Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:47:49 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/11_2022/6nt7_0504_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/11_2022/6nt7_0504.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/11_2022/6nt7_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_0504/11_2022/6nt7_0504_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/11_2022/6nt7_0504_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/11_2022/6nt7_0504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/11_2022/6nt7_0504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/11_2022/6nt7_0504_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nt7_0504/11_2022/6nt7_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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 315": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/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: 3.11, per 1000 atoms: 0.66 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: 1.99 Conformation dependent library (CDL) restraints added in 694.0 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: 1.52 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: 1.17 Time building geometry restraints manager: 2.16 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=" O26 1SY A 401 " pdb=" P27 1SY A 401 " ideal model delta sigma weight residual 1.723 1.599 0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" O28 1SY A 401 " pdb=" P27 1SY A 401 " ideal model delta sigma weight residual 1.770 1.648 0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C1' 1SY A 401 " pdb=" N9 1SY A 401 " ideal model delta sigma weight residual 1.432 1.362 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C32 1SY A 401 " pdb=" N33 1SY A 401 " ideal model delta sigma weight residual 1.482 1.413 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C21 1SY A 401 " pdb=" O20 1SY A 401 " ideal model delta sigma weight residual 1.508 1.442 0.066 2.00e-02 2.50e+03 1.08e+01 ... (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=" C32 1SY A 401 " pdb=" N33 1SY A 401 " pdb=" C36 1SY A 401 " ideal model delta sigma weight residual 131.33 121.64 9.69 3.00e+00 1.11e-01 1.04e+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 ... (remaining 6535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.65: 2806 30.65 - 61.30: 68 61.30 - 91.96: 6 91.96 - 122.61: 0 122.61 - 153.26: 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 269.52 116.26 153.26 1 3.00e+01 1.11e-03 2.02e+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 - 0.049: 582 0.049 - 0.097: 147 0.097 - 0.145: 27 0.145 - 0.194: 5 0.194 - 0.242: 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 -2.56 -2.32 -0.24 2.00e-01 2.50e+01 1.47e+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 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. 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: 0.010 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.220 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.050 Process input model: 16.840 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 0.124 4827 Z= 0.543 Angle : 0.906 9.686 6540 Z= 0.486 Chirality : 0.046 0.242 762 Planarity : 0.007 0.064 796 Dihedral : 14.130 153.258 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 : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2026 time to fit residues: 20.2639 Evaluate side-chains 33 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7076 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS A 337 HIS B 78 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2210 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= 0.202 Angle : 0.611 9.608 6540 Z= 0.289 Chirality : 0.039 0.157 762 Planarity : 0.005 0.052 796 Dihedral : 8.541 148.849 639 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 3.12 % 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: -1.62 (0.33), residues: 560 helix: -0.28 (0.27), residues: 320 sheet: -1.93 (0.63), residues: 80 loop : -1.95 (0.39), residues: 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 47 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 55 average time/residue: 0.1695 time to fit residues: 12.1526 Evaluate side-chains 40 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 30 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0527 time to fit residues: 1.6305 ------------------------------------------------------------------------------- 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: 9.9990 chunk 16 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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: 0.8507 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 4827 Z= 0.341 Angle : 0.706 10.102 6540 Z= 0.326 Chirality : 0.042 0.182 762 Planarity : 0.005 0.048 796 Dihedral : 8.471 150.365 639 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer Outliers : 2.15 % 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: -0.47 (0.35), residues: 560 helix: 0.56 (0.28), residues: 308 sheet: -1.68 (0.68), residues: 74 loop : -1.05 (0.46), residues: 178 *********************** 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 45 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 34 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 45 average time/residue: 0.1382 time to fit residues: 8.7725 Evaluate side-chains 32 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.625 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0464 time to fit residues: 1.1527 ------------------------------------------------------------------------------- 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: 4.9990 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.8475 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4827 Z= 0.228 Angle : 0.633 10.562 6540 Z= 0.284 Chirality : 0.040 0.143 762 Planarity : 0.004 0.044 796 Dihedral : 8.335 151.085 639 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 1.37 % 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: -0.05 (0.36), residues: 560 helix: 1.04 (0.29), residues: 310 sheet: -1.91 (0.65), residues: 80 loop : -0.91 (0.46), 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 44 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 43 average time/residue: 0.1359 time to fit residues: 8.3846 Evaluate side-chains 34 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.608 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0460 time to fit residues: 1.1195 ------------------------------------------------------------------------------- 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: 9.9990 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- 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: 0.8515 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 