Starting phenix.real_space_refine on Tue Sep 24 07:04:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/09_2024/8t03_40933.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/09_2024/8t03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/09_2024/8t03_40933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/09_2024/8t03_40933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/09_2024/8t03_40933.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/09_2024/8t03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.99, per 1000 atoms: 0.73 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: 1.61 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.91 Time building geometry restraints manager: 1.90 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.450 Find NCS groups from input model: 0.190 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:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 0.786 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: 1.1558 time to fit residues: 163.2622 Evaluate side-chains 100 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 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 fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 0.776 Fit side-chains REVERT: A 27 LYS cc_start: 0.6987 (ttmt) cc_final: 0.6472 (mttt) REVERT: A 134 LEU cc_start: 0.6749 (mt) cc_final: 0.6510 (mm) REVERT: A 138 LYS cc_start: 0.6355 (mptt) cc_final: 0.6122 (mptt) REVERT: A 139 GLU cc_start: 0.6559 (tt0) cc_final: 0.6238 (tt0) REVERT: B 27 LYS cc_start: 0.7020 (ttmt) cc_final: 0.6425 (mttt) REVERT: B 87 ASP cc_start: 0.7471 (t0) cc_final: 0.7220 (t0) REVERT: B 134 LEU cc_start: 0.6773 (mt) cc_final: 0.6545 (mm) REVERT: B 138 LYS cc_start: 0.6352 (mptt) cc_final: 0.6118 (mptt) REVERT: B 139 GLU cc_start: 0.6557 (tt0) cc_final: 0.6236 (tt0) REVERT: C 41 LYS cc_start: 0.7038 (tttt) cc_final: 0.6721 (tttp) REVERT: C 48 GLU cc_start: 0.7272 (tt0) cc_final: 0.6994 (tt0) REVERT: C 97 CYS cc_start: 0.8153 (t) cc_final: 0.7696 (p) REVERT: D 31 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6573 (mp0) REVERT: D 42 LYS cc_start: 0.7290 (mtpp) cc_final: 0.6860 (mtmm) REVERT: D 45 ARG cc_start: 0.6998 (mtm180) cc_final: 0.6607 (mtp180) REVERT: D 67 SER cc_start: 0.7015 (OUTLIER) cc_final: 0.6285 (p) REVERT: E 41 LYS cc_start: 0.7030 (tttt) cc_final: 0.6334 (tptp) REVERT: E 48 GLU cc_start: 0.7241 (tt0) cc_final: 0.6985 (tt0) REVERT: E 61 TYR cc_start: 0.8247 (m-80) cc_final: 0.8002 (m-80) REVERT: E 97 CYS cc_start: 0.8183 (t) cc_final: 0.7724 (p) REVERT: F 31 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6544 (mp0) REVERT: F 42 LYS cc_start: 0.7266 (mtpp) cc_final: 0.6770 (mtmm) REVERT: F 67 SER cc_start: 0.7156 (OUTLIER) cc_final: 0.6481 (p) outliers start: 19 outliers final: 4 residues processed: 126 average time/residue: 1.2980 time to fit residues: 171.7003 Evaluate side-chains 121 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 41 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2450 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= 0.313 Angle : 0.622 6.761 9564 Z= 0.320 Chirality : 0.045 0.151 1054 Planarity : 0.005 0.033 1156 Dihedral : 13.500 165.999 1136 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.59 % Allowed : 11.85 % Favored : 85.56 % 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: 