Starting phenix.real_space_refine on Wed Feb 12 04:56:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t03_40933/02_2025/8t03_40933.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t03_40933/02_2025/8t03_40933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t03_40933/02_2025/8t03_40933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t03_40933/02_2025/8t03_40933.map" model { file = "/net/cci-nas-00/data/ceres_data/8t03_40933/02_2025/8t03_40933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t03_40933/02_2025/8t03_40933.cif" } resolution = 2.72 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= 0.002 sd= 0.094 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 44 5.16 5 C 4492 2.51 5 N 1092 2.21 5 O 1246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6878 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1593 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "C" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: E, F, B Time building chain proxies: 5.07, per 1000 atoms: 0.74 Number of scatterers: 6878 At special positions: 0 Unit cell: (92.13, 103.75, 103.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 44 16.00 P 2 15.00 O 1246 8.00 N 1092 7.00 C 4492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 59 " distance=2.04 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: 1.71 Conformation dependent library (CDL) restraints added in 962.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 184 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 180 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 184 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 180 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 12 sheets defined 41.0% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 removed outlier: 3.975A pdb=" N LEU A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 18 through 28 Processing helix chain 'A' and resid 30 through 52 Processing helix chain 'A' and resid 62 through 87 Processing helix chain 'A' and resid 91 through 111 Processing helix chain 'A' and resid 118 through 141 Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 153 through 170 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 176 through 195 removed outlier: 3.704A pdb=" N SER A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 15 Proline residue: B 11 - end of helix Processing helix chain 'B' and resid 18 through 28 Processing helix chain 'B' and resid 30 through 52 Processing helix chain 'B' and resid 62 through 87 Processing helix chain 'B' and resid 91 through 111 Processing helix chain 'B' and resid 118 through 141 Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 153 through 170 Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 176 through 195 removed outlier: 3.704A pdb=" N SER B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.516A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.515A pdb=" N ILE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.597A pdb=" N LEU C 12 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL C 36 " --> pdb=" O HIS C 52 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N HIS C 52 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP C 38 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.597A pdb=" N LEU C 12 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.419A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE D 33 " --> pdb=" O HIS D 49 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N HIS D 49 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.419A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.598A pdb=" N LEU E 12 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL E 36 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N HIS E 52 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TRP E 38 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.598A pdb=" N LEU E 12 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR E 109 