Starting phenix.real_space_refine on Sun Mar 10 20:11:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/03_2024/6nt7_0504_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/03_2024/6nt7_0504.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/03_2024/6nt7_0504_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/03_2024/6nt7_0504_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/03_2024/6nt7_0504_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/03_2024/6nt7_0504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/03_2024/6nt7_0504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/03_2024/6nt7_0504_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/03_2024/6nt7_0504_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 36 5.16 5 C 3040 2.51 5 N 834 2.21 5 O 817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 315": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4729 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2342 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 6 Chain: "B" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2342 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 6 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.27, per 1000 atoms: 0.69 Number of scatterers: 4729 At special positions: 0 Unit cell: (79.8, 57.96, 103.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 2 15.00 O 817 8.00 N 834 7.00 C 3040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.86 Conformation dependent library (CDL) restraints added in 809.0 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 6 sheets defined 54.1% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 24 through 40 Processing helix chain 'A' and resid 50 through 82 removed outlier: 4.547A pdb=" N ALA A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A 73 " --> pdb=" O CYS A 69 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU A 74 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU A 75 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N SER A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 127 through 139 removed outlier: 3.633A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'A' and resid 173 through 188 removed outlier: 3.728A pdb=" N LEU A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 5.005A pdb=" N LYS A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 286 through 305 Processing helix chain 'A' and resid 330 through 340 Processing helix chain 'B' and resid 24 through 40 Processing helix chain 'B' and resid 50 through 82 removed outlier: 4.547A pdb=" N ALA B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B 73 " --> pdb=" O CYS B 69 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 75 " --> pdb=" O CYS B 71 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N HIS B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N SER B 81 " --> pdb=" O PHE B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 94 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 127 through 139 removed outlier: 3.632A pdb=" N LEU B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 155 Processing helix chain 'B' and resid 160 through 171 Processing helix chain 'B' and resid 173 through 188 removed outlier: 3.728A pdb=" N LEU B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 5.005A pdb=" N LYS B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLU B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS B 183 " --> pdb=" O ARG B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 268 through 276 Processing helix chain 'B' and resid 286 through 305 Processing helix chain 'B' and resid 330 through 340 Processing sheet with id= A, first strand: chain 'A' and resid 314 through 319 removed outlier: 6.386A pdb=" N LEU A 203 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE A 317 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE A 205 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TYR A 319 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 207 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 233 through 235 Processing sheet with id= C, first strand: chain 'A' and resid 260 through 263 removed outlier: 3.675A pdb=" N ALA A 228 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 251 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TYR A 226 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 314 through 319 removed outlier: 6.386A pdb=" N LEU B 203 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 317 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE B 205 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TYR B 319 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 207 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 233 through 235 Processing sheet with id= F, first strand: chain 'B' and resid 260 through 263 removed outlier: 3.675A pdb=" N ALA B 228 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL B 251 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TYR B 226 " --> pdb=" O VAL B 251 " (cutoff:3.500A) 210 hydrogen bonds defined for protein. 