1.22 (0.30), residues: 840 helix: 1.75 (0.28), residues: 302 sheet: 0.65 (0.34), residues: 242 loop : 0.09 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 110 HIS 0.005 0.001 HIS F 38 PHE 0.019 0.002 PHE B 69 TYR 0.015 0.002 TYR D 91 ARG 0.003 0.000 ARG A 107 *********************** 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 130 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 0.746 Fit side-chains REVERT: A 27 LYS cc_start: 0.6801 (ttmt) cc_final: 0.6303 (mttt) REVERT: A 103 THR cc_start: 0.8195 (m) cc_final: 0.7858 (p) REVERT: A 138 LYS cc_start: 0.6535 (mptt) cc_final: 0.6291 (mptt) REVERT: A 139 GLU cc_start: 0.6609 (tt0) cc_final: 0.6284 (tt0) REVERT: B 27 LYS cc_start: 0.6802 (ttmt) cc_final: 0.6299 (mttt) REVERT: B 103 THR cc_start: 0.8206 (m) cc_final: 0.7867 (p) REVERT: B 138 LYS cc_start: 0.6535 (mptt) cc_final: 0.6283 (mptt) REVERT: B 139 GLU cc_start: 0.6609 (tt0) cc_final: 0.6287 (tt0) REVERT: C 48 GLU cc_start: 0.7271 (tt0) cc_final: 0.7014 (tt0) REVERT: C 97 CYS cc_start: 0.8325 (t) cc_final: 0.7519 (p) REVERT: D 31 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6664 (mp0) REVERT: D 42 LYS cc_start: 0.7320 (mtpp) cc_final: 0.6772 (mtmm) REVERT: E 48 GLU cc_start: 0.7251 (tt0) cc_final: 0.6991 (tt0) REVERT: E 97 CYS cc_start: 0.8317 (t) cc_final: 0.7530 (p) REVERT: F 31 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6551 (mp0) REVERT: F 42 LYS cc_start: 0.7272 (mtpp) cc_final: 0.6790 (mtmm) outliers start: 19 outliers final: 7 residues processed: 113 average time/residue: 1.3836 time to fit residues: 163.7200 Evaluate side-chains 114 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 LEU 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 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 73 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 0.0050 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2715 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= 0.145 Angle : 0.521 6.135 9564 Z= 0.268 Chirality : 0.041 0.157 1054 Planarity : 0.004 0.039 1156 Dihedral : 11.995 158.901 1136 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.18 % Allowed : 12.94 % Favored : 84.88 % 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: 1.58 (0.30), residues: 840 helix: 2.19 (0.28), residues: 306 sheet: 0.85 (0.35), residues: 242 loop : 0.05 (0.40), residues: 292 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 0.001 PHE B 39 TYR 0.010 0.001 TYR F 91 ARG 0.001 0.000 ARG E 99 *********************** 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 131 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.664 Fit side-chains REVERT: A 27 LYS cc_start: 0.7026 (ttmt) cc_final: 0.6520 (mttt) REVERT: A 103 THR cc_start: 0.8225 (m) cc_final: 0.7986 (p) REVERT: A 134 LEU cc_start: 0.6764 (mt) cc_final: 0.6523 (mm) REVERT: A 138 LYS cc_start: 0.6453 (mptt) cc_final: 0.6207 (mptt) REVERT: A 139 GLU cc_start: 0.6586 (tt0) cc_final: 0.6266 (tt0) REVERT: B 27 LYS cc_start: 0.7027 (ttmt) cc_final: 0.6518 (mttt) REVERT: B 103 THR cc_start: 0.8226 (m) cc_final: 0.7986 (p) REVERT: B 134 LEU cc_start: 0.6758 (mt) cc_final: 0.6523 (mm) REVERT: B 138 LYS cc_start: 0.6571 (mptt) cc_final: 0.6307 (mptt) REVERT: B 139 GLU cc_start: 0.6602 (tt0) cc_final: 0.6316 (tt0) REVERT: C 48 GLU cc_start: 0.7197 (tt0) cc_final: 0.6858 (tt0) REVERT: C 97 CYS cc_start: 0.8172 (t) cc_final: 0.7773 (p) REVERT: D 5 THR cc_start: 0.6631 (m) cc_final: 0.6384 (p) REVERT: D 31 GLU cc_start: 0.7531 (mt-10) cc_final: 0.6688 (mp0) REVERT: D 42 LYS cc_start: 0.7297 (mtpp) cc_final: 0.6802 (mtmm) REVERT: D 45 ARG cc_start: 0.6926 (mtm180) cc_final: 0.6588 (mtp180) REVERT: D 61 ARG cc_start: 0.6806 (ptt90) cc_final: 0.6565 (ptp90) REVERT: E 48 GLU cc_start: 0.7223 (tt0) cc_final: 0.6887 (tt0) REVERT: E 97 CYS cc_start: 0.8181 (t) cc_final: 0.7809 (p) REVERT: E 112 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7120 (tt0) REVERT: F 5 THR cc_start: 0.6628 (m) cc_final: 0.6407 (p) REVERT: F 31 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6656 (mp0) REVERT: F 42 LYS cc_start: 0.7238 (mtpp) cc_final: 0.6739 (mtmm) REVERT: F 61 ARG cc_start: 0.6742 (ptt90) cc_final: 0.6471 (ptp90) outliers start: 16 outliers final: 7 residues processed: 119 average time/residue: 1.2809 time to fit residues: 159.9862 Evaluate side-chains 117 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 D residue 12 SER 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 66 optimal weight: 0.0980 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 54 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7058 Z= 0.256 Angle : 0.567 6.505 9564 Z= 0.293 Chirality : 0.043 0.146 1054 Planarity : 0.005 0.045 1156 Dihedral : 12.049 151.834 1136 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.41 % Allowed : 12.81 % Favored : 83.79 % 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: 1.61 (0.30), residues: 840 helix: 2.06 (0.28), residues: 306 sheet: 1.07 (0.35), residues: 240 loop : 0.07 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 110 HIS 0.003 0.001 HIS D 38 PHE 0.018 0.002 PHE A 69 TYR 0.013 0.002 TYR F 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 fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 0.678 Fit side-chains REVERT: A 103 THR cc_start: 0.8260 (m) cc_final: 0.7988 (p) REVERT: A 134 LEU cc_start: 0.6772 (mt) cc_final: 0.6511 (mm) REVERT: A 138 LYS cc_start: 0.6466 (mptt) cc_final: 0.6245 (mptt) REVERT: A 139 GLU cc_start: 0.6623 (tt0) cc_final: 0.6328 (tt0) REVERT: B 63 ARG cc_start: 0.6263 (OUTLIER) cc_final: 0.5940 (mtp85) REVERT: B 103 THR cc_start: 0.8261 (m) cc_final: 0.7988 (p) REVERT: B 134 LEU cc_start: 0.6766 (mt) cc_final: 0.6500 (mm) REVERT: B 138 LYS cc_start: 0.6563 (mptt) cc_final: 0.6338 (mptt) REVERT: B 139 GLU cc_start: 0.6619 (tt0) cc_final: 0.6315 (tt0) REVERT: C 48 GLU cc_start: 0.7234 (tt0) cc_final: 0.6917 (tt0) REVERT: C 97 CYS cc_start: 0.8305 (t) cc_final: 0.7676 (p) REVERT: D 5 THR cc_start: 0.6501 (m) cc_final: 0.6270 (p) REVERT: D 31 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6651 (mp0) REVERT: D 42 LYS cc_start: 0.7257 (mtpp) cc_final: 0.6782 (mtmm) REVERT: D 45 ARG cc_start: 0.6961 (mtm180) cc_final: 0.6525 (mtp180) REVERT: E 48 GLU cc_start: 0.7219 (tt0) cc_final: 0.6913 (tt0) REVERT: E 97 CYS cc_start: 0.8347 (t) cc_final: 0.7681 (p) REVERT: F 5 THR cc_start: 0.6503 (m) cc_final: 0.6296 (p) REVERT: F 31 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6581 (mp0) REVERT: F 42 LYS cc_start: 0.7268 (mtpp) cc_final: 0.6786 (mtmm) outliers start: 25 outliers final: 7 residues processed: 115 average time/residue: 1.3231 time to fit residues: 159.4340 Evaluate