cc_final: 0.7971 (mtt180) REVERT: A 208 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.5678 (mtt90) REVERT: A 226 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: A 270 LYS cc_start: 0.7455 (ttpt) cc_final: 0.6823 (ttpp) REVERT: A 272 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7011 (pp) REVERT: B 69 TYR cc_start: 0.8089 (m-80) cc_final: 0.7837 (m-80) REVERT: D 53 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8578 (m) REVERT: E 42 ARG cc_start: 0.8640 (ttm-80) cc_final: 0.8423 (ttp-170) REVERT: F 14 MET cc_start: 0.6367 (mmp) cc_final: 0.6158 (tmm) REVERT: F 15 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6522 (pp) REVERT: F 47 LYS cc_start: 0.8361 (ttmm) cc_final: 0.8016 (mttm) outliers start: 66 outliers final: 25 residues processed: 278 average time/residue: 0.1186 time to fit residues: 43.0896 Evaluate side-chains 233 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 208 ARG 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 276 SER Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D 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 85 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 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 113 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 62 optimal weight: 0.2980 chunk 67 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 77 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** E 52 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.177392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136430 restraints weight = 15674.171| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.66 r_work: 0.3563 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 10881 Z= 0.197 Angle : 0.736 13.469 15424 Z= 0.376 Chirality : 0.042 0.265 1832 Planarity : 0.008 0.158 1399 Dihedral : 24.361 173.256 3371 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 26.38 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.42 % Favored : 90.67 % Rotamer: Outliers : 5.77 % Allowed : 21.61 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.27), residues: 879 helix: -0.22 (0.19), residues: 666 sheet: -2.51 (1.05), residues: 26 loop : -3.08 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 111 TYR 0.018 0.002 TYR F 28 PHE 0.032 0.003 PHE A 231 TRP 0.011 0.002 TRP F 116 HIS 0.013 0.002 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00439 (10881) covalent geometry : angle 0.73557 (15424) hydrogen bonds : bond 0.05971 ( 589) hydrogen bonds : angle 5.21101 ( 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 269 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.7058 (m-80) cc_final: 0.6851 (m-80) REVERT: A 165 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7804 (mtt180) REVERT: A 263 TYR cc_start: 0.6789 (m-80) cc_final: 0.6552 (m-80) REVERT: A 272 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7151 (pp) REVERT: B 69 TYR cc_start: 0.7832 (m-80) cc_final: 0.7597 (m-80) REVERT: B 103 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8067 (mm-40) REVERT: D 18 GLU cc_start: 0.8077 (tp30) cc_final: 0.7834 (tp30) REVERT: D 19 ARG cc_start: 0.7817 (mmt-90) cc_final: 0.7523 (mmp80) REVERT: F 47 LYS cc_start: 0.8322 (ttmm) cc_final: 0.7957 (mttm) outliers start: 43 outliers final: 25 residues processed: 252 average time/residue: 0.1156 time to fit residues: 38.1779 Evaluate side-chains 228 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 227 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 44 optimal weight: 0.1980 chunk 48 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 68 optimal weight: 0.1980 chunk 94 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 187 GLN B 32 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.178138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.137428 restraints weight = 15686.062| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.65 r_work: 0.3582 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 10881 Z= 0.186 Angle : 0.697 9.834 15424 Z= 0.354 Chirality : 0.039 0.199 1832 Planarity : 0.007 0.133 1399 Dihedral : 23.917 173.644 3361 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 24.39 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.17 % Favored : 92.15 % Rotamer: Outliers : 5.23 % Allowed : 22.68 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.28), residues: 879 helix: 0.09 (0.19), residues: 665 sheet: -1.93 (1.12), residues: 26 loop : -2.76 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 119 TYR 0.022 0.002 TYR C 28 PHE 0.028 0.002 