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.418A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE F 33 " --> pdb=" O HIS F 49 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N HIS F 49 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.418A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 2.00 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: 1145 1.33 - 1.45: 1929 1.45 - 1.57: 3908 1.57 - 1.69: 4 1.69 - 1.82: 72 Bond restraints: 7058 Sorted by residual: bond pdb=" N LEU A 55 " pdb=" CA LEU A 55 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.00e-02 1.00e+04 1.37e+01 bond pdb=" N LEU B 55 " pdb=" CA LEU B 55 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.00e-02 1.00e+04 1.33e+01 bond pdb=" N LEU B 10 " pdb=" CA LEU B 10 " ideal model delta sigma weight residual 1.461 1.495 -0.034 9.20e-03 1.18e+04 1.33e+01 bond pdb=" N LEU A 10 " pdb=" CA LEU A 10 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.20e-03 1.18e+04 1.28e+01 bond pdb=" N ARG E 68 " pdb=" CA ARG E 68 " ideal model delta sigma weight residual 1.454 1.504 -0.050 1.42e-02 4.96e+03 1.24e+01 ... (remaining 7053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 7570 2.25 - 4.50: 1874 4.50 - 6.75: 114 6.75 - 9.00: 4 9.00 - 11.25: 2 Bond angle restraints: 9564 Sorted by residual: angle pdb=" C PHE E 54 " pdb=" N TRP E 55 " pdb=" CA TRP E 55 " ideal model delta sigma weight residual 120.38 127.50 -7.12 1.37e+00 5.33e-01 2.70e+01 angle pdb=" C PHE C 54 " pdb=" N TRP C 55 " pdb=" CA TRP C 55 " ideal model delta sigma weight residual 120.38 127.48 -7.10 1.37e+00 5.33e-01 2.68e+01 angle pdb=" CA GLY C 113 " pdb=" C GLY C 113 " pdb=" O GLY C 113 " ideal model delta sigma weight residual 122.24 117.94 4.30 8.70e-01 1.32e+00 2.44e+01 angle pdb=" CA GLY E 113 " pdb=" C GLY E 113 " pdb=" O GLY E 113 " ideal model delta sigma weight residual 122.24 117.97 4.27 8.70e-01 1.32e+00 2.41e+01 angle pdb=" CA GLY D 101 " pdb=" C GLY D 101 " pdb=" O GLY D 101 " ideal model delta sigma weight residual 122.29 118.46 3.83 8.10e-01 1.52e+00 2.24e+01 ... (remaining 9559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 4115 35.87 - 71.74: 116 71.74 - 107.61: 4 107.61 - 143.48: 2 143.48 - 179.35: 4 Dihedral angle restraints: 4241 sinusoidal: 1779 harmonic: 2462 Sorted by residual: dihedral pdb=" CA GLU A 90 " pdb=" C GLU A 90 " pdb=" N PRO A 91 " pdb=" CA PRO A 91 " ideal model delta harmonic sigma weight residual 0.00 38.51 -38.51 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CA GLU B 90 " pdb=" C GLU B 90 " pdb=" N PRO B 91 " pdb=" CA PRO B 91 " ideal model delta harmonic sigma weight residual 0.00 38.43 -38.43 0 5.00e+00 4.00e-02 5.91e+01 dihedral pdb=" C1 LBN B 303 " pdb=" O1 LBN B 303 " pdb=" P1 LBN B 303 " pdb=" O3 LBN B 303 " ideal model delta sinusoidal sigma weight residual 275.40 96.05 179.35 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.970: 1052 0.970 - 1.939: 0 1.939 - 2.909: 0 2.909 - 3.879: 0 3.879 - 4.848: 2 Chirality restraints: 1054 Sorted by residual: chirality pdb=" C2 LBN B 303 " pdb=" C1 LBN B 303 " pdb=" C3 LBN B 303 " pdb=" O7 LBN B 303 " both_signs ideal model delta sigma weight residual False -2.36 2.48 -4.85 2.00e-01 2.50e+01 5.88e+02 chirality pdb=" C2 LBN A 303 " pdb=" C1 LBN A 303 " pdb=" C3 LBN A 303 " pdb=" O7 LBN A 303 " both_signs ideal model delta sigma weight residual False -2.36 2.48 -4.85 2.00e-01 2.50e+01 5.87e+02 chirality pdb=" CA ILE D 75 " pdb=" N ILE D 75 " pdb=" C ILE D 75 " pdb=" CB ILE D 75 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1051 not shown) Planarity restraints: 1156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN B 303 " -0.038 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C42 LBN B 303 " 0.038 2.00e-02 2.50e+03 pdb=" C5 LBN B 303 " 0.039 2.00e-02 2.50e+03 pdb=" C8 LBN B 303 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN A 303 " 0.038 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C42 LBN A 303 " -0.038 2.00e-02 2.50e+03 pdb=" C5 LBN A 303 " -0.039 