Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 03:21:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/04_2023/6nt7_0504_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/04_2023/6nt7_0504.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/04_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_0504/04_2023/6nt7_0504_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/04_2023/6nt7_0504_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/04_2023/6nt7_0504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/04_2023/6nt7_0504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/04_2023/6nt7_0504_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/04_2023/6nt7_0504_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 3.16, per 1000 atoms: 0.67 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: 2.31 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: 0.46 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: 1.15 Time building geometry restraints manager: 2.42 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 - 30.11: 2800 30.11 - 60.23: 74 60.23 - 90.34: 5 90.34 - 120.45: 1 120.45 - 150.57: 1 Dihedral angle restraints: 2881 sinusoidal: 1163 harmonic: 1718 Sorted by residual: 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 dihedral pdb=" CA GLN A 56 " pdb=" C GLN A 56 " pdb=" N LEU A 57 " pdb=" CA LEU A 57 " ideal model delta harmonic sigma weight residual -180.00 -160.45 -19.55 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 2878 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: 0.310 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: 1.960 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.420 Find NCS groups from input model: 0.260 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: 23.000 ------------------------------------------------------------------------------- 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 : 14.163 150.568 1757 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 % 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 *********************** 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 : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2139 time to fit residues: 21.3513 Evaluate side-chains 33 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7360 ------------------------------------------------------------------------------- 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: 0.8426 moved from start: 0.2141 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= 0.252 Angle : 0.641 8.740 6540 Z= 0.307 Chirality : 0.039 0.147 762 Planarity : 0.005 0.054 796 Dihedral : 8.784 147.275 639 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 3.32 % 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: -1.58 (0.33), residues: 560 helix: -0.32 (0.27), residues: 320 sheet: -1.58 (0.68), residues: 74 loop : -1.98 (0.39), residues: 166 *********************** 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 62 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 45 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 55 average time/residue: 0.1894 time to fit residues: 13.5115 Evaluate side-chains 42 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 30 time to evaluate : 0.600 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0555 time to fit residues: 1.9352 ------------------------------------------------------------------------------- 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: 7.9990 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.8408 moved from start: 0.2591 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 : 0.595 10.485 6540 Z= 0.275 Chirality : 0.040 0.160 762 Planarity : 0.004 0.047 796 Dihedral : 8.530 147.178 639 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 1.17 % 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: -0.45 (0.35), residues: 560 helix: 0.73 (0.29), residues: 308 sheet: -1.89 (0.65), residues: 80 loop : -1.21 (0.43), residues: 172 *********************** 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 47 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 46 average time/residue: 0.1417 time to fit residues: 9.2035 Evaluate side-chains 36 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.597 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0461 time to fit residues: 0.9707 ------------------------------------------------------------------------------- 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: 5.9990 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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: 0.8439 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 4827 Z= 0.292 Angle : 0.619 8.525 6540 Z= 0.291 Chirality : 0.040 0.160 762 Planarity : 0.004 0.045 796 Dihedral : 8.435 146.042 639 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer Outliers : 3.52 % 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: -0.15 (0.36), residues: 560 helix: 0.93 (0.29), residues: 310 sheet: -1.92 (0.65), residues: 80 loop : -0.90 (0.47), residues: 170 *********************** 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 54 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 36 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 50 average time/residue: 0.1348 time to fit residues: 9.6330 Evaluate side-chains 40 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0467 time to fit residues: 1.4279 ------------------------------------------------------------------------------- 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: 8.9990 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 0.0060 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.1980 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- 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: 0.8380 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 4827 Z= 0.144 Angle : 0.588 11.143 6540 Z= 0.262 Chirality : 0.040 0.174 762 Planarity : 0.004 0.043 796 Dihedral : 8.247 145.046 639 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 1.17 % 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: 0.31 (0.37), residues: 560 helix: 1.41 (0.30), residues: 306 sheet: -1.78 (0.66), residues: 80 loop : -0.85 (0.46), residues: 174 *********************** 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 49 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.1446 time to fit residues: 9.3655 Evaluate side-chains 40 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.586 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0578 time to fit residues: 1.1693 ------------------------------------------------------------------------------- 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: 8.9990 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 0.0370 chunk 29 optimal weight: 0.0270 chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- 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: 0.8360 moved from start: 0.3431 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= 0.140 Angle : 0.564 10.284 6540 Z= 0.258 Chirality : 0.039 0.182 762 Planarity : 0.003 0.041 796 Dihedral : 8.031 142.631 639 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 0.59 % 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: 0.55 (0.37), residues: 560 helix: 1.62 (0.30), residues: 306 sheet: -1.72 (0.65), residues: 80 loop : -0.75 (0.46), residues: 174 *********************** 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: 3 poor density : 39 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.1402 time to fit residues: 8.1417 Evaluate side-chains 35 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.612 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0479 time to fit residues: 0.9024 ------------------------------------------------------------------------------- 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: 10.0000 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 34 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.8366 moved from start: 0.3588 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= 0.159 Angle : 0.592 10.915 6540 Z= 0.265 Chirality : 0.040 0.184 762 Planarity : 0.003 0.041 796 Dihedral : 7.910 140.616 639 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 0.39 % 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: 0.81 (0.38), residues: 560 helix: 1.83 (0.31), residues: 308 sheet: -1.66 (0.65), residues: 80 loop : -0.64 (0.47), residues: 172 *********************** 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 36 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 36 average time/residue: 0.1462 time to fit residues: 7.7507 Evaluate side-chains 33 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.592 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7843 ------------------------------------------------------------------------------- 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: 5.9990 chunk 5 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 22 optimal weight: 0.0870 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- 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: 0.8340 moved from start: 0.3746 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: