Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 05:16:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/04_2023/8cth_26990_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/04_2023/8cth_26990.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/04_2023/8cth_26990_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/04_2023/8cth_26990_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/04_2023/8cth_26990_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/04_2023/8cth_26990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/04_2023/8cth_26990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/04_2023/8cth_26990_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/04_2023/8cth_26990_updated.pdb" } resolution = 3.3 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= 0.077 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 74 5.49 5 S 22 5.16 5 C 3250 2.51 5 N 969 2.21 5 O 1229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 82": "OD1" <-> "OD2" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 114": "OD1" <-> "OD2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 5544 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1750 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2175 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 8, 'TRANS': 269} Chain breaks: 3 Chain: "C" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1593 Classifications: {'RNA': 74} Modifications used: {'p5*END': 1, 'rna2p': 2, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p': 10, 'rna3p_pur': 32, 'rna3p_pyr': 23} Link IDs: {'rna2p': 9, 'rna3p': 64} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 3.96, per 1000 atoms: 0.71 Number of scatterers: 5544 At special positions: 0 Unit cell: (81, 100.44, 118.8, 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 22 16.00 P 74 15.00 O 1229 8.00 N 969 7.00 C 3250 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: 2.96 Conformation dependent library (CDL) restraints added in 686.7 milliseconds 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 926 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 10 helices and 8 sheets defined 14.7% alpha, 27.7% beta 20 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 89 through 95 removed outlier: 3.606A pdb=" N GLU A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 124 Processing helix chain 'A' and resid 145 through 148 No H-bonds generated for 'chain 'A' and resid 145 through 148' Processing helix chain 'A' and resid 169 through 173 removed outlier: 3.904A pdb=" N LYS A 172 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 201 through 213 removed outlier: 3.599A pdb=" N HIS A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 239 through 247 Processing sheet with id= A, first strand: chain 'A' and resid 217 through 219 removed outlier: 3.537A pdb=" N THR A 198 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU A 160 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU A 102 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ALA A 81 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A 104 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE A 83 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU A 106 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 7 through 10 Processing sheet with id= C, first strand: chain 'B' and resid 66 through 69 removed outlier: 4.133A pdb=" N ALA B 66 " --> pdb=" O THR B 79 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE B 76 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 97 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG B 89 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N CYS B 95 " --> pdb=" O ARG B 89 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 107 through 110 removed outlier: 3.975A pdb=" N ALA B 107 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 109 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 126 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 142 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER B 128 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU B 140 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 148 through 153 removed outlier: 6.588A pdb=" N ALA B 163 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL B 151 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B 161 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL B 153 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE B 159 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N TRP B 173 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE B 180 " --> pdb=" O TRP B 173 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 191 through 196 removed outlier: 7.195A pdb=" N SER B 207 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE B 194 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU B 205 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER B 206 " --> pdb=" O ARG B 214 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU B 217 " --> pdb=" O GLN B 223 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN B 223 " --> pdb=" O GLU B 217 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 248 through 252 removed outlier: 4.199A pdb=" N ARG B 248 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE B 270 " --> pdb=" O GLN B 284 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN B 284 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN B 272 " --> pdb=" O TYR B 282 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR B 282 " --> pdb=" O GLN B 272 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP B 274 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU B 280 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 314 through 317 removed outlier: 3.506A pdb=" N VAL B 305 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 303 " --> pdb=" O TYR B 317 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 294 " --> pdb=" O LEU B 306 " (cutoff:3.500A) 101 hydrogen bonds defined for protein. 