Starting phenix.real_space_refine on Thu May 1 02:46:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubb_42081/05_2025/8ubb_42081.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubb_42081/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ubb_42081/05_2025/8ubb_42081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubb_42081/05_2025/8ubb_42081.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubb_42081/05_2025/8ubb_42081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubb_42081/05_2025/8ubb_42081.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 7.44, per 1000 atoms: 0.72 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: 2.70 Conformation dependent library (CDL) restraints added in 931.5 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: 4.50 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: 3.54 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1685 1.33 - 1.45: 3592 1.45 - 1.57: 5249 1.57 - 1.69: 294 1.69 - 1.81: 61 Bond restraints: 10881 Sorted by residual: bond pdb=" 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: 2.550 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 31.360 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.024 0.005 TRP D 81 HIS 0.015 0.003 HIS E 38 PHE 0.054 0.006 PHE A 231 TYR 0.026 0.004 TYR A 41 ARG 0.014 0.001 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.22640 ( 589) hydrogen bonds : angle 9.80307 ( 1616) covalent geometry : bond 0.01040 (10881) covalent geometry : angle 1.20614 (15424) *********************** 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 : 0.922 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: A 1 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6612 (ppp) REVERT: A 3 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6719 (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: 0.7899 (t) REVERT: A 123 GLN cc_start: 0.7862 (tt0) cc_final: 0.7647 (tt0) 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: 0.8367 (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: 0.7762 (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: 0.8245 (mmm) REVERT: A 226 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: A 256 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7570 (mmm-85) REVERT: A 270 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8152 (ttpp) REVERT: A 272 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7202 (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: 0.7987 (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: 0.8289 (tt0) REVERT: C 20 TYR cc_start: 0.8729 (t80) cc_final: 0.8527 (t80) REVERT: C 48 CYS cc_start: 0.8823 (t) cc_final: 0.8613 (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 38 HIS cc_start: 0.8698 (m-70) cc_final: 0.7821 (m-70) 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: 0.6069 (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: 0.7994 (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: 0.7640 (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: 0.6752 (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: 0.7749 (tm-30) REVERT: F 55 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7198 (mp) REVERT: F 92 HIS cc_start: 0.6308 (m-70) cc_final: 0.5962 (m90) outliers start: 149 outliers final: 33 residues processed: 356 average time/residue: 0.3307 time to fit residues: 149.1387 Evaluate side-chains 271 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 214 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 85 optimal weight: 0.4980 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 87 GLN A 290 HIS A 306 HIS ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN C 92 HIS C 121 ASN D 13 GLN E 32 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN F 97 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.177035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.135787 restraints weight = 15321.573| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.58 r_work: 0.3547 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 10881 Z= 0.238 Angle : 0.820 9.577 15424 Z= 0.420 Chirality : 0.043 0.233 1832 Planarity : 0.008 0.123 1399 Dihedral : 24.948 173.756 3470 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 28.52 Ramachandran Plot: Outliers : 1.02 % Allowed : 7.74 % Favored : 91.24 % Rotamer: Outliers : 8.86 % Allowed : 18.93 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.27), residues: 879 helix: -0.61 (0.19), residues: 658 sheet: -3.02 (1.07), residues: 26 loop : -3.37 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 116 HIS 0.010 0.002 HIS C 92 PHE 0.040 0.003 PHE A 231 TYR 0.020 0.002 TYR C 28 ARG 0.007 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.06758 ( 589) hydrogen bonds : angle 5.58672 ( 1616) covalent geometry : bond 0.00540 (10881) covalent geometry : angle 0.81981 (15424) *********************** 