2.00e-02 2.50e+03 pdb=" C8 LBN A 303 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 90 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO A 91 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " 0.026 5.00e-02 4.00e+02 ... (remaining 1153 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 34 2.60 - 3.18: 5349 3.18 - 3.75: 10509 3.75 - 4.33: 15424 4.33 - 4.90: 26178 Nonbonded interactions: 57494 Sorted by model distance: nonbonded pdb=" SG CYS C 22 " pdb=" SG CYS C 97 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS E 22 " pdb=" SG CYS E 97 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B 50 " pdb=" SG CYS B 59 " model vdw 2.040 3.760 nonbonded pdb=" OD1 ASP D 28 " pdb=" O GLY D 68 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASP F 28 " pdb=" O GLY F 68 " model vdw 2.206 3.040 ... (remaining 57489 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: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 19.980 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 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 : 0.014 0.050 7058 Z= 0.882 Angle : 1.758 11.254 9564 Z= 1.287 Chirality : 0.227 4.848 1054 Planarity : 0.004 0.051 1156 Dihedral : 17.024 179.354 2666 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.63 % Allowed : 4.90 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -0.46 (0.29), residues: 840 helix: -0.62 (0.26), residues: 294 sheet: 0.45 (0.39), residues: 196 loop : -0.27 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 110 HIS 0.008 0.002 HIS B 110 PHE 0.022 0.003 PHE A 46 TYR 0.027 0.003 TYR F 71 ARG 0.003 0.001 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.768 Fit side-chains REVERT: A 29 ARG cc_start: 0.7286 (mmm160) cc_final: 0.7076 (mtp180) REVERT: A 61 MET cc_start: 0.7701 (mtm) cc_final: 0.7328 (mtp) REVERT: A 134 LEU cc_start: 0.7325 (mt) cc_final: 0.7024 (mm) REVERT: A 138 LYS cc_start: 0.6890 (mptt) cc_final: 0.6518 (mptt) REVERT: A 139 GLU cc_start: 0.6813 (tt0) cc_final: 0.6456 (tt0) REVERT: B 29 ARG cc_start: 0.7294 (mmm160) cc_final: 0.7089 (mtp180) REVERT: B 61 MET cc_start: 0.7670 (mtm) cc_final: 0.7319 (mtp) REVERT: B 134 LEU cc_start: 0.7320 (mt) cc_final: 0.7023 (mm) REVERT: B 138 LYS cc_start: 0.6891 (mptt) cc_final: 0.6506 (mptt) REVERT: B 139 GLU cc_start: 0.6827 (tt0) cc_final: 0.6470 (tt0) REVERT: C 41 LYS cc_start: 0.7093 (tttt) cc_final: 0.6753 (ttpp) REVERT: C 61 TYR cc_start: 0.8446 (m-80) cc_final: 0.8099 (m-80) REVERT: C 112 GLN cc_start: 0.7583 (tt0) cc_final: 0.7178 (tt0) REVERT: D 31 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6359 (mp0) REVERT: D 42 LYS cc_start: 0.7527 (mtpp) cc_final: 0.6803 (mtmt) REVERT: E 41 LYS cc_start: 0.7062 (tttt) cc_final: 0.6705 (ttpp) REVERT: E 61 TYR cc_start: 0.8424 (m-80) cc_final: 0.8081 (m-80) REVERT: E 83 MET cc_start: 0.6350 (mmm) cc_final: 0.6123 (mpt) REVERT: F 31 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6297 (mp0) REVERT: F 42 LYS cc_start: 0.7644 (mtpp) cc_final: 0.6966 (mtmt) outliers start: 12 outliers final: 2 residues processed: 134 average time/residue: 1.2308 time to fit residues: 173.6562 Evaluate side-chains 100 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain F residue 61 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 0.0870 chunk 64 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.162362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.116394 restraints weight = 6886.883| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.38 r_work: 0.3105 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7058 Z= 0.184 Angle : 0.588 6.400 9564 Z= 0.305 Chirality : 0.043 0.147 1054 Planarity : 0.004 0.034 1156 Dihedral : 13.858 163.239 1144 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.59 % Allowed : 8.86 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.02 (0.30), residues: 840 helix: 1.61 (0.28), residues: 304 sheet: 0.65 (0.35), residues: 230 loop : -0.14 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 110 HIS 0.003 0.001 HIS E 52 PHE 0.018 0.002 PHE A 39 TYR 0.012 0.001 TYR F 91 ARG 0.002 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.785 Fit side-chains REVERT: A 27 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7782 (mttt) REVERT: A 139 GLU cc_start: 0.7842 (tt0) cc_final: 0.7594 (tt0) REVERT: B 27 LYS cc_start: 0.8295 (ttmt) cc_final: 0.7756 (mttt) REVERT: B 139 GLU cc_start: 0.7825 (tt0) cc_final: 0.7578 (tt0) REVERT: D 31 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8035 (mp0) REVERT: D 42 LYS cc_start: 0.8267 (mtpp) cc_final: 0.7881 (mtmm) REVERT: D 45 ARG cc_start: 0.8253 (mtm180) cc_final: 0.8004 (mtp180) REVERT: D 67 SER cc_start: 0.7252 (OUTLIER) cc_final: 0.6773 (p) REVERT: E 41 LYS cc_start: 0.7885 (tttt) cc_final: 0.7298 (tptp) REVERT: F 31 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8009 (mp0) REVERT: F 42 LYS cc_start: 0.8258 (mtpp) cc_final: 0.7816 (mtmm) REVERT: F 67 SER cc_start: 0.7431 (OUTLIER) cc_final: 0.6983 (p) outliers start: 19 outliers final: 4 residues processed: 126 average time/residue: 1.3051 time to fit residues: 172.4612 Evaluate side-chains 116 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain F residue 67 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 61 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 0.0070 chunk 3 optimal weight: 0.5980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN D 30 ASN F 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.161547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113044 restraints weight = 7032.104| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.07 r_work: 0.3076 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7058 Z= 0.165 Angle : 0.537 6.265 9564 Z= 0.277 Chirality : 0.042 0.138 1054 Planarity : 0.004 0.032 1156 Dihedral : 12.744 162.883 1136 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.72 % Allowed : 12.81 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.43 (0.30), residues: 840 helix: 2.03 (0.28), residues: 306 sheet: 0.73 (0.34), residues: 240 loop : 0.09 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 110 HIS 0.003 0.001 HIS E 52 PHE 0.015 0.002 PHE B 46 TYR 0.012 0.001 TYR D 91 ARG 0.002 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.734 Fit side-chains REVERT: A 27 LYS cc_start: 0.8374 (ttmt) cc_final: 0.7909 (mttt) REVERT: A 139 GLU cc_start: 0.7875 (tt0) cc_final: 0.7594 (tt0) REVERT: B 27 LYS cc_start: 0.8381 (ttmt) cc_final: 0.7911 (mttt) REVERT: B 139 GLU cc_start: 0.7868 (tt0) cc_final: 0.7589 (tt0) REVERT: C 41 LYS cc_start: 0.8129 (tttp) cc_final: 0.7771 (tptm) REVERT: D 31 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8037 (mp0) REVERT: D 42 LYS cc_start: 0.8301 (mtpp) cc_final: 0.7824 (mtpt) REVERT: D 45 ARG cc_start: 0.8182 (mtm180) cc_final: 0.7977 (mtp180) REVERT: F 5 THR cc_start: 0.7693 (m) cc_final: 0.7412 (p) REVERT: F 31 GLU cc_start: 0.8570 (mt-10) cc_final: 0.7990 (mp0) REVERT: F 42 LYS cc_start: 0.8293 (mtpp) cc_final: 0.7843 (mtmm) outliers start: 20 outliers final: 7 residues processed: 112 average time/residue: 1.4281 time to fit residues: 167.6110 Evaluate side-chains 111 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain F residue 45 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 43 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN D 30 ASN F 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.161308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112803 restraints weight = 7085.047| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.10 r_work: 0.3084 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7058 Z= 0.168 Angle : 0.527 6.224 9564 Z= 0.271 Chirality : 0.041 0.138 1054 Planarity : 0.004 0.038 1156 Dihedral : 12.321 157.316 1136 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.45 % Allowed : 13.62 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.63 (0.30), residues: 840 helix: 2.23 (0.28), residues: 306 sheet: 0.93 (0.35), residues: 