282 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1036 1.33 - 1.45: 1792 1.45 - 1.57: 2826 1.57 - 1.69: 147 1.69 - 1.81: 29 Bond restraints: 5830 Sorted by residual: bond pdb=" C4 5MU C 54 " pdb=" C5 5MU C 54 " ideal model delta sigma weight residual 1.802 1.443 0.359 2.00e-02 2.50e+03 3.22e+02 bond pdb=" N1 5MU C 54 " pdb=" C6 5MU C 54 " ideal model delta sigma weight residual 1.635 1.371 0.264 2.00e-02 2.50e+03 1.75e+02 bond pdb=" N3 5MU C 54 " pdb=" C4 5MU C 54 " ideal model delta sigma weight residual 1.182 1.380 -0.198 2.00e-02 2.50e+03 9.75e+01 bond pdb=" C5 5MU C 54 " pdb=" C6 5MU C 54 " ideal model delta sigma weight residual 1.155 1.342 -0.187 2.00e-02 2.50e+03 8.74e+01 bond pdb=" C2 1MA C 58 " pdb=" N3 1MA C 58 " ideal model delta sigma weight residual 1.465 1.290 0.175 2.00e-02 2.50e+03 7.65e+01 ... (remaining 5825 not shown) Histogram of bond angle deviations from ideal: 89.25 - 98.22: 1 98.22 - 107.19: 576 107.19 - 116.15: 3804 116.15 - 125.12: 3527 125.12 - 134.08: 360 Bond angle restraints: 8268 Sorted by residual: angle pdb=" C1' 1MA C 58 " pdb=" N9 1MA C 58 " pdb=" C8 1MA C 58 " ideal model delta sigma weight residual 100.68 128.08 -27.40 3.00e+00 1.11e-01 8.34e+01 angle pdb=" C1' OMG C 34 " pdb=" N9 OMG C 34 " pdb=" C4 OMG C 34 " ideal model delta sigma weight residual 108.29 126.75 -18.46 3.00e+00 1.11e-01 3.79e+01 angle pdb=" C1' M2G C 26 " pdb=" N9 M2G C 26 " pdb=" C4 M2G C 26 " ideal model delta sigma weight residual 108.14 126.04 -17.90 3.00e+00 1.11e-01 3.56e+01 angle pdb=" C6 5MU C 54 " pdb=" C5 5MU C 54 " pdb=" C5M 5MU C 54 " ideal model delta sigma weight residual 106.09 123.76 -17.67 3.00e+00 1.11e-01 3.47e+01 angle pdb=" C1' 1MA C 58 " pdb=" N9 1MA C 58 " pdb=" C4 1MA C 58 " ideal model delta sigma weight residual 142.33 125.34 16.99 3.00e+00 1.11e-01 3.21e+01 ... (remaining 8263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 2847 17.65 - 35.31: 282 35.31 - 52.96: 100 52.96 - 70.62: 22 70.62 - 88.27: 10 Dihedral angle restraints: 3261 sinusoidal: 1832 harmonic: 1429 Sorted by residual: dihedral pdb=" CA ARG B 89 " pdb=" C ARG B 89 " pdb=" N THR B 90 " pdb=" CA THR B 90 " ideal model delta harmonic sigma weight residual -180.00 -161.34 -18.66 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CG ARG B 318 " pdb=" CD ARG B 318 " pdb=" NE ARG B 318 " pdb=" CZ ARG B 318 " ideal model delta sinusoidal sigma weight residual 90.00 133.52 -43.52 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CA ASP B 150 " pdb=" CB ASP B 150 " pdb=" CG ASP B 150 " pdb=" OD1 ASP B 150 " ideal model delta sinusoidal sigma weight residual -30.00 -83.66 53.66 1 2.00e+01 2.50e-03 9.78e+00 ... (remaining 3258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 707 0.040 - 0.080: 153 0.080 - 0.120: 57 0.120 - 0.160: 9 0.160 - 0.200: 1 Chirality restraints: 927 Sorted by residual: chirality pdb=" C1' U C 59 " pdb=" O4' U C 59 " pdb=" C2' U C 59 " pdb=" N1 U C 59 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE A 259 " pdb=" N ILE A 259 " pdb=" C ILE A 259 " pdb=" CB ILE A 259 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE B 160 " pdb=" N ILE B 160 " pdb=" C ILE B 160 " pdb=" CB ILE B 160 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 924 not shown) Planarity restraints: 784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' H2U C 17 " -0.031 2.00e-02 2.50e+03 6.09e-01 8.33e+03 pdb=" C4' H2U C 17 " -0.469 2.00e-02 2.50e+03 pdb=" O4' H2U C 17 " -0.820 2.00e-02 2.50e+03 pdb=" C3' H2U C 17 " 0.583 2.00e-02 2.50e+03 pdb=" O3' H2U C 17 " 0.566 2.00e-02 2.50e+03 pdb=" C2' H2U C 17 " 0.250 2.00e-02 2.50e+03 pdb=" O2' H2U C 17 " -0.864 2.00e-02 2.50e+03 pdb=" C1' H2U C 17 " -0.183 2.00e-02 2.50e+03 pdb=" N1 H2U C 17 " 0.969 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 1MA C 58 " 0.845 2.00e-02 2.50e+03 5.82e-01 7.62e+03 pdb=" C4' 1MA C 58 " -0.228 2.00e-02 2.50e+03 pdb=" O4' 1MA C 58 " -0.623 2.00e-02 2.50e+03 pdb=" C3' 1MA C 58 " 0.193 2.00e-02 2.50e+03 pdb=" O3' 1MA C 58 " -0.950 2.00e-02 2.50e+03 pdb=" C2' 1MA C 58 " 0.619 2.00e-02 2.50e+03 pdb=" O2' 1MA C 58 " 0.617 2.00e-02 2.50e+03 pdb=" C1' 1MA C 58 " -0.431 2.00e-02 2.50e+03 pdb=" N9 1MA C 58 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU C 54 " 0.053 2.00e-02 2.50e+03 5.81e-01 7.59e+03 pdb=" C4' 5MU C 54 " 0.430 2.00e-02 2.50e+03 pdb=" O4' 5MU C 54 " 0.606 2.00e-02 2.50e+03 pdb=" C3' 5MU C 54 " -0.596 2.00e-02 2.50e+03 pdb=" O3' 5MU C 54 " -0.607 2.00e-02 2.50e+03 pdb=" C2' 5MU C 54 " -0.189 2.00e-02 2.50e+03 pdb=" O2' 5MU C 54 " 0.950 2.00e-02 2.50e+03 pdb=" C1' 5MU C 54 " 0.230 2.00e-02 2.50e+03 pdb=" N1 5MU C 54 " -0.877 2.00e-02 2.50e+03 ... (remaining 781 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1179 2.79 - 3.31: 4874 3.31 - 3.84: 10031 3.84 - 4.37: 11737 4.37 - 4.90: 18144 Nonbonded interactions: 