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 304 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 238 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7188 (mmtp) REVERT: A 7 ASN cc_start: 0.7338 (OUTLIER) cc_final: 0.6743 (m-40) REVERT: A 115 THR cc_start: 0.9009 (m) cc_final: 0.8621 (p) REVERT: A 165 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7942 (mtt180) REVERT: A 272 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7100 (pp) REVERT: B 22 ARG cc_start: 0.8282 (mtm110) cc_final: 0.7798 (mtm110) REVERT: B 69 TYR cc_start: 0.7950 (m-80) cc_final: 0.7720 (m-80) REVERT: D 54 GLU cc_start: 0.7619 (tp30) cc_final: 0.7396 (tp30) REVERT: E 42 ARG cc_start: 0.8570 (ttm-80) cc_final: 0.8366 (ttp-170) REVERT: F 15 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6601 (pp) REVERT: F 20 TYR cc_start: 0.8415 (t80) cc_final: 0.8133 (t80) REVERT: F 47 LYS cc_start: 0.8375 (ttmm) cc_final: 0.8006 (mttm) outliers start: 66 outliers final: 23 residues processed: 276 average time/residue: 0.3568 time to fit residues: 130.4290 Evaluate side-chains 227 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 7 ASN 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 227 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 77 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 83 optimal weight: 0.3980 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** 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 = 0.4254 r_free = 0.4254 target = 0.175097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133146 restraints weight = 15825.742| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.68 r_work: 0.3518 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 10881 Z= 0.224 Angle : 0.750 13.990 15424 Z= 0.379 Chirality : 0.042 0.277 1832 Planarity : 0.008 0.159 1399 Dihedral : 24.373 173.819 3369 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 25.70 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.42 % Favored : 90.67 % Rotamer: Outliers : 5.37 % Allowed : 21.07 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.27), residues: 879 helix: -0.15 (0.19), residues: 666 sheet: -1.30 (1.33), residues: 14 loop : -3.23 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 309 HIS 0.006 0.002 HIS A 121 PHE 0.032 0.003 PHE A 231 TYR 0.025 0.002 TYR C 28 ARG 0.010 0.001 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.06201 ( 589) hydrogen bonds : angle 5.21922 ( 1616) covalent geometry : bond 0.00505 (10881) covalent geometry : angle 0.74960 (15424) *********************** 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: 40 poor density : 229 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7561 (mmtp) REVERT: A 115 THR cc_start: 0.8979 (m) cc_final: 0.8748 (p) REVERT: A 165 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7768 (mtt180) REVERT: A 272 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7248 (pp) REVERT: B 69 TYR cc_start: 0.7962 (m-80) cc_final: 0.7688 (m-80) REVERT: C 42 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7832 (ttp-170) REVERT: C 98 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8008 (mt0) REVERT: D 19 ARG cc_start: 0.7950 (mmt-90) cc_final: 0.7606 (mmm160) REVERT: E 16 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7883 (pt) REVERT: E 52 GLN cc_start: 0.7337 (tm-30) cc_final: 0.6794 (tm-30) REVERT: F 47 LYS cc_start: 0.8414 (ttmm) cc_final: 0.8111 (mttm) outliers start: 40 outliers final: 24 residues processed: 251 average time/residue: 0.3383 time to fit residues: 112.1352 Evaluate side-chains 239 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS 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 293 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 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 C residue 98 GLN 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 27 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 187 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.174693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.132885 restraints weight = 15559.522| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.66 r_work: 0.3510 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 10881 Z= 0.228 Angle : 0.719 8.927 15424 Z= 0.365 Chirality : 0.040 0.200 1832 Planarity : 0.008 0.137 1399 Dihedral : 24.046 174.952 3362 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 25.28 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.62 % Favored : 91.47 % Rotamer: Outliers : 4.43 % Allowed : 22.82 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.27), residues: 879 helix: -0.03 (0.19), residues: 664 sheet: -2.29 (1.05), residues: 26 loop : -2.76 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 116 HIS 0.006 0.001 HIS A 121 PHE 0.030 0.003 PHE A 231 TYR 0.025 0.002 TYR C 28 ARG 0.009 0.001 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.05943 ( 589) hydrogen bonds : angle 5.12220 ( 1616) covalent geometry : bond 0.00519 (10881) covalent geometry : angle 0.71931 (15424) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7353 (m-40) cc_final: 0.6875 (m-40) REVERT: A 165 ARG cc_start: 0.8287 (mtp85) cc_final: 0.7808 (mtt180) REVERT: A 187 GLN cc_start: 0.8644 (mm110) cc_final: 0.8413 (mm-40) REVERT: A 224 PRO cc_start: 0.6862 (Cg_exo) cc_final: 0.6626 (Cg_endo) REVERT: A 272 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7454 (pp) REVERT: C 77 MET cc_start: 0.8534 (tpt) cc_final: 0.7950 (tpt) REVERT: D 19 ARG cc_start: 0.7861 (mmt-90) cc_final: 0.7522 (mmm160) REVERT: E 16 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7863 (pt) REVERT: E 52 GLN cc_start: 0.7466 (tm-30) cc_final: 0.6872 (tm-30) REVERT: E 53 VAL cc_start: 0.8561 (t) cc_final: 0.8142 (t) REVERT: E 92 HIS cc_start: 0.8079 (m170) cc_final: 0.7204 (m170) REVERT: F 20 TYR cc_start: 0.8478 (t80) cc_final: 0.8082 (t80) REVERT: F 47 LYS cc_start: 0.8436 (ttmm) cc_final: 0.8183 (mttm) outliers start: 33 outliers final: 22 residues processed: 251 average time/residue: 0.3534 time to fit residues: 117.6500 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 : 2.812 ------------------------------------------------------------------------------- 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 B residue 8 THR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 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 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 76 optimal weight: 0.5980 chunk 94 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 61 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** C 13 GLN E 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.177333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136838 restraints weight = 15575.437| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.61 r_work: 0.3557 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.5351 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= 0.193 Angle : 0.696 10.147 15424 Z= 0.353 Chirality : 0.039 0.196 1832 Planarity : 0.007 0.124 1399 Dihedral : 23.742 173.692 3354 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.85 % Favored : 91.47 % Rotamer: Outliers : 4.56 % Allowed : 23.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.28), residues: 879 helix: 0.12 (0.19), residues: 663 sheet: -1.83 (1.13), residues: 26 loop : -2.66 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 116 HIS 0.007 0.001 HIS A 121 PHE 0.029 0.002 PHE A 231 TYR 0.022 0.002 TYR C 28 ARG 0.015 0.001 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.05652 ( 589) hydrogen bonds : angle 5.00752 ( 1616) covalent geometry : bond 0.00438 (10881) covalent geometry : angle 0.69621 (15424) *********************** 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 272 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 1.498 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: 0.7302 (m-40) cc_final: 0.6767 (m-40) REVERT: A 199 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6083 (mtt-85) REVERT: A 224 PRO cc_start: 0.6748 (Cg_exo) cc_final: 0.6509 (Cg_endo) REVERT: A 272 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7447 (pp) REVERT: D 19 ARG cc_start: 0.7720 (mmt-90) cc_final: 0.7432 (mmm160) REVERT: D 37 LYS cc_start: 0.7916 (mtpp) cc_final: 0.7299 (mmmt) REVERT: D 79 ARG cc_start: 0.8140 (ttm110) cc_final: 0.7595 (mtt180) REVERT: E 16 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7729 (pt) REVERT: E 52 GLN cc_start: 0.7280 (tm-30) cc_final: 0.6793 (tm-30) REVERT: E 53 VAL cc_start: 0.8553 (t) cc_final: 0.8146 (t) REVERT: E 77 MET cc_start: 0.8412 (tpt) cc_final: 0.7770 (tpt) REVERT: E 92 HIS cc_start: 0.7991 (m170) cc_final: 0.7255 (m170) REVERT: F 47 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8168 (mttm) outliers start: 34 outliers final: 18 residues processed: 253 average time/residue: 0.3292 time to fit residues: 110.0306 Evaluate side-chains 236 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 115 THR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 199 ARG Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 272 LEU 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 67 LYS Chi-restraints excluded: chain E residue 85 LEU 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 0 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 93 optimal weight: 20.0000 chunk 35 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN E 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.177026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.136305 restraints weight = 15678.701| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.61 r_work: 0.3541 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.5658 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= 0.211 Angle : 0.705 10.066 15424 Z= 0.357 Chirality : 0.039 