PHE A 231 TRP 0.015 0.002 TRP D 116 HIS 0.007 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00422 (10881) covalent geometry : angle 0.69669 (15424) hydrogen bonds : bond 0.05631 ( 589) hydrogen bonds : angle 5.02694 ( 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 269 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7261 (m-40) cc_final: 0.6606 (m-40) REVERT: A 107 TYR cc_start: 0.7167 (m-80) cc_final: 0.6941 (m-80) REVERT: A 165 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7859 (mtt180) REVERT: A 224 PRO cc_start: 0.6636 (Cg_exo) cc_final: 0.6410 (Cg_endo) REVERT: A 272 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7427 (pp) REVERT: B 69 TYR cc_start: 0.7759 (m-10) cc_final: 0.7525 (m-80) REVERT: D 18 GLU cc_start: 0.7856 (tp30) cc_final: 0.7634 (tp30) REVERT: D 19 ARG cc_start: 0.7746 (mmt-90) cc_final: 0.7507 (mmm160) REVERT: D 37 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7314 (mmmt) REVERT: D 47 LYS cc_start: 0.8322 (mttm) cc_final: 0.7967 (mmtt) REVERT: F 47 LYS cc_start: 0.8369 (ttmm) cc_final: 0.8082 (mttm) outliers start: 39 outliers final: 26 residues processed: 250 average time/residue: 0.1137 time to fit residues: 37.1840 Evaluate side-chains 240 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 14 THR 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 227 LEU 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 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 100 GLU 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 E residue 16 ILE 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 16 ILE Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 95 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 0.0570 chunk 89 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 0.0970 chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 38 HIS ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.179363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.138889 restraints weight = 15718.589| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.63 r_work: 0.3579 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.5464 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= 0.184 Angle : 0.689 9.217 15424 Z= 0.348 Chirality : 0.039 0.195 1832 Planarity : 0.007 0.123 1399 Dihedral : 23.638 171.152 3359 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.74 % Favored : 91.58 % Rotamer: Outliers : 4.16 % Allowed : 24.97 % Favored : 70.87 % 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 aren not related in a simple way. whole: -0.80 (0.28), residues: 879 helix: 0.15 (0.19), residues: 663 sheet: -1.39 (1.21), residues: 26 loop : -2.53 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 36 TYR 0.024 0.002 TYR F 20 PHE 0.027 0.002 PHE A 231 TRP 0.019 0.002 TRP D 116 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00421 (10881) covalent geometry : angle 0.68886 (15424) hydrogen bonds : bond 0.05455 ( 589) hydrogen bonds : angle 4.91045 ( 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 253 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7193 (m-40) cc_final: 0.6552 (m-40) REVERT: A 224 PRO cc_start: 0.6611 (Cg_exo) cc_final: 0.6339 (Cg_endo) REVERT: B 11 TYR cc_start: 0.7210 (t80) cc_final: 0.6943 (t80) REVERT: C 20 TYR cc_start: 0.8264 (t80) cc_final: 0.7970 (t80) REVERT: D 18 GLU cc_start: 0.7854 (tp30) cc_final: 0.7587 (tp30) REVERT: D 19 ARG cc_start: 0.7724 (mmt-90) cc_final: 0.7465 (mmm160) REVERT: D 37 LYS cc_start: 0.7924 (mtpp) cc_final: 0.7348 (mmmt) REVERT: D 47 LYS cc_start: 0.8386 (mttm) cc_final: 0.8082 (mmtt) REVERT: D 79 ARG cc_start: 0.8173 (ttm110) cc_final: 0.7611 (mtt180) REVERT: E 47 LYS cc_start: 0.8189 (mttp) cc_final: 0.7869 (mttm) REVERT: F 47 LYS cc_start: 0.8345 (ttmm) cc_final: 0.8111 (mttm) outliers start: 31 outliers final: 22 residues processed: 240 average time/residue: 0.1219 time to fit residues: 38.0756 Evaluate side-chains 234 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 202 HIS Chi-restraints excluded: chain A residue 227 LEU 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 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 100 GLU 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 E residue 16 ILE 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 16 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 83 optimal weight: 0.4980 chunk 88 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 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 = 0.4247 r_free = 0.4247 target = 