570 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: 1.18 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 744 1.32 - 1.44: 1271 1.44 - 1.56: 2767 1.56 - 1.69: 5 1.69 - 1.81: 40 Bond restraints: 4827 Sorted by residual: bond pdb=" C16 1SY A 401 " pdb=" O17 1SY A 401 " ideal model delta sigma weight residual 1.402 1.472 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C32 1SY A 401 " pdb=" N33 1SY A 401 " ideal model delta sigma weight residual 1.474 1.413 0.061 2.00e-02 2.50e+03 9.33e+00 bond pdb=" O26 1SY A 401 " pdb=" P27 1SY A 401 " ideal model delta sigma weight residual 1.658 1.599 0.059 2.00e-02 2.50e+03 8.57e+00 bond pdb=" O20 1SY A 401 " pdb=" P18 1SY A 401 " ideal model delta sigma weight residual 1.630 1.686 -0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" C4' 1SY A 401 " pdb=" O4' 1SY A 401 " ideal model delta sigma weight residual 1.459 1.407 0.052 2.00e-02 2.50e+03 6.87e+00 ... (remaining 4822 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.23: 196 107.23 - 113.94: 2857 113.94 - 120.66: 1980 120.66 - 127.37: 1444 127.37 - 134.09: 63 Bond angle restraints: 6540 Sorted by residual: angle pdb=" C VAL A 176 " pdb=" N LEU A 177 " pdb=" CA LEU A 177 " ideal model delta sigma weight residual 120.58 125.95 -5.37 1.32e+00 5.74e-01 1.66e+01 angle pdb=" C VAL B 176 " pdb=" N LEU B 177 " pdb=" CA LEU B 177 " ideal model delta sigma weight residual 120.58 125.93 -5.35 1.32e+00 5.74e-01 1.64e+01 angle pdb=" N SER B 268 " pdb=" CA SER B 268 " pdb=" C SER B 268 " ideal model delta sigma weight residual 112.75 117.15 -4.40 1.36e+00 5.41e-01 1.05e+01 angle pdb=" N SER A 268 " pdb=" CA SER A 268 " pdb=" C SER A 268 " ideal model delta sigma weight residual 112.75 117.13 -4.38 1.36e+00 5.41e-01 1.04e+01 angle pdb=" N LEU A 177 " pdb=" CA LEU A 177 " pdb=" C LEU A 177 " ideal model delta sigma weight residual 113.45 117.84 -4.39 1.39e+00 5.18e-01 9.98e+00 ... (remaining 6535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 2850 35.78 - 71.56: 36 71.56 - 107.34: 5 107.34 - 143.12: 0 143.12 - 178.90: 2 Dihedral angle restraints: 2893 sinusoidal: 1175 harmonic: 1718 Sorted by residual: dihedral pdb=" C3' 1SY A 401 " pdb=" C16 1SY A 401 " pdb=" C4' 1SY A 401 " pdb=" O17 1SY A 401 " ideal model delta sinusoidal sigma weight residual 116.11 -64.99 -178.90 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C16 1SY A 401 " pdb=" O17 1SY A 401 " pdb=" P18 1SY A 401 " pdb=" O20 1SY A 401 " ideal model delta sinusoidal sigma weight residual 266.83 116.26 150.57 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" CA GLN B 56 " pdb=" C GLN B 56 " pdb=" N LEU B 57 " pdb=" CA LEU B 57 " ideal model delta harmonic sigma weight residual -180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 2890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 580 0.048 - 0.095: 149 0.095 - 0.142: 27 0.142 - 0.190: 5 0.190 - 0.237: 1 Chirality restraints: 762 Sorted by residual: chirality pdb=" C24 1SY A 401 " pdb=" C22 1SY A 401 " pdb=" C25 1SY A 401 " pdb=" O31 1SY A 401 " both_signs ideal model delta sigma weight residual False -2.55 -2.32 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA LEU B 177 " pdb=" N LEU B 177 " pdb=" C LEU B 177 " pdb=" CB LEU B 177 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA LEU A 177 " pdb=" N LEU A 177 " pdb=" C LEU A 177 " pdb=" CB LEU A 177 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 759 not shown) Planarity restraints: 796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 95 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.47e+00 pdb=" N PRO B 96 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 96 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 96 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 95 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.42e+00 pdb=" N PRO A 96 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 230 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO A 231 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " 0.025 5.00e-02 4.00e+02 ... (remaining 793 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 930 2.77 - 3.30: 4200 3.30 - 3.84: 7199 3.84 - 4.37: 7969 4.37 - 4.90: 13665 Nonbonded