0.193 1832 Planarity : 0.007 0.121 1399 Dihedral : 23.587 174.365 3346 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.51 % Favored : 91.92 % Rotamer: Outliers : 5.37 % Allowed : 23.89 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.28), residues: 879 helix: 0.08 (0.19), residues: 660 sheet: -1.49 (1.18), residues: 26 loop : -2.45 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 116 HIS 0.010 0.001 HIS A 121 PHE 0.028 0.002 PHE A 231 TYR 0.025 0.002 TYR C 28 ARG 0.006 0.001 ARG E 36 Details of bonding type rmsd hydrogen bonds : bond 0.05582 ( 589) hydrogen bonds : angle 4.97228 ( 1616) covalent geometry : bond 0.00484 (10881) covalent geometry : angle 0.70524 (15424) *********************** 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 259 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7131 (m-40) cc_final: 0.6622 (m-40) REVERT: A 123 GLN cc_start: 0.6761 (mt0) cc_final: 0.6253 (mm-40) REVERT: A 224 PRO cc_start: 0.6724 (Cg_exo) cc_final: 0.6448 (Cg_endo) REVERT: A 272 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7236 (pp) REVERT: B 11 TYR cc_start: 0.7206 (t80) cc_final: 0.6966 (t80) REVERT: C 19 ARG cc_start: 0.6469 (mmm-85) cc_final: 0.6129 (mmm-85) REVERT: D 19 ARG cc_start: 0.7666 (mmt-90) cc_final: 0.7377 (mmm160) REVERT: D 37 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7310 (mmmt) REVERT: D 79 ARG cc_start: 0.8236 (ttm110) cc_final: 0.7883 (mtm-85) REVERT: E 16 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7714 (pt) REVERT: E 52 GLN cc_start: 0.7363 (tm-30) cc_final: 0.6875 (tm-30) REVERT: E 53 VAL cc_start: 0.8512 (t) cc_final: 0.8079 (t) REVERT: E 77 MET cc_start: 0.8414 (tpt) cc_final: 0.7746 (tpt) REVERT: E 92 HIS cc_start: 0.7872 (m170) cc_final: 0.7108 (m170) REVERT: F 47 LYS cc_start: 0.8468 (ttmm) cc_final: 0.8197 (mttm) outliers start: 40 outliers final: 20 residues processed: 242 average time/residue: 0.2910 time to fit residues: 91.7343 Evaluate side-chains 237 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 200 LEU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 272 LEU 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 D residue 121 ASN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 65 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 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** ** 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 = 0.4270 r_free = 0.4270 target = 0.177640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137112 restraints weight = 15718.631| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.62 r_work: 0.3556 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.5905 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= 0.208 Angle : 0.700 9.759 15424 Z= 0.355 Chirality : 0.039 0.235 1832 Planarity : 0.007 0.113 1399 Dihedral : 23.505 178.803 3344 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 25.17 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.62 % Favored : 91.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.28), residues: 879 helix: 0.08 (0.19), residues: 657 sheet: 0.79 (1.48), residues: 14 loop : -2.53 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 116 HIS 0.008 0.001 HIS A 121 PHE 0.029 0.002 PHE A 231 TYR 0.024 0.002 TYR C 28 ARG 0.014 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.05534 ( 589) hydrogen bonds : angle 4.99750 ( 1616) covalent geometry : bond 0.00478 (10881) covalent geometry : angle 0.69973 (15424) *********************** 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 251 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7176 (m-40) cc_final: 0.6641 (m-40) REVERT: A 224 PRO cc_start: 0.6636 (Cg_exo) cc_final: 0.6420 (Cg_endo) REVERT: A 272 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7200 (pp) REVERT: B 82 LEU cc_start: 0.8697 (mt) cc_final: 0.8466 (mp) REVERT: C 103 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7947 (mt0) REVERT: D 19 ARG cc_start: 0.7666 (mmt-90) cc_final: 0.7388 (mmm160) REVERT: D 37 LYS cc_start: 0.7827 (mtpp) cc_final: 0.7323 (mmmt) REVERT: D 79 ARG cc_start: 0.8318 (ttm110) cc_final: 0.7985 (mtm-85) REVERT: E 16 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7719 (pt) REVERT: E 52 GLN cc_start: 0.7341 (tm-30) cc_final: 0.6857 (tm-30) REVERT: E 77 MET cc_start: 0.8428 (tpt) cc_final: 0.7763 (tpt) REVERT: E 92 HIS cc_start: 0.7914 (m170) cc_final: 0.7148 (m170) REVERT: F 47 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8210 (mttm) REVERT: F 92 HIS cc_start: 0.6112 (m-70) cc_final: 0.5713 (m170) outliers start: 28 outliers final: 18 residues processed: 237 average time/residue: 0.2806 time to fit residues: 87.4373 Evaluate side-chains 238 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 200 LEU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 272 LEU 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 66 SER 