4827 Z= 0.371 Angle : 0.712 9.815 6540 Z= 0.327 Chirality : 0.043 0.168 762 Planarity : 0.004 0.043 796 Dihedral : 8.365 150.903 639 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 2.34 % 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: 0.09 (0.38), residues: 560 helix: 1.10 (0.30), residues: 306 sheet: -1.64 (0.70), residues: 74 loop : -0.86 (0.49), residues: 180 *********************** 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 40 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 28 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 38 average time/residue: 0.1527 time to fit residues: 8.2573 Evaluate side-chains 32 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 27 time to evaluate : 0.615 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0536 time to fit residues: 1.2785 ------------------------------------------------------------------------------- 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: 2.9990 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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: 0.8462 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 4827 Z= 0.174 Angle : 0.605 10.766 6540 Z= 0.272 Chirality : 0.041 0.176 762 Planarity : 0.003 0.042 796 Dihedral : 8.222 150.735 639 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 0.78 % 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: 0.44 (0.38), residues: 560 helix: 1.43 (0.30), residues: 310 sheet: -1.84 (0.66), residues: 80 loop : -0.60 (0.49), residues: 170 *********************** 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 44 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 0.1383 time to fit residues: 8.7531 Evaluate side-chains 32 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.615 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0538 time to fit residues: 0.9851 ------------------------------------------------------------------------------- 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: 0.1980 chunk 55 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.0040 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.0196 ------------------------------------------------------------------------------- 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: 0.8435 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 4827 Z= 0.152 Angle : 0.588 11.227 6540 Z= 0.270 Chirality : 0.040 0.185 762 Planarity : 0.003 0.040 796 Dihedral : 8.054 148.853 639 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 1.76 % 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: 0.66 (0.38), residues: 560 helix: 1.67 (0.30), residues: 308 sheet: -1.79 (0.66), residues: 80 loop : -0.61 (0.49), 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 45 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 44 average time/residue: 0.1265 time to fit residues: 8.0340 Evaluate side-chains 35 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0542 time to fit residues: 0.9823 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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: 0.8432 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 4827 Z= 0.175 Angle : 0.629 10.556 6540 Z= 0.282 Chirality : 0.040 0.190 762 Planarity : 0.003 0.040 796 Dihedral : 7.958 147.144 639 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: 0.80 (0.38), residues: 560 helix: 1.79 (0.30), residues: 308 sheet: -1.76 (0.65), residues: 80 loop : -0.53 (0.49), residues: 172 *********************** 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 38 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 37 average time/residue: 0.1316 time to fit residues: 7.0762 Evaluate side-chains 34 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.617 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8092 ------------------------------------------------------------------------------- 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: 5.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 0.0060 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- 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: 0.8414 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4827 Z= 0.167 Angle : 0.632 11.134 6540 Z= 0.282 Chirality : 0.040 0.188 762 Planarity : 0.003 0.040 796 Dihedral : 7.802 145.106 639 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: 0.88 (0.38), residues: 560 helix: 1.86 (0.31), residues: 310 sheet: -1.71 (0.64), residues: 80 loop : -0.55 (0.48), residues: 170 *********************** 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 40 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 0.1398 time to fit residues: 8.0385 Evaluate side-chains 37 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0543 time to fit residues: 1.0632 ------------------------------------------------------------------------------- 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: 10.0000 chunk 35 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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: 0.8466 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 4827 Z= 0.289 Angle : 0.665 9.063 6540 Z= 0.306 Chirality : 0.042 0.189 762 Planarity : 0.004 0.041 796 Dihedral : 7.855 144.181 639 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % 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: 0.87 (0.38), residues: 560 helix: 1.87 (0.30), residues: 306 sheet: -1.83 (0.65), residues: 80 loop : -0.45 (0.49), residues: 174 ********************** 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 35 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1452 time to fit residues: 7.3835 Evaluate side-chains 30 residues out of total 512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9385 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN B 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.081911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.065069 restraints weight = 17195.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.066719 restraints weight = 11138.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.067820 restraints weight = 8418.785| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 4827 Z= 0.356 Angle : 0.711 8.439 6540 Z= 0.333 Chirality : 0.043 0.191 762 Planarity : 0.004 0.040 796 Dihedral : 8.067 144.710 639 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.78 % 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: 0.58 (0.38), residues: 560 helix: 1.57 (0.30), residues: 306 sheet: -1.98 (0.64), residues: 80 loop : -0.42 (0.50), residues: 174 =============================================================================== Job complete usr+sys time: 941.35 seconds wall clock time: 18 minutes 9.04 seconds (1089.04 seconds total)