240 loop : 0.06 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 110 HIS 0.003 0.001 HIS E 52 PHE 0.015 0.001 PHE B 39 TYR 0.011 0.001 TYR F 91 ARG 0.002 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.879 Fit side-chains REVERT: A 27 LYS cc_start: 0.8392 (ttmt) cc_final: 0.7942 (mttt) REVERT: A 139 GLU cc_start: 0.7912 (tt0) cc_final: 0.7647 (tt0) REVERT: B 27 LYS cc_start: 0.8401 (ttmt) cc_final: 0.7949 (mttt) REVERT: B 139 GLU cc_start: 0.7911 (tt0) cc_final: 0.7645 (tt0) REVERT: C 41 LYS cc_start: 0.8158 (tttp) cc_final: 0.7669 (tptp) REVERT: C 48 GLU cc_start: 0.8169 (tt0) cc_final: 0.7968 (tt0) REVERT: D 5 THR cc_start: 0.7667 (m) cc_final: 0.7459 (p) REVERT: D 31 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8082 (mp0) REVERT: D 42 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7838 (mtpt) REVERT: D 45 ARG cc_start: 0.8197 (mtm180) cc_final: 0.7892 (mtp180) REVERT: E 48 GLU cc_start: 0.8187 (tt0) cc_final: 0.7978 (tt0) REVERT: F 31 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8053 (mp0) REVERT: F 42 LYS cc_start: 0.8298 (mtpp) cc_final: 0.7846 (mtmm) outliers start: 18 outliers final: 7 residues processed: 117 average time/residue: 1.4529 time to fit residues: 177.9060 Evaluate side-chains 111 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 112 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 63 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 79 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.158241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112753 restraints weight = 6968.533| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.44 r_work: 0.3043 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7058 Z= 0.238 Angle : 0.561 6.386 9564 Z= 0.290 Chirality : 0.043 0.146 1054 Planarity : 0.005 0.044 1156 Dihedral : 12.106 152.972 1136 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.00 % Allowed : 14.03 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.66 (0.30), residues: 840 helix: 2.16 (0.28), residues: 304 sheet: 1.03 (0.35), residues: 240 loop : 0.12 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 110 HIS 0.003 0.001 HIS D 38 PHE 0.018 0.002 PHE B 69 TYR 0.013 0.002 TYR D 91 ARG 0.003 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.733 Fit side-chains REVERT: A 27 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7757 (mttt) REVERT: A 139 GLU cc_start: 0.7891 (tt0) cc_final: 0.7597 (tt0) REVERT: B 27 LYS cc_start: 0.8240 (ttmt) cc_final: 0.7763 (mttt) REVERT: B 63 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7577 (mtp85) REVERT: B 139 GLU cc_start: 0.7883 (tt0) cc_final: 0.7591 (tt0) REVERT: C 41 LYS cc_start: 0.8171 (tttp) cc_final: 0.7801 (tptp) REVERT: C 48 GLU cc_start: 0.8169 (tt0) cc_final: 0.7952 (tt0) REVERT: D 31 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8094 (mp0) REVERT: D 42 LYS cc_start: 0.8319 (mtpp) cc_final: 0.7867 (mtmm) REVERT: D 45 ARG cc_start: 0.8309 (mtm180) cc_final: 0.8080 (mtp180) REVERT: D 61 ARG cc_start: 0.7260 (ptp-170) cc_final: 0.6967 (ptp90) REVERT: E 48 GLU cc_start: 0.8209 (tt0) cc_final: 0.7968 (tt0) REVERT: F 31 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8044 (mp0) REVERT: F 42 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7838 (mtmm) REVERT: F 61 ARG cc_start: 0.7289 (ptp90) cc_final: 0.6938 (ptp90) outliers start: 22 outliers final: 10 residues processed: 116 average time/residue: 1.4933 time to fit residues: 181.0792 Evaluate side-chains 113 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 112 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 70 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.159401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113420 restraints weight = 7009.745| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.32 r_work: 0.3071 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7058 Z= 0.203 Angle : 0.540 6.293 9564 Z= 0.279 Chirality : 0.042 0.138 1054 Planarity : 0.005 0.048 1156 Dihedral : 11.624 147.028 1136 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.32 % Allowed : 14.85 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.73 (0.30), residues: 840 helix: 2.24 (0.28), residues: 304 sheet: 1.10 (0.35), residues: 240 loop : 0.10 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 110 HIS 0.003 0.001 HIS E 52 PHE 0.016 0.002 PHE A 39 TYR 0.012 0.001 TYR F 86 ARG 0.002 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.696 Fit side-chains REVERT: A 27 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7677 (mttt) REVERT: A 139 GLU cc_start: 0.7817 (tt0) cc_final: 0.7540 (tt0) REVERT: B 27 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7668 (mttt) REVERT: B 139 GLU cc_start: 0.7806 (tt0) cc_final: 0.7529 (tt0) REVERT: B 166 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7591 (mmm) REVERT: C 41 LYS cc_start: 0.8138 (tttp) cc_final: 0.7732 (tptp) REVERT: C 48 GLU cc_start: 0.8123 (tt0) cc_final: 0.7891 (tt0) REVERT: D 31 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8006 (mp0) REVERT: D 42 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7765 (mtmm) REVERT: E 48 GLU cc_start: 0.8149 (tt0) cc_final: 0.7917 (tt0) REVERT: F 31 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7969 (mp0) REVERT: F 42 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7751 (mtmm) REVERT: F 61 ARG cc_start: 0.7247 (ptp90) cc_final: 0.7046 (ptp90) outliers start: 17 outliers final: 8 residues processed: 109 average time/residue: 1.4881 time to fit residues: 169.4366 Evaluate side-chains 112 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 79 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN D 30 ASN E 112 GLN F 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.159409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113267 restraints weight = 6913.906| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.25 r_work: 0.3077 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7058 Z= 0.200 Angle : 0.538 6.294 9564 Z= 0.277 Chirality : 0.042 0.139 1054 Planarity : 0.005 0.050 1156 Dihedral : 11.433 143.675 1136 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.45 % Allowed : 14.44 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.77 (0.30), residues: 840 helix: 2.24 (0.28), residues: 304 sheet: 1.16 (0.35), residues: 240 loop : 0.13 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 110 HIS 0.003 0.001 HIS E 52 PHE 0.016 0.002 PHE B 69 TYR 0.012 0.001 TYR F 86 ARG 0.002 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.740 Fit side-chains REVERT: A 27 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7689 (mttt) REVERT: A 63 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7420 (mtp-110) REVERT: A 138 LYS cc_start: 0.7825 (mptt) cc_final: 0.7543 (mptt) REVERT: A 139 GLU cc_start: 0.7825 (tt0) cc_final: 0.7542 (tt0) REVERT: B 27 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7682 (mttt) REVERT: B 63 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7493 (mtp85) REVERT: B 138 LYS cc_start: 0.7820 (mptt) cc_final: 0.7539 (mptt) REVERT: B 139 GLU cc_start: 0.7812 (tt0) cc_final: 0.7529 (tt0) REVERT: B 166 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7612 (mmm) REVERT: C 17 THR cc_start: 0.6712 (p) cc_final: 0.6478 (m) REVERT: C 41 LYS cc_start: 0.8111 (tttp) cc_final: 0.7716 (tptp) REVERT: C 48 GLU cc_start: 0.8105 (tt0) cc_final: 0.7876 (tt0) REVERT: D 31 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8011 (mp0) REVERT: D 42 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7777 (mtmm) REVERT: E 48 GLU cc_start: 0.8153 (tt0) cc_final: 0.7927 (tt0) REVERT: F 31 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7979 (mp0) REVERT: F 42 LYS cc_start: 0.8224 (mtpp) cc_final: 0.7768 (mtmm) REVERT: F 61 ARG cc_start: 0.7227 (ptp90) cc_final: 0.7015 (ptp90) outliers start: 18 outliers final: 11 residues processed: 119 average time/residue: 1.4388 time to fit residues: 178.9687 Evaluate side-chains 118 