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 C residue 103 GLN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN ** B 89 GLN ** 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 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.173863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132086 restraints weight = 15498.334| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.61 r_work: 0.3487 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 10881 Z= 0.301 Angle : 0.763 8.773 15424 Z= 0.385 Chirality : 0.041 0.224 1832 Planarity : 0.007 0.113 1399 Dihedral : 23.531 179.640 3344 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 27.48 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.05 % Favored : 92.26 % Rotamer: Outliers : 4.30 % Allowed : 25.50 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.28), residues: 879 helix: -0.04 (0.19), residues: 656 sheet: 0.39 (1.39), residues: 14 loop : -2.30 (0.45), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 15 HIS 0.012 0.002 HIS C 38 PHE 0.030 0.003 PHE A 231 TYR 0.030 0.003 TYR C 28 ARG 0.007 0.001 ARG F 19 Details of bonding type rmsd hydrogen bonds : bond 0.06037 ( 589) hydrogen bonds : angle 5.17656 ( 1616) covalent geometry : bond 0.00697 (10881) covalent geometry : angle 0.76344 (15424) *********************** 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 247 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7529 (m-40) cc_final: 0.7088 (m-40) REVERT: A 264 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6883 (ttm170) REVERT: A 272 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7366 (pp) REVERT: B 43 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7911 (mt-10) REVERT: B 82 LEU cc_start: 0.8743 (mt) cc_final: 0.8521 (mp) REVERT: C 98 GLN cc_start: 0.8483 (tt0) cc_final: 0.8186 (mt0) REVERT: D 19 ARG cc_start: 0.7970 (mmt-90) cc_final: 0.7584 (mmm160) REVERT: D 79 ARG cc_start: 0.8525 (ttm110) cc_final: 0.8015 (mtm-85) REVERT: E 16 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7942 (pt) REVERT: E 52 GLN cc_start: 0.7642 (tm-30) cc_final: 0.7002 (tm-30) REVERT: E 67 LYS cc_start: 0.9146 (tppt) cc_final: 0.8890 (tppt) REVERT: E 92 HIS cc_start: 0.8153 (m170) cc_final: 0.7392 (m170) REVERT: F 47 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8395 (mttm) outliers start: 32 outliers final: 22 residues processed: 234 average time/residue: 0.3183 time to fit residues: 100.5667 Evaluate side-chains 234 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 115 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 272 LEU 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 97 HIS Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 97 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 20.0000 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN ** A 133 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** ** E 32 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 = 0.4272 r_free = 0.4272 target = 0.177891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.137217 restraints weight = 15707.782| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.62 r_work: 0.3564 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 10881 Z= 0.200 Angle : 0.717 8.637 15424 Z= 0.363 Chirality : 0.039 0.228 1832 Planarity : 0.007 0.112 1399 Dihedral : 23.458 178.162 3344 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 25.23 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.28 % Favored : 91.92 % Rotamer: Outliers : 3.49 % Allowed : 25.37 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.28), residues: 879 helix: -0.02 (0.19), residues: 662 sheet: 0.79 (1.46), residues: 14 loop : -2.45 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 116 HIS 0.008 0.001 HIS A 121 PHE 0.027 0.002 PHE A 231 TYR 0.024 0.002 TYR C 28 ARG 0.009 0.001 ARG F 19 Details of bonding type rmsd hydrogen bonds : bond 0.05519 ( 589) hydrogen bonds : angle 5.09573 ( 1616) covalent geometry : bond 0.00464 (10881) covalent geometry : angle 0.71689 (15424) *********************** 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: 26 poor density : 219 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6616 (mm-40) REVERT: A 224 PRO cc_start: 0.6727 (Cg_exo) cc_final: 0.6435 (Cg_endo) REVERT: A 264 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6681 (ttm170) REVERT: A 272 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7133 (pp) REVERT: B 11 TYR cc_start: 0.7034 (t80) cc_final: 0.6737 (t80) REVERT: C 42 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7656 (ttp-170) REVERT: D 37 LYS cc_start: 0.7988 (mtpp) cc_final: 0.7473 (mmmt) REVERT: D 79 ARG cc_start: 0.8315 (ttm110) cc_final: 0.7687 (mtt180) REVERT: E 16 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7697 (pt) REVERT: E 52 GLN cc_start: 0.7334 (tm-30) cc_final: 0.6839 (tm-30) REVERT: E 67 LYS cc_start: 