interactions: 33963 Sorted by model distance: nonbonded pdb=" OG SER B 268 " pdb=" O2' 1SY A 401 " model vdw 2.238 2.440 nonbonded pdb=" O SER A 52 " pdb=" OG1 THR A 55 " model vdw 2.281 2.440 nonbonded pdb=" O SER B 52 " pdb=" OG1 THR B 55 " model vdw 2.281 2.440 nonbonded pdb=" O LEU B 187 " pdb=" OG1 THR B 190 " model vdw 2.313 2.440 nonbonded pdb=" O LEU A 187 " pdb=" OG1 THR A 190 " model vdw 2.314 2.440 ... (remaining 33958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 342) 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 group one per residue 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: 0.470 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: 1.830 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.880 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:3.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 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 : 0.008 0.070 4827 Z= 0.510 Angle : 0.902 8.226 6540 Z= 0.485 Chirality : 0.045 0.237 762 Planarity : 0.007 0.064 796 Dihedral : 14.875 178.904 1769 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.28), residues: 560 helix: -2.00 (0.22), residues: 308 sheet: -1.47 (0.65), residues: 74 loop : -2.45 (0.36), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 88 HIS 0.008 0.002 HIS B 80 PHE 0.012 0.002 PHE B 329 TYR 0.008 0.001 TYR A 100 ARG 0.003 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 ILE cc_start: 0.9436 (mt) cc_final: 0.9222 (mm) REVERT: B 303 ILE cc_start: 0.9381 (mt) cc_final: 0.9157 (mm) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2076 time to fit residues: 20.6860 Evaluate side-chains 35 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS B 78 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4827 Z= 0.248 Angle : 0.641 9.305 6540 Z= 0.304 Chirality : 0.040 0.157 762 Planarity : 0.005 0.053 796 Dihedral : 11.581 178.237 651 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.12 % Allowed : 10.35 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.33), residues: 560 helix: -0.30 (0.27), residues: 320 sheet: -1.60 (0.68), residues: 74 loop : -1.95 (0.39), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 99 HIS 0.003 0.001 HIS A 204 PHE 0.012 0.002 PHE B 95 TYR 0.004 0.001 TYR B 100 ARG 0.003 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 47 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7135 (tp) REVERT: A 54 CYS cc_start: 0.9025 (m) cc_final: 0.8559 (t) REVERT: A 70 CYS cc_start: 0.8699 (m) cc_final: 0.8301 (p) REVERT: B 49 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.6849 (tp) REVERT: B 54 CYS cc_start: 0.9079 (m) cc_final: 0.8676 (t) outliers start: 16 outliers final: 12 residues processed: 56 average time/residue: 0.2035 time to fit residues: 14.9753 Evaluate side-chains 47 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 33 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 284 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN B 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4827 Z= 0.265 Angle : 0.631 10.229 6540 Z= 0.292 Chirality : 0.040 0.153 762 Planarity : 0.004 0.046 796 Dihedral : 11.423 179.308 651 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.10 % Allowed : 12.30 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.36), residues: 560 helix: 0.75 (0.29), residues: 310 sheet: -1.95 (0.65), residues: 80 loop : -1.01 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 99 HIS 0.003 0.001 HIS A 78 PHE 0.014 0.001 PHE B 95 TYR 0.004 0.001 TYR B 314 ARG 0.004 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 39 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.9030 (m) cc_final: 0.8383 (t) REVERT: A 284 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7051 (m-80) REVERT: B 54 CYS cc_start: 0.9008 (m) cc_final: 0.8559 (t) outliers start: 21 outliers final: 8 residues processed: 54 average time/residue: 0.1371 time to fit residues: 10.4476 Evaluate side-chains 44 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 284 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.2980 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN B 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4827 Z= 0.174 Angle : 0.580 10.596 6540 Z= 0.263 Chirality : 0.040 0.169 762 Planarity : 0.004 0.044 796 Dihedral : 11.241 179.146 651 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.12 % Allowed : 14.45 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.36), residues: 560 helix: 1.19 (0.29), residues: 310 sheet: -1.82 (0.66), residues: 80 loop : -0.87 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 99 HIS 0.002 0.001 HIS B 162 PHE 0.008 