Starting phenix.real_space_refine on Thu Dec 7 21:09:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/12_2023/6nt7_0504_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/12_2023/6nt7_0504.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/12_2023/6nt7_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_0504/12_2023/6nt7_0504_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/12_2023/6nt7_0504_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/12_2023/6nt7_0504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/12_2023/6nt7_0504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/12_2023/6nt7_0504_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/12_2023/6nt7_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-1.21rc1-5172/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: 3.23, per 1000 atoms: 0.68 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: 1.79 Conformation dependent library (CDL) restraints added in 836.0 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: 0.95 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: 1.21 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.790 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.870 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.310 ------------------------------------------------------------------------------- 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 : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2138 time to fit residues: 21.3815 Evaluate side-chains 33 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8268 ------------------------------------------------------------------------------- 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 B 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4827 Z= 0.250 Angle : 0.641 9.006 6540 Z= 0.306 Chirality : 0.040 0.155 762 Planarity : 0.005 0.053 796 Dihedral : 11.611 178.852 651 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.32 % Allowed : 10.55 % Favored : 86.13 % 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: -1.27 (0.33), residues: 560 helix: -0.10 (0.27), residues: 308 sheet: -1.56 (0.68), residues: 74 loop : -1.63 (0.39), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 99 HIS 0.002 0.001 HIS B 204 PHE 0.012 0.001 PHE B 95 TYR 0.004 0.001 TYR A 314 ARG 0.004 0.000 ARG A 13 *********************** 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: 17 poor density : 46 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 56 average time/residue: 0.1802 time to fit residues: 13.0749 Evaluate side-chains 40 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 28 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0535 time to fit residues: 1.8580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.8396 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4827 Z= 0.167 Angle : 0.587 10.888 6540 Z= 0.271 Chirality : 0.040 0.168 762 Planarity : 0.004 0.046 796 Dihedral : 11.375 178.610 651 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.98 % Allowed : 12.89 % Favored : 86.13 % 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: -0.50 (0.35), residues: 560 helix: 0.70 (0.29), residues: 308 sheet: -1.88 (0.65), residues: 80 loop : -1.28 (0.42), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 99 HIS 0.002 0.001 HIS B 78 PHE 0.009 0.001 PHE B 95 TYR 0.004 0.001 TYR A 100 ARG 0.002 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 48 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 48 average time/residue: 0.1271 time to fit residues: 8.6650 Evaluate side-chains 34 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.517 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0438 time to fit residues: 0.8495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.8446 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4827 Z= 0.318 Angle : 0.648 8.422 6540 Z= 0.305 Chirality : 0.041 0.165 762 Planarity : 0.004 0.045 796 Dihedral : 11.340 179.328 651 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.32 % Allowed : 14.06 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.08 (0.36), residues: 560 helix: 0.94 (0.29), residues: 310 sheet: -1.65 (0.69), residues: 74 loop : -0.95 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 99 HIS 0.004 0.001 HIS A 162 PHE 0.015 0.002 PHE B 95 TYR 0.004 0.001 TYR B 100 ARG 0.003 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 51 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 34 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 47 average time/residue: 0.1427 time to fit residues: 9.6292 Evaluate side-chains 41 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.604 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0505 time to fit residues: 1.6333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 0.0570 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.0170 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4827 Z= 0.161 Angle : 0.586 10.449 6540 Z= 0.264 Chirality : 0.040 0.172 762 Planarity : 0.004 0.042 796 Dihedral : 11.213 179.949 651 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.37 % Allowed : 15.43 % Favored : 83.20 % 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: 0.32 (0.37), residues: 560 helix: 1.39 (0.30), residues: 310 sheet: -1.83 (0.66), residues: 80 loop : -0.84 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 99 HIS 0.002 0.001 HIS A 247 PHE 0.007 0.001 PHE B 95 TYR 0.004 0.001 TYR B 314 ARG 0.001 0.000 ARG A 286 *********************** 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 47 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 44 average time/residue: 0.1415 time to fit residues: 8.7274 Evaluate side-chains 35 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.574 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0544 time to fit residues: 1.0335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 0.0670 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 18 optimal weight: 0.1980 chunk 29 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4827 Z= 0.143 Angle : 0.544 7.440 6540 Z= 0.253 Chirality : 0.039 0.176 762 Planarity : 0.003 0.041 796 Dihedral : 10.959 178.498 651 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.39 % Allowed : 16.60 % Favored : 83.01 % 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: 0.59 (0.38), residues: 560 helix: 1.62 (0.30), residues: 310 sheet: -1.76 (0.65), residues: 80 loop : -0.69 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 99 HIS 0.001 0.000 HIS A 247 PHE 0.005 0.001 PHE B 95 TYR 0.005 0.001 TYR A 314 ARG 0.002 0.000 ARG A 13 *********************** 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 42 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 41 average time/residue: 0.1383 time to fit residues: 8.1131 Evaluate side-chains 35 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.576 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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: 0.8390 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4827 Z= 0.208 Angle : 0.612 10.871 6540 Z= 0.274 Chirality : 0.040 0.182 762 Planarity : 0.004 0.041 796 Dihedral : 10.830 175.870 651 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.78 % Allowed : 17.58 % 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: 0.78 (0.38), residues: 560 helix: 1.75 (0.30), residues: 310 sheet: -1.74 (0.65), residues: 80 loop : -0.52 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 99 HIS 0.002 0.001 HIS A 78 PHE 0.009 0.001 PHE A 95 TYR 0.004 0.001 TYR A 100 ARG 0.001 0.000 ARG B 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 39 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 38 average time/residue: 0.1435 time to fit residues: 7.8702 Evaluate side-chains 33 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.591 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0457 time to fit residues: 0.8642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 43 optimal weight: 0.0170 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 22 optimal weight: 0.0570 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN B 337 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4827 Z= 0.192 Angle : 0.623 11.284 6540 Z= 0.282 Chirality : 0.040 0.185 762 Planarity : 0.003 0.040 796 Dihedral : 10.738 173.741 651 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.17 % Allowed : 16.99 % Favored : 81.84 % 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: 0.84 (0.38), residues: 560 helix: 1.83 (0.31), residues: 308 sheet: -1.74 (0.65), residues: 80 loop : -0.52 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 99 HIS 0.002 0.001 HIS A 78 PHE 0.009 0.001 PHE B 95 TYR 0.004 0.001 TYR A 314 ARG 0.002 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 41 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 41 average time/residue: 0.1427 time to fit residues: 8.3970 Evaluate side-chains 34 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0557 time to fit residues: 0.8660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 0.0470 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 HIS B 337 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4827 Z= 0.198 Angle : 0.633 10.716 6540 Z= 0.286 Chirality : 0.040 0.188 762 Planarity : 0.003 0.040 796 Dihedral : 10.668 172.259 651 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.39 % Allowed : 18.16 % Favored : 81.45 % 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: 0.85 (0.38), residues: 560 helix: 1.84 (0.31), residues: 308 sheet: -1.75 (0.65), residues: 80 loop : -0.50 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 99 HIS 0.002 0.001 HIS A 337 PHE 0.009 0.001 PHE B 95 TYR 0.003 0.001 TYR B 314 ARG 0.002 0.000 ARG A 198 *********************** 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 35 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.1418 time to fit residues: 7.1017 Evaluate side-chains 35 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0524 time to fit residues: 0.7665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 0.0570 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 0.0020 chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.2112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4827 Z= 0.208 Angle : 0.632 11.562 6540 Z= 0.287 Chirality : 0.041 0.191 762 Planarity : 0.004 0.040 796 Dihedral : 10.550 169.598 651 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.20 % Allowed : 17.77 % Favored : 82.03 % 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: 1.75 (0.30), residues: 312 sheet: -1.75 (0.65), residues: 80 loop : -0.53 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 99 HIS 0.002 0.001 HIS A 337 PHE 0.010 0.001 PHE B 95 TYR 0.004 0.001 TYR B 314 ARG 0.002 0.000 ARG A 198 ********************** 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 37 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.1497 time to fit residues: 7.7220 Evaluate side-chains 32 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 36 optimal weight: 0.3980 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN A 337 HIS B 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.083583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.066682 restraints weight = 17450.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.068421 restraints weight = 11268.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.069612 restraints weight = 8453.780| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4827 Z= 0.222 Angle : 0.604 7.806 6540 Z= 0.281 Chirality : 0.040 0.191 762 Planarity : 0.003 0.039 796 Dihedral : 10.493 168.231 651 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.20 % Allowed : 17.77 % Favored : 82.03 % 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: 0.95 (0.38), residues: 560 helix: 1.91 (0.30), residues: 308 sheet: -1.81 (0.64), residues: 80 loop : -0.38 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 99 HIS 0.002 0.001 HIS B 78 PHE 0.010 0.001 PHE B 95 TYR 0.005 0.001 TYR A 319 ARG 0.001 0.000 ARG B 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1074.50 seconds wall clock time: 20 minutes 18.70 seconds (1218.70 seconds total)