0.175342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133526 restraints weight = 15741.624| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.64 r_work: 0.3504 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 10881 Z= 0.262 Angle : 0.728 10.316 15424 Z= 0.367 Chirality : 0.040 0.192 1832 Planarity : 0.007 0.123 1399 Dihedral : 23.621 177.093 3353 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 25.38 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.28 % Favored : 92.04 % 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 aren not related in a simple way. whole: -0.80 (0.28), residues: 879 helix: 0.12 (0.19), residues: 664 sheet: -1.41 (1.20), residues: 26 loop : -2.43 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 36 TYR 0.026 0.003 TYR C 28 PHE 0.029 0.003 PHE A 231 TRP 0.012 0.002 TRP A 15 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00605 (10881) covalent geometry : angle 0.72845 (15424) hydrogen bonds : bond 0.05865 ( 589) hydrogen bonds : angle 5.06804 ( 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 251 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.6092 (mtt-85) REVERT: A 272 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7549 (pp) REVERT: D 18 GLU cc_start: 0.7873 (tp30) cc_final: 0.7640 (tp30) REVERT: D 19 ARG cc_start: 0.7740 (mmt-90) cc_final: 0.7474 (mmm160) REVERT: D 47 LYS cc_start: 0.8526 (mttm) cc_final: 0.8122 (mmtt) REVERT: D 79 ARG cc_start: 0.8378 (ttm110) cc_final: 0.7953 (mtm-85) REVERT: E 52 GLN cc_start: 0.7460 (tm-30) cc_final: 0.6892 (tm-30) REVERT: F 47 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8197 (mttm) outliers start: 38 outliers final: 23 residues processed: 237 average time/residue: 0.1234 time to fit residues: 38.6459 Evaluate side-chains 231 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 271 LEU 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 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain E residue 16 ILE 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 65 VAL Chi-restraints excluded: chain F residue 66 SER 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: 0.6980 chunk 41 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 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 32 GLN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.177910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.137113 restraints weight = 15593.444| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.63 r_work: 0.3558 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 10881 Z= 0.201 Angle : 0.696 10.921 15424 Z= 0.353 Chirality : 0.039 0.200 1832 Planarity : 0.006 0.114 1399 Dihedral : 23.566 178.351 3350 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 24.65 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.05 % Favored : 92.26 % Rotamer: Outliers : 4.70 % Allowed : 23.36 % Favored : 71.95 % 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 aren not related in a simple way. whole: -0.77 (0.28), residues: 879 helix: 0.16 (0.19), residues: 663 sheet: 0.90 (1.54), residues: 14 loop : -2.68 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 36 TYR 0.021 0.002 TYR C 28 PHE 0.026 0.002 PHE A 231 TRP 0.014 0.002 TRP A 210 HIS 0.008 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00463 (10881) covalent geometry : angle 0.69584 (15424) hydrogen bonds : bond 0.05552 ( 589) hydrogen bonds : angle 5.01213 ( 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 255 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 0.203 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 272 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7371 (pp) REVERT: C 20 TYR cc_start: 0.8325 (t80) cc_final: 0.8055 (t80) REVERT: D 18 GLU cc_start: 0.7905 (tp30) cc_final: 0.7660 (tp30) REVERT: D 19 ARG cc_start: 0.7647 (mmt-90) cc_final: 0.7429 (mmm160) REVERT: D 37 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7547 (mmmt) REVERT: D 47 LYS cc_start: 0.8419 (mttm) cc_final: 0.8096 (mmtt) REVERT: D 79 ARG cc_start: 0.8242 (ttm110) cc_final: 0.7670 (mtt180) REVERT: E 52 GLN cc_start: 0.7242 (tm-30) cc_final: 0.6777 (tm-30) REVERT: F 47 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8197 (mttm) outliers start: 35 outliers final: 23 residues processed: 241 average time/residue: 0.1197 time to fit residues: 38.0149 Evaluate side-chains 236 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG 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 271 LEU 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 