0.001 PHE B 95 TYR 0.005 0.001 TYR B 314 ARG 0.004 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 40 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 CYS cc_start: 0.8641 (m) cc_final: 0.8285 (p) REVERT: A 284 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7045 (m-80) REVERT: B 54 CYS cc_start: 0.8965 (m) cc_final: 0.8461 (t) REVERT: B 284 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.6940 (m-80) outliers start: 16 outliers final: 5 residues processed: 51 average time/residue: 0.1319 time to fit residues: 9.5226 Evaluate side-chains 41 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 284 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 47 optimal weight: 0.0070 chunk 38 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4827 Z= 0.169 Angle : 0.592 10.649 6540 Z= 0.264 Chirality : 0.040 0.174 762 Planarity : 0.004 0.042 796 Dihedral : 11.061 179.283 651 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.32 % Allowed : 15.04 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.37), residues: 560 helix: 1.48 (0.30), residues: 310 sheet: -1.75 (0.66), residues: 80 loop : -0.71 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 99 HIS 0.002 0.001 HIS B 78 PHE 0.008 0.001 PHE B 95 TYR 0.004 0.001 TYR B 314 ARG 0.001 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 42 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 CYS cc_start: 0.8664 (m) cc_final: 0.8311 (p) REVERT: A 128 LEU cc_start: 0.8570 (pp) cc_final: 0.8120 (tp) REVERT: A 284 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7237 (m-80) REVERT: B 54 CYS cc_start: 0.8906 (m) cc_final: 0.8404 (t) REVERT: B 70 CYS cc_start: 0.8674 (m) cc_final: 0.8292 (p) REVERT: B 284 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7090 (m-80) outliers start: 17 outliers final: 6 residues processed: 52 average time/residue: 0.1291 time to fit residues: 9.5153 Evaluate side-chains 43 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 284 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN B 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4827 Z= 0.323 Angle : 0.671 10.028 6540 Z= 0.307 Chirality : 0.041 0.174 762 Planarity : 0.004 0.042 796 Dihedral : 11.030 176.658 651 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.91 % Allowed : 15.62 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.37), residues: 560 helix: 1.48 (0.29), residues: 310 sheet: -1.82 (0.66), residues: 80 loop : -0.54 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 99 HIS 0.003 0.001 HIS B 162 PHE 0.014 0.001 PHE B 95 TYR 0.005 0.001 TYR B 168 ARG 0.002 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 35 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.8575 (pp) cc_final: 0.8018 (tp) REVERT: A 284 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: B 54 CYS cc_start: 0.8909 (m) cc_final: 0.8399 (t) REVERT: B 284 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7201 (m-80) outliers start: 20 outliers final: 9 residues processed: 49 average time/residue: 0.1341 time to fit residues: 9.3407 Evaluate side-chains 45 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 34 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 284 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN B 223 ASN B 337 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4827 Z= 0.145 Angle : 0.581 10.177 6540 Z= 0.262 Chirality : 0.040 0.178 762 Planarity : 0.003 0.040 796 Dihedral : 10.913 177.167 651 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.71 % Allowed : 15.62 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.38), residues: 560 helix: 1.82 (0.30), residues: 308 sheet: -1.71 (0.65), residues: 80 loop : -0.66 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 99 HIS 0.002 0.000 HIS A 247 PHE 0.005 0.001 PHE B 266 TYR 0.006 0.001 TYR A 172 ARG 0.002 0.000 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 41 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 CYS cc_start: 0.8662 (m) cc_final: 0.8252 (p) REVERT: A 128 LEU cc_start: 0.8508 (pp) cc_final: 0.8045 (tp) REVERT: A 284 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: B 54 CYS cc_start: 0.8876 (m) cc_final: 0.8399 (t) REVERT: B 128 LEU cc_start: 0.8559 (pp) cc_final: 0.8161 (tt) REVERT: B 284 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7186 (m-80) outliers start: 19 outliers final: 7 residues processed: 55 average time/residue: 0.1255 time to fit residues: 9.8424 Evaluate side-chains 48 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 337 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4827 Z= 0.307 Angle : 0.678 10.158 6540 Z= 0.312 Chirality : 0.041 0.184 762 Planarity : 0.004 0.040 796 Dihedral : 10.899 175.632 651 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.91 % Allowed : 16.41 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.38), residues: 560 helix: 1.63 (0.29), residues: 310 sheet: -1.81 (0.65), residues: 80 loop : -0.41 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 99 HIS 0.013 0.001 HIS B 337 PHE 0.013 0.001 PHE A 95 TYR 0.005 0.001 TYR B 168 ARG 0.003 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 37 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.8531 (pp) cc_final: 0.8047 (tp) REVERT: A 279 ASP cc_start: 0.6278 (OUTLIER) cc_final: 0.5822 (p0) REVERT: A 284 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7405 (m-80) REVERT: B 54 CYS cc_start: 0.8909 (m) cc_final: 0.8385 (t) REVERT: B 128 LEU cc_start: 0.8606 (pp) cc_final: 0.8200 (tt) REVERT: B 284 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7249 (m-80) outliers start: 20 outliers final: 13 residues processed: 49 average time/residue: 0.1348 time to fit residues: 9.3219 Evaluate side-chains 51 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 35 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 337 HIS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 337 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 0.0020 chunk 51 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.5048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4827 Z= 0.151 Angle : 0.623 9.825 6540 Z= 0.279 Chirality : 0.039 0.193 762 Planarity : 0.003 0.039 796 Dihedral : 10.806 174.886 651 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.34 % Allowed : 18.36 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.38), residues: 560 helix: 1.87 (0.30), residues: 308 sheet: -1.76 (0.64), residues: 80 loop : -0.48 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 99 HIS 0.011 0.001 HIS A 337 PHE 0.005 0.001 PHE B 95 TYR 0.006 0.001 TYR B 314 ARG 0.003 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 37 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7446 (m-80) REVERT: B 54 CYS cc_start: 0.8932 (m) cc_final: 0.8388 (t) REVERT: B 284 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7243 (m-80) outliers start: 12 outliers final: 7 residues processed: 44 average time/residue: 0.1394 time to fit residues: 8.6846 Evaluate side-chains 46 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 284 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 0.2980 chunk 46 optimal weight: 0.0670 chunk 19 optimal weight: 8.9990 overall best weight: 1.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4827 Z= 0.170 Angle : 0.572 6.921 6540 Z= 0.265 Chirality : 0.039 0.195 762 Planarity : 0.003 0.039 796 Dihedral : 10.587 172.665 651 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.34 % Allowed : 17.97 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.38), residues: 560 helix: 2.01 (0.30), residues: 310 sheet: -1.72 (0.64), residues: 80 loop : -0.41 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 99 HIS 0.002 0.000 HIS A 337 PHE 0.006 0.001 PHE B 95 TYR 0.004 0.001 TYR B 314 ARG 0.001 0.000 ARG B 301 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7546 (m-80) REVERT: B 54 CYS cc_start: 0.8911 (m) cc_final: 0.8380 (t) REVERT: B 284 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7288 (m-80) outliers start: 12 outliers final: 9 residues processed: 48 average time/residue: 0.1350 time to fit residues: 9.2688 Evaluate side-chains 49 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 337 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN B 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.082467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.066147 restraints weight = 17575.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.067868 restraints weight = 11132.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.069025 restraints weight = 8305.918| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4827 Z= 0.281 Angle : 0.626 6.999 6540 Z= 0.293 Chirality : 0.040 0.189 762 Planarity : 0.004 0.040 796 Dihedral : 10.593 170.976 651 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.12 % Allowed : 17.19 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.38), residues: 560 helix: 2.00 (0.30), residues: 308 sheet: -1.79 (0.64), residues: 80 loop : -0.28 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 99 HIS 0.003 0.001 HIS B 162 PHE 0.012 0.001 PHE A 95 TYR 0.004 0.001 TYR B 168 ARG 0.001 0.000 ARG B 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1083.34 seconds wall clock time: 20 minutes 25.10 seconds (1225.10 seconds total)