0.9111 (tppt) cc_final: 0.8874 (tppt) REVERT: E 92 HIS cc_start: 0.7912 (m170) cc_final: 0.7138 (m170) REVERT: F 47 LYS cc_start: 0.8515 (ttmm) cc_final: 0.8237 (mttm) outliers start: 26 outliers final: 16 residues processed: 231 average time/residue: 0.2787 time to fit residues: 85.5475 Evaluate side-chains 225 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 123 GLN 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 202 HIS Chi-restraints excluded: chain A residue 264 ARG Chi-restraints excluded: chain A residue 272 LEU 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 97 HIS 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 97 HIS 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 49 optimal weight: 0.9990 chunk 72 optimal weight: 0.3980 chunk 71 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN ** A 133 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 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.177660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.136997 restraints weight = 15548.840| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.60 r_work: 0.3562 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 10881 Z= 0.208 Angle : 0.761 22.056 15424 Z= 0.374 Chirality : 0.040 0.281 1832 Planarity : 0.008 0.188 1399 Dihedral : 23.387 177.581 3343 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.62 % Favored : 91.58 % Rotamer: Outliers : 2.82 % Allowed : 25.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.28), residues: 879 helix: -0.03 (0.19), residues: 656 sheet: 0.84 (1.50), residues: 14 loop : -2.35 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 116 HIS 0.010 0.001 HIS A 121 PHE 0.026 0.002 PHE B 80 TYR 0.023 0.003 TYR C 28 ARG 0.008 0.001 ARG F 19 Details of bonding type rmsd hydrogen bonds : bond 0.05595 ( 589) hydrogen bonds : angle 5.11815 ( 1616) covalent geometry : bond 0.00485 (10881) covalent geometry : angle 0.76103 (15424) ********************** 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 231 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7299 (m-40) cc_final: 0.6754 (m-40) REVERT: A 224 PRO cc_start: 0.6654 (Cg_exo) cc_final: 0.6326 (Cg_endo) REVERT: B 11 TYR cc_start: 0.7068 (t80) cc_final: 0.6776 (t80) REVERT: C 42 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7701 (ttp-170) REVERT: C 98 GLN cc_start: 0.8272 (tt0) cc_final: 0.8048 (tt0) REVERT: D 37 LYS cc_start: 0.7987 (mtpp) cc_final: 0.7485 (mmmt) REVERT: D 79 ARG cc_start: 0.8339 (ttm110) cc_final: 0.7706 (mtt180) REVERT: E 16 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7719 (pt) REVERT: E 52 GLN cc_start: 0.7375 (tm-30) cc_final: 0.6867 (tm-30) REVERT: E 67 LYS cc_start: 0.9097 (tppt) cc_final: 0.8873 (tppt) REVERT: E 92 HIS cc_start: 0.7938 (m170) cc_final: 0.7187 (m170) REVERT: F 20 TYR cc_start: 0.8362 (t80) cc_final: 0.8116 (t80) REVERT: F 47 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8215 (mttm) outliers start: 21 outliers final: 19 residues processed: 220 average time/residue: 0.2700 time to fit residues: 79.3413 Evaluate side-chains 222 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 200 LEU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 272 LEU 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 97 HIS 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 97 HIS Chi-restraints excluded: chain E residue 100 GLU 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 28 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 30 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** 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 32 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 = 0.4274 r_free = 0.4274 target = 0.177832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.137423 restraints weight = 15557.851| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.60 r_work: 0.3571 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 10881 Z= 0.211 Angle : 0.755 18.056 15424 Z= 0.374 Chirality : 0.040 0.285 1832 Planarity : 0.007 0.172 1399 Dihedral : 23.321 176.982 3343 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 25.23 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.39 % Favored : 91.81 % Rotamer: Outliers : 2.82 % Allowed : 26.71 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.28), residues: 879 helix: -0.05 (0.19), residues: 655 sheet: 0.92 (1.43), residues: 14 loop : -2.37 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 81 HIS 0.009 0.001 HIS A 121 PHE 0.025 0.002 PHE A 231 TYR 0.028 0.003 TYR A 105 ARG 0.008 0.001 ARG F 19 Details of bonding type rmsd hydrogen bonds : bond 0.05595 ( 589) hydrogen bonds : angle 5.15811 ( 1616) covalent geometry : bond 0.00489 (10881) covalent geometry : angle 0.75485 (15424) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5501.87 seconds wall clock time: 98 minutes 14.33 seconds (5894.33 seconds total)