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 100 GLU 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 E residue 16 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 66 optimal weight: 0.0060 chunk 67 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 87 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.180222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.140253 restraints weight = 15668.413| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.62 r_work: 0.3605 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 10881 Z= 0.177 Angle : 0.714 18.895 15424 Z= 0.355 Chirality : 0.039 0.238 1832 Planarity : 0.008 0.175 1399 Dihedral : 23.460 179.147 3350 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.83 % Favored : 92.49 % Rotamer: Outliers : 3.89 % Allowed : 24.56 % 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 aren not related in a simple way. whole: -0.68 (0.28), residues: 879 helix: 0.20 (0.19), residues: 661 sheet: 1.37 (1.59), residues: 14 loop : -2.53 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 22 TYR 0.029 0.002 TYR F 20 PHE 0.024 0.002 PHE A 231 TRP 0.018 0.002 TRP A 210 HIS 0.008 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00403 (10881) covalent geometry : angle 0.71425 (15424) hydrogen bonds : bond 0.05330 ( 589) hydrogen bonds : angle 4.93574 ( 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 246 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 PRO cc_start: 0.6631 (Cg_exo) cc_final: 0.6381 (Cg_endo) REVERT: B 11 TYR cc_start: 0.7188 (t80) cc_final: 0.6824 (t80) REVERT: C 77 MET cc_start: 0.8448 (tpt) cc_final: 0.7770 (tpp) REVERT: D 18 GLU cc_start: 0.7858 (tp30) cc_final: 0.7549 (tp30) REVERT: D 37 LYS cc_start: 0.7691 (mtpp) cc_final: 0.7277 (mmmt) REVERT: D 47 LYS cc_start: 0.8319 (mttm) cc_final: 0.7975 (mmtt) REVERT: D 79 ARG cc_start: 0.8222 (ttm110) cc_final: 0.7690 (mtt180) REVERT: E 47 LYS cc_start: 0.8139 (mttp) cc_final: 0.7752 (mttm) REVERT: F 19 ARG cc_start: 0.7943 (mtp85) cc_final: 0.7739 (mmm-85) REVERT: F 47 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8158 (mttm) outliers start: 29 outliers final: 21 residues processed: 233 average time/residue: 0.1298 time to fit residues: 39.5359 Evaluate side-chains 225 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 271 LEU 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 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 95 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 50 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN B 32 GLN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.180126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140049 restraints weight = 15603.212| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.64 r_work: 0.3597 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.6349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10881 Z= 0.194 Angle : 0.734 17.019 15424 Z= 0.366 Chirality : 0.040 0.253 1832 Planarity : 0.007 0.167 1399 Dihedral : 23.358 179.584 3350 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 25.33 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.83 % Favored : 92.49 % Rotamer: Outliers : 3.76 % Allowed : 24.56 % Favored : 71.68 % 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 aren not related in a simple way. whole: -0.70 (0.28), residues: 879 helix: 0.18 (0.19), residues: 659 sheet: 1.36 (1.54), residues: 14 loop : -2.51 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 233 TYR 0.023 0.002 TYR A 107 PHE 0.026 0.002 PHE A 231 TRP 0.023 0.002 TRP A 15 HIS 0.012 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00449 (10881) covalent geometry : angle 0.73356 (15424) hydrogen bonds : bond 0.05468 ( 589) hydrogen bonds : angle 4.97639 ( 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 245 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 TYR cc_start: 0.7255 (t80) cc_final: 0.7004 (t80) REVERT: B 43 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7307 (mt-10) REVERT: B 122 ARG cc_start: 0.7252 (mtt90) cc_final: 0.6862 (mpp80) REVERT: C 42 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7702 (ttp-170) REVERT: C 77 MET cc_start: 0.8450 (tpt) cc_final: 0.7753 (tpp) REVERT: D 18 GLU cc_start: 0.7871 (tp30) cc_final: 0.7613 (tp30) REVERT: D 37 LYS cc_start: 0.7609 (mtpp) cc_final: 0.7235 (mmmt) REVERT: D 47 LYS cc_start: 0.8353 (mttm) cc_final: 0.8107 (mmtt) REVERT: D 79 ARG cc_start: 0.8205 (ttm110) cc_final: 0.7684 (mtt180) REVERT: F 19 ARG cc_start: 0.7880 (mtp85) cc_final: 0.7673 (mtp85) REVERT: F 47 LYS cc_start: 0.8375 (ttmm) cc_final: 0.8138 (mttm) outliers start: 28 outliers final: 20 residues processed: 231 average time/residue: 0.1316 time to fit residues: 39.5776 Evaluate side-chains 224 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 271 LEU 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 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 50 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: 0.5980 chunk 88 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 83 optimal weight: 0.0270 chunk 87 optimal weight: 20.0000 chunk 64 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 HIS ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.181098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.141429 restraints weight = 15529.307| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.60 r_work: 0.3617 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10881 Z= 0.192 Angle : 0.737 15.920 15424 Z= 0.371 Chirality : 0.040 0.264 1832 Planarity : 0.007 0.162 1399 Dihedral : 23.234 178.804 3349 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 24.81 Ramachandran Plot: Outliers : 0.80 % Allowed : 6.48 % Favored : 92.72 % Rotamer: Outliers : 3.22 % Allowed : 25.50 % Favored : 71.28 % 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 aren not related in a simple way. whole: -0.69 (0.28), residues: 879 helix: 0.18 (0.20), residues: 657 sheet: 1.60 (1.53), residues: 14 loop : -2.46 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 79 TYR 0.030 0.003 TYR A 107 PHE 0.024 0.002 PHE A 231 TRP 0.022 0.002 TRP A 210 HIS 0.009 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00444 (10881) covalent geometry : angle 0.73654 (15424) hydrogen bonds : bond 0.05413 ( 589) hydrogen bonds : angle 5.00008 ( 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 239 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 THR cc_start: 0.8591 (p) cc_final: 0.8225 (t) REVERT: A 198 ASP cc_start: 0.7426 (m-30) cc_final: 0.7010 (m-30) REVERT: B 11 TYR cc_start: 0.7230 (t80) cc_final: 0.6916 (t80) REVERT: B 122 ARG cc_start: 0.7244 (mtt90) cc_final: 0.6852 (mpp80) REVERT: C 42 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7677 (ttp-170) REVERT: C 77 MET cc_start: 0.8485 (tpt) cc_final: 0.7786 (tpp) REVERT: D 18 GLU cc_start: 0.7858 (tp30) cc_final: 0.7564 (tp30) REVERT: D 37 LYS cc_start: 0.7565 (mtpp) cc_final: 0.7161 (mmmt) REVERT: D 47 LYS cc_start: 0.8346 (mttm) cc_final: 0.8123 (mmtt) REVERT: D 79 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7618 (mtt180) REVERT: E 108 GLU cc_start: 0.5864 (pt0) cc_final: 0.5541 (pt0) REVERT: F 47 LYS cc_start: 0.8410 (ttmm) cc_final: 0.8186 (mttm) outliers start: 24 outliers final: 19 residues processed: 225 average time/residue: 0.1381 time to fit residues: 40.1955 Evaluate side-chains 221 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 271 LEU 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 C residue 14 MET Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 50 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 45 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 0.0050 chunk 74 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 87 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.181932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.142849 restraints weight = 15776.132| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.62 r_work: 0.3630 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.6843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10881 Z= 0.187 Angle : 0.724 12.524 15424 Z= 0.365 Chirality : 0.040 0.272 1832 Planarity : 0.007 0.147 1399 Dihedral : 23.115 177.896 3349 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 23.50 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.60 % Favored : 92.72 % Rotamer: Outliers : 2.68 % Allowed : 25.77 % 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 aren not related in a simple way. whole: -0.63 (0.28), residues: 879 helix: 0.21 (0.20), residues: 658 sheet: 1.87 (1.51), residues: 14 loop : -2.41 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 22 TYR 0.027 0.002 TYR A 105 PHE 0.021 0.002 PHE A 231 TRP 0.016 0.002 TRP A 15 HIS 0.016 0.002 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00435 (10881) covalent geometry : angle 0.72355 (15424) hydrogen bonds : bond 0.05389 ( 589) hydrogen bonds : angle 5.02732 ( 1616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2353.34 seconds wall clock time: 41 minutes 37.52 seconds (2497.52 seconds total)