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 24 optimal weight: 0.0270 chunk 40 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN D 30 ASN F 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.162686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114721 restraints weight = 7031.986| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.10 r_work: 0.3053 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7058 Z= 0.131 Angle : 0.497 6.037 9564 Z= 0.255 Chirality : 0.040 0.146 1054 Planarity : 0.004 0.050 1156 Dihedral : 10.773 136.184 1136 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.77 % Allowed : 15.53 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.04 (0.30), residues: 840 helix: 2.53 (0.28), residues: 304 sheet: 1.30 (0.35), residues: 240 loop : 0.20 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 110 HIS 0.004 0.001 HIS E 52 PHE 0.015 0.001 PHE B 39 TYR 0.010 0.001 TYR C 96 ARG 0.001 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.658 Fit side-chains REVERT: A 27 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7817 (mttt) REVERT: A 63 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7405 (mtp-110) REVERT: A 139 GLU cc_start: 0.7831 (tt0) cc_final: 0.7573 (tt0) REVERT: B 27 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7818 (mttt) REVERT: B 63 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7525 (mtp85) REVERT: B 139 GLU cc_start: 0.7818 (tt0) cc_final: 0.7563 (tt0) REVERT: C 41 LYS cc_start: 0.8116 (tttp) cc_final: 0.7540 (tptp) REVERT: C 48 GLU cc_start: 0.8099 (tt0) cc_final: 0.7886 (tt0) REVERT: D 31 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7981 (mp0) REVERT: D 42 LYS cc_start: 0.8197 (mtpp) cc_final: 0.7748 (mtmm) REVERT: E 48 GLU cc_start: 0.8110 (tt0) cc_final: 0.7870 (tt0) REVERT: F 31 GLU cc_start: 0.8561 (mt-10) cc_final: 0.7947 (mp0) REVERT: F 42 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7711 (mtmm) REVERT: F 61 ARG cc_start: 0.7218 (ptp90) cc_final: 0.6944 (ptp90) outliers start: 13 outliers final: 6 residues processed: 118 average time/residue: 1.3767 time to fit residues: 170.0744 Evaluate side-chains 115 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 81 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN D 30 ASN E 112 GLN F 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.158709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109649 restraints weight = 7016.526| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.11 r_work: 0.3043 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7058 Z= 0.227 Angle : 0.550 6.372 9564 Z= 0.282 Chirality : 0.042 0.142 1054 Planarity : 0.005 0.051 1156 Dihedral : 11.047 138.702 1136 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.32 % Allowed : 15.12 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.89 (0.30), residues: 840 helix: 2.25 (0.27), residues: 304 sheet: 1.29 (0.35), residues: 240 loop : 0.23 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 110 HIS 0.003 0.001 HIS D 38 PHE 0.019 0.002 PHE B 46 TYR 0.012 0.002 TYR F 86 ARG 0.002 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.782 Fit side-chains REVERT: A 27 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7800 (mttt) REVERT: A 63 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7505 (mtp-110) REVERT: A 103 THR cc_start: 0.9242 (m) cc_final: 0.9035 (p) REVERT: A 139 GLU cc_start: 0.7902 (tt0) cc_final: 0.7621 (tt0) REVERT: B 27 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7788 (mttt) REVERT: B 63 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7614 (mtp85) REVERT: B 103 THR cc_start: 0.9240 (m) cc_final: 0.9029 (p) REVERT: B 139 GLU cc_start: 0.7891 (tt0) cc_final: 0.7613 (tt0) REVERT: B 152 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8189 (mt0) REVERT: B 166 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7738 (mmm) REVERT: C 17 THR cc_start: 0.6818 (p) cc_final: 0.6617 (m) REVERT: C 41 LYS cc_start: 0.8160 (tttp) cc_final: 0.7942 (ttpp) REVERT: C 48 GLU cc_start: 0.8135 (tt0) cc_final: 0.7922 (tt0) REVERT: D 31 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8055 (mp0) REVERT: D 42 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7836 (mtmm) REVERT: E 48 GLU cc_start: 0.8174 (tt0) cc_final: 0.7960 (tt0) REVERT: F 31 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8042 (mp0) REVERT: F 42 LYS cc_start: 0.8258 (mtpp) cc_final: 0.7795 (mtmm) REVERT: F 61 ARG cc_start: 0.7298 (ptp90) cc_final: 0.7065 (ptp90) outliers start: 17 outliers final: 6 residues processed: 118 average time/residue: 1.4842 time to fit residues: 182.8794 Evaluate side-chains 117 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN D 30 ASN E 112 GLN F 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.160042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.111268 restraints weight = 7026.593| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.11 r_work: 0.3064 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7058 Z= 0.182 Angle : 0.539 7.756 9564 Z= 0.274 Chirality : 0.041 0.165 1054 Planarity : 0.005 0.050 1156 Dihedral : 10.861 139.085 1136 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.36 % Allowed : 16.35 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.96 (0.30), residues: 840 helix: 2.28 (0.27), residues: 304 sheet: 1.35 (0.35), residues: 240 loop : 0.30 (0.41), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 110 HIS 0.003 0.001 HIS E 52 PHE 0.016 0.002 PHE B 39 TYR 0.011 0.001 TYR D 86 ARG 0.003 0.000 ARG D 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.736 Fit side-chains REVERT: A 27 LYS cc_start: 0.8251 (ttmt) cc_final: 0.7799 (mttt) REVERT: A 63 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7504 (mtp-110) REVERT: A 103 THR cc_start: 0.9272 (m) cc_final: 0.9053 (p) REVERT: A 139 GLU cc_start: 0.7853 (tt0) cc_final: 0.7567 (tt0) REVERT: B 27 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7786 (mttt) REVERT: B 63 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7591 (mtp85) REVERT: B 103 THR cc_start: 0.9274 (m) cc_final: 0.9051 (p) REVERT: B 139 GLU cc_start: 0.7841 (tt0) cc_final: 0.7557 (tt0) REVERT: C 41 LYS cc_start: 0.8163 (tttp) cc_final: 0.7761 (tptp) REVERT: C 48 GLU cc_start: 0.8133 (tt0) cc_final: 0.7913 (tt0) REVERT: D 31 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8041 (mp0) REVERT: D 42 LYS cc_start: 0.8257 (mtpp) cc_final: 0.7820 (mtmm) REVERT: E 17 THR cc_start: 0.6559 (p) cc_final: 0.6263 (m) REVERT: E 48 GLU cc_start: 0.8151 (tt0) cc_final: 0.7922 (tt0) REVERT: F 31 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8024 (mp0) REVERT: F 42 LYS cc_start: 0.8259 (mtpp) cc_final: 0.7728 (mtmm) REVERT: F 61 ARG cc_start: 0.7295 (ptp90) cc_final: 0.7004 (ptp90) outliers start: 10 outliers final: 6 residues processed: 117 average time/residue: 1.4531 time to fit residues: 177.8213 Evaluate side-chains 118 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 9 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN D 30 ASN D 49 HIS E 112 GLN F 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.157108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.111828 restraints weight = 6992.742| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.05 r_work: 0.3004 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7058 Z= 0.295 Angle : 0.604 7.073 9564 Z= 0.307 Chirality : 0.044 0.179 1054 Planarity : 0.005 0.050 1156 Dihedral : 11.392 142.076 1136 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.91 % Allowed : 15.40 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.71 (0.30), residues: 840 helix: 1.98 (0.28), residues: 304 sheet: 1.26 (0.35), residues: 240 loop : 0.24 (0.41), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 110 HIS 0.005 0.001 HIS D 38 PHE 0.020 0.002 PHE A 69 TYR 0.015 0.002 TYR F 91 ARG 0.003 0.000 ARG A 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6324.29 seconds wall clock time: 112 minutes 2.66 seconds (6722.66 seconds total)