side-chains 109 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 63 ARG 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 F residue 45 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.7980 chunk 71 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7058 Z= 0.166 Angle : 0.519 6.243 9564 Z= 0.268 Chirality : 0.041 0.151 1054 Planarity : 0.005 0.048 1156 Dihedral : 11.377 146.154 1136 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.63 % Allowed : 13.76 % Favored : 84.60 % 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: 1.80 (0.30), residues: 840 helix: 2.28 (0.28), residues: 306 sheet: 1.18 (0.35), residues: 240 loop : 0.11 (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 0.010 0.001 TYR D 86 ARG 0.002 0.000 ARG B 29 *********************** 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 123 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.775 Fit side-chains REVERT: A 27 LYS cc_start: 0.6892 (ttmt) cc_final: 0.6404 (mttt) REVERT: A 103 THR cc_start: 0.8247 (m) cc_final: 0.7995 (p) REVERT: A 134 LEU cc_start: 0.6736 (mt) cc_final: 0.6499 (mm) REVERT: A 138 LYS cc_start: 0.6463 (mptt) cc_final: 0.6249 (mptt) REVERT: A 139 GLU cc_start: 0.6614 (tt0) cc_final: 0.6303 (tt0) REVERT: B 27 LYS cc_start: 0.6893 (ttmt) cc_final: 0.6404 (mttt) REVERT: B 63 ARG cc_start: 0.6268 (OUTLIER) cc_final: 0.5946 (mtp85) REVERT: B 103 THR cc_start: 0.8252 (m) cc_final: 0.7997 (p) REVERT: B 134 LEU cc_start: 0.6744 (mt) cc_final: 0.6504 (mm) REVERT: B 138 LYS cc_start: 0.6649 (mptt) cc_final: 0.6379 (mptt) REVERT: B 139 GLU cc_start: 0.6625 (tt0) cc_final: 0.6337 (tt0) REVERT: C 48 GLU cc_start: 0.7184 (tt0) cc_final: 0.6904 (tt0) REVERT: C 97 CYS cc_start: 0.8313 (t) cc_final: 0.7675 (p) REVERT: D 31 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6692 (mp0) REVERT: D 42 LYS cc_start: 0.7256 (mtpp) cc_final: 0.6775 (mtmm) REVERT: D 45 ARG cc_start: 0.6885 (mtm180) cc_final: 0.6520 (mtp180) REVERT: E 48 GLU cc_start: 0.7195 (tt0) cc_final: 0.6910 (tt0) REVERT: E 97 CYS cc_start: 0.8285 (t) cc_final: 0.7683 (p) REVERT: F 31 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6657 (mp0) REVERT: F 42 LYS cc_start: 0.7247 (mtpp) cc_final: 0.6781 (mtmm) outliers start: 12 outliers final: 6 residues processed: 114 average time/residue: 1.3265 time to fit residues: 158.4815 Evaluate side-chains 115 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain D residue 12 SER 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 8 optimal weight: 0.3980 chunk 45 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3032 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 : 0.529 6.274 9564 Z= 0.272 Chirality : 0.041 0.147 1054 Planarity : 0.005 0.048 1156 Dihedral : 11.229 142.867 1136 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.50 % Allowed : 13.62 % Favored : 84.88 % 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: 1.86 (0.30), residues: 840 helix: 2.34 (0.28), residues: 304 sheet: 1.23 (0.35), residues: 240 loop : 0.12 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 110 HIS 0.003 0.001 HIS E 52 PHE 0.016 0.001 PHE B 69 TYR 0.011 0.001 TYR D 86 ARG 0.002 0.000 ARG A 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 118 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 0.813 Fit side-chains REVERT: A 27 LYS cc_start: 0.6887 (ttmt) cc_final: 0.6413 (mttt) REVERT: A 103 THR cc_start: 0.8258 (m) cc_final: 0.8000 (p) REVERT: A 134 LEU cc_start: 0.6752 (mt) cc_final: 0.6502 (mm) REVERT: A 138 LYS cc_start: 0.6552 (mptt) cc_final: 0.6348 (mptt) REVERT: A 139 GLU cc_start: 0.6718 (tt0) cc_final: 0.6401 (tt0) REVERT: A 166 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.6033 (mmm) REVERT: B 27 LYS cc_start: 0.6886 (ttmt) cc_final: 0.6413 (mttt) REVERT: B 63 ARG cc_start: 0.6280 (OUTLIER) cc_final: 0.5957 (mtp85) REVERT: B 103 THR cc_start: 0.8260 (m) cc_final: 0.8001 (p) REVERT: B 134 LEU cc_start: 0.6737 (mt) cc_final: 0.6494 (mm) REVERT: B 138 LYS cc_start: 0.6637 (mptt) cc_final: 0.6363 (mptt) REVERT: B 139 GLU cc_start: 0.6710 (tt0) cc_final: 0.6382 (tt0) REVERT: C 17 THR cc_start: 0.6663 (p) cc_final: 0.6417 (m) REVERT: C 48 GLU cc_start: 0.7173 (tt0) cc_final: 0.6897 (tt0) REVERT: C 97 CYS cc_start: 0.8321 (t) cc_final: 0.7609 (p) REVERT: C 114 THR cc_start: 0.7298 (t) cc_final: 0.6987 (p) REVERT: D 31 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6652 (mp0) REVERT: D 42 LYS cc_start: 0.7241 (mtpp) cc_final: 0.6764 (mtmm) REVERT: D 61 ARG cc_start: 0.6861 (ptp-170) cc_final: 0.6520 (ptp90) REVERT: E 48 GLU cc_start: 0.7177 (tt0) cc_final: 0.6634 (tt0) REVERT: E 97 CYS cc_start: 0.8324 (t) cc_final: 0.7646 (p) REVERT: F 31 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6603 (mp0) REVERT: F 42 LYS cc_start: 0.7286 (mtpp) cc_final: 0.6708 (mtmm) outliers start: 11 outliers final: 4 residues processed: 109 average time/residue: 1.3078 time to fit residues: 149.6347 Evaluate side-chains 111 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7058 Z= 0.226 Angle : 0.553 6.393 9564 Z= 0.284 Chirality : 0.042 0.158 1054 Planarity : 0.005 0.050 1156 Dihedral : 11.244 142.996 1136 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.63 % Allowed : 13.62 % Favored : 84.74 % 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: 2.19 (0.28), residues: 304 sheet: 1.22 (0.35), residues: 240 loop : 0.12 (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 F 38 PHE 0.017 0.002 PHE B 69 TYR 0.012 0.002 TYR D 86 ARG 0.002 0.000 ARG A 107 *********************** 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 125 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.752 Fit side-chains REVERT: A 103 THR cc_start: 0.8276 (m) cc_final: 0.7956 (p) REVERT: A 134 LEU cc_start: 0.6743 (mt) cc_final: 0.6492 (mm) REVERT: A 138 LYS cc_start: 0.6578 (mptt) cc_final: 0.6362 (mptt) REVERT: A 139 GLU cc_start: 0.6656 (tt0) cc_final: 0.6329 (tt0) REVERT: A 166 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.5956 (mmm) REVERT: B 63 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5929 (mtp85) REVERT: B 103 THR cc_start: 0.8281 (m) cc_final: 0.7957 (p) REVERT: B 134 LEU cc_start: 0.6758 (mt) cc_final: 0.6500 (mm) REVERT: B 138 LYS cc_start: 0.6567 (mptt) cc_final: 0.6349 (mptt) REVERT: B 139 GLU cc_start: 0.6694 (tt0) cc_final: 0.6365 (tt0) REVERT: C 17 THR cc_start: 0.6790 (p) cc_final: 0.6549 (m) REVERT: C 48 GLU cc_start: 0.7186 (tt0) cc_final: 0.6652 (tt0) REVERT: C 97 CYS cc_start: 0.8302 (t) cc_final: 0.7576 (p) REVERT: C 114 THR cc_start: 0.7289 (t) cc_final: 0.6979 (p) REVERT: D 31 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6637 (mp0) REVERT: D 42 LYS cc_start: 0.7252 (mtpp) cc_final: 0.6787 (mtmm) REVERT: D 61 ARG cc_start: 0.6740 (ptp-170) cc_final: 0.6488 (ptp90) REVERT: E 48 GLU cc_start: 0.7201 (tt0) cc_final: 0.6662 (tt0) REVERT: E 97 CYS cc_start: 0.8313 (t) cc_final: 0.7542 (p) REVERT: F 31 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6596 (mp0) REVERT: F 42 LYS cc_start: 0.7303 (mtpp) cc_final: 0.6729 (mtmm) REVERT: F 61 ARG cc_start: 0.6715 (ptp-170) cc_final: 0.6376 (ptp90) outliers start: 12 outliers final: 6 residues processed: 117 average time/residue: 1.2670 time to fit residues: 155.7555 Evaluate side-chains 118 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 63 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 0.0170 chunk 32 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 16 GLN E 112 GLN F 30 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7058 Z= 0.165 Angle : 0.517 6.214 9564 Z= 0.266 Chirality : 0.041 0.171 1054 Planarity : 0.005 0.050 1156 Dihedral : 10.818 141.106 1136 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.50 % Allowed : 14.85 % Favored : 83.65 % 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: 1.94 (0.30), residues: 840 helix: 2.36 (0.27), residues: 304 sheet: 1.29 (0.35), residues: 240 loop : 0.19 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 110 HIS 0.003 0.001 HIS E 52 PHE 0.016 0.001 PHE B 39 TYR 0.011 0.001 TYR D 86 ARG 0.001 0.000 ARG C 68 *********************** 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 fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.717 Fit side-chains REVERT: A 27 LYS cc_start: 0.6874 (ttmt) cc_final: 0.6412 (mttt) REVERT: A 103 THR cc_start: 0.8299 (m) cc_final: 0.8027 (p) REVERT: A 134 LEU cc_start: 0.6750 (mt) cc_final: 0.6509 (mm) REVERT: A 138 LYS cc_start: 0.6612 (mptt) cc_final: 0.6357 (mptt) REVERT: A 139 GLU cc_start: 0.6702 (tt0) cc_final: 0.6433 (tt0) REVERT: B 27 LYS cc_start: 0.6874 (ttmt) cc_final: 0.6411 (mttt) REVERT: B 63 ARG cc_start: 0.6239 (OUTLIER) cc_final: 0.5915 (mtp85) REVERT: B 103 THR cc_start: 0.8302 (m) cc_final: 0.8027 (p) REVERT: B 134 LEU cc_start: 0.6734 (mt) cc_final: 0.6497 (mm) REVERT: B 138 LYS cc_start: 0.6603 (mptt) cc_final: 0.6341 (mptt) REVERT: B 139 GLU cc_start: 0.6697 (tt0) cc_final: 0.6425 (tt0) REVERT: C 17 THR cc_start: 0.6812 (p) cc_final: 0.6608 (m) REVERT: C 48 GLU cc_start: 0.7135 (tt0) cc_final: 0.6863 (tt0) REVERT: C 97 CYS cc_start: 0.8240 (t) cc_final: 0.7738 (p) REVERT: C 114 THR cc_start: 0.7286 (t) cc_final: 0.6996 (p) REVERT: D 31 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6643 (mp0) REVERT: D 42 LYS cc_start: 0.7237 (mtpp) cc_final: 0.6767 (mtmm) REVERT: D 61 ARG cc_start: 0.6779 (ptp-170) cc_final: 0.6519 (ptp90) REVERT: E 48 GLU cc_start: 0.7137 (tt0) cc_final: 0.6611 (tt0) REVERT: E 97 CYS cc_start: 0.8246 (t) cc_final: 0.7719 (p) REVERT: F 31 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6619 (mp0) REVERT: F 42 LYS cc_start: 0.7255 (mtpp) cc_final: 0.6679 (mtmm) REVERT: F 61 ARG cc_start: 0.6768 (ptp-170) cc_final: 0.6477 (ptp90) outliers start: 11 outliers final: 5 residues processed: 119 average time/residue: 1.3967 time to fit residues: 174.3944 Evaluate side-chains 116 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 81 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 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 : 0.003 0.024 7058 Z= 0.171 Angle : 0.521 6.211 9564 Z= 0.269 Chirality : 0.041 0.170 1054 Planarity : 0.005 0.050 1156 Dihedral : 10.707 139.251 1136 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.23 % Allowed : 15.12 % Favored : 83.65 % 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: 1.98 (0.30), residues: 840 helix: 2.35 (0.27), residues: 304 sheet: 1.35 (0.35), residues: 240 loop : 0.24 (0.40), 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 0.001 PHE B 39 TYR 0.012 0.001 TYR D 91 ARG 0.001 0.000 ARG B 107 ********************** 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 123 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.802 Fit side-chains REVERT: A 27 LYS cc_start: 0.7000 (ttmt) cc_final: 0.6529 (mttt) REVERT: A 103 THR cc_start: 0.8302 (m) cc_final: 0.8029 (p) REVERT: A 134 LEU cc_start: 0.6746 (mt) cc_final: 0.6502 (mm) REVERT: A 138 LYS cc_start: 0.6613 (mptt) cc_final: 0.6349 (mptt) REVERT: A 139 GLU cc_start: 0.6712 (tt0) cc_final: 0.6447 (tt0) REVERT: A 166 MET cc_start: 0.6353 (OUTLIER) cc_final: 0.6003 (mmm) REVERT: B 27 LYS cc_start: 0.7000 (ttmt) cc_final: 0.6528 (mttt) REVERT: B 63 ARG cc_start: 0.6249 (OUTLIER) cc_final: 0.5925 (mtp85) REVERT: B 103 THR cc_start: 0.8303 (m) cc_final: 0.8029 (p) REVERT: B 134 LEU cc_start: 0.6747 (mt) cc_final: 0.6504 (mm) REVERT: B 138 LYS cc_start: 0.6609 (mptt) cc_final: 0.6346 (mptt) REVERT: B 139 GLU cc_start: 0.6712 (tt0) cc_final: 0.6441 (tt0) REVERT: C 48 GLU cc_start: 0.7114 (tt0) cc_final: 0.6595 (tt0) REVERT: C 97 CYS cc_start: 0.8253 (t) cc_final: 0.7657 (p) REVERT: C 114 THR cc_start: 0.7295 (t) cc_final: 0.7019 (p) REVERT: D 31 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6599 (mp0) REVERT: D 42 LYS cc_start: 0.7236 (mtpp) cc_final: 0.6764 (mtmm) REVERT: D 61 ARG cc_start: 0.6769 (ptp-170) cc_final: 0.6508 (ptp90) REVERT: E 48 GLU cc_start: 0.7105 (tt0) cc_final: 0.6597 (tt0) REVERT: E 97 CYS cc_start: 0.8288 (t) cc_final: 0.7708 (p) REVERT: F 31 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6574 (mp0) REVERT: F 42 LYS cc_start: 0.7248 (mtpp) cc_final: 0.6754 (mtmm) REVERT: F 61 ARG cc_start: 0.6777 (ptp-170) cc_final: 0.6542 (ptp90) outliers start: 9 outliers final: 6 residues processed: 118 average time/residue: 1.3664 time to fit residues: 169.1369 Evaluate side-chains 120 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.160135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.111053 restraints weight = 6856.292| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.07 r_work: 0.3068 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3233 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 : 0.530 6.243 9564 Z= 0.273 Chirality : 0.041 0.173 1054 Planarity : 0.005 0.050 1156 Dihedral : 10.720 139.459 1136 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.09 % Allowed : 15.94 % 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: 1.99 (0.30), residues: 840 helix: 2.32 (0.27), residues: 304 sheet: 1.40 (0.35), residues: 240 loop : 0.26 (0.41), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 110 HIS 0.003 0.001 HIS E 52 PHE 0.016 0.002 PHE A 39 TYR 0.012 0.001 TYR D 86 ARG 0.002 0.000 ARG B 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3204.90 seconds wall clock time: 56 minutes 32.85 seconds (3392.85 seconds total)