45965 Sorted by model distance: nonbonded pdb=" O2' 1MA C 58 " pdb=" OP2 C C 60 " model vdw 2.257 3.040 nonbonded pdb=" NZ LYS B 83 " pdb=" OP1 5MU C 54 " model vdw 2.286 2.520 nonbonded pdb=" OH TYR A 50 " pdb=" O ILE A 103 " model vdw 2.289 2.440 nonbonded pdb=" OG SER B 146 " pdb=" OD2 ASP B 166 " model vdw 2.326 2.440 nonbonded pdb=" OG SER B 146 " pdb=" OD2 ASP B 164 " model vdw 2.367 2.440 ... (remaining 45960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 4.010 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.610 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 0.359 5830 Z= 0.753 Angle : 1.049 27.400 8268 Z= 0.405 Chirality : 0.039 0.200 927 Planarity : 0.065 0.609 784 Dihedral : 15.979 88.269 2335 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: -1.68 (0.34), residues: 482 helix: -0.05 (0.58), residues: 65 sheet: -0.84 (0.43), residues: 147 loop : -1.55 (0.31), residues: 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.650 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2002 time to fit residues: 13.2740 Evaluate side-chains 46 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 23 optimal weight: 0.0370 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5830 Z= 0.199 Angle : 1.289 14.113 8268 Z= 0.798 Chirality : 0.041 0.250 927 Planarity : 0.014 0.126 784 Dihedral : 16.480 168.812 1421 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 4.02 % 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: -1.09 (0.36), residues: 482 helix: 1.08 (0.65), residues: 64 sheet: -0.56 (0.44), residues: 155 loop : -1.28 (0.32), residues: 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.493 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 65 average time/residue: 0.1719 time to fit residues: 14.9380 Evaluate side-chains 54 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1159 time to fit residues: 1.9799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.0670 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.0020 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 50 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 17 optimal weight: 0.0970 chunk 40 optimal weight: 0.5980 overall best weight: 0.2124 ------------------------------------------------------------------------------- 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: 0.6427 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 5830 Z= 0.146 Angle : 1.241 13.817 8268 Z= 0.780 Chirality : 0.038 0.167 927 Planarity : 0.014 0.123 784 Dihedral : 15.976 170.022 1421 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.37), residues: 482 helix: 1.29 (0.65), residues: 69 sheet: -0.40 (0.42), residues: 168 loop : -1.17 (0.35), residues: 245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.480 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 58 average time/residue: 0.2059 time to fit residues: 15.4150 Evaluate side-chains 49 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0619 time to fit residues: 1.0407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.6592 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5830 Z= 0.210 Angle : 1.259 14.153 8268 Z= 0.787 Chirality : 0.040 0.216 927 Planarity : 0.014 0.126 784 Dihedral : 15.908 172.751 1421 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 1.18 % 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: -0.75 (0.37), residues: 482 helix: 2.15 (0.69), residues: 60 sheet: -0.50 (0.41), residues: 166 loop : -1.13 (0.33), residues: 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.516 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 54 average time/residue: 0.1862 time to fit residues: 13.3329 Evaluate side-chains 47 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.528 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2894 time to fit residues: 1.3282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 45 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.6610 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5830 Z= 0.214 Angle : 1.258 14.303 8268 Z= 0.788 Chirality : 0.040 0.230 927 Planarity : 0.014 0.126 784 Dihedral : 15.921 175.075 1421 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 1.65 % 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: -1.06 (0.36), residues: 482 helix: 1.65 (0.67), residues: 66 sheet: -0.49 (0.43), residues: 150 loop : -1.47 (0.31), residues: 266 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.471 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 56 average time/residue: 0.1488 time to fit residues: 11.6860 Evaluate side-chains 49 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.528 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0556 time to fit residues: 1.1068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.0670 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 51 optimal weight: 20.0000 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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: 0.6614 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5830 Z= 0.203 Angle : 1.258 14.366 8268 Z= 0.788 Chirality : 0.039 0.231 927 Planarity : 0.014 0.124 784 Dihedral : 15.834 177.510 1421 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 1.18 % 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: -1.10 (0.35), residues: 482 helix: 1.72 (0.67), residues: 66 sheet: -0.48 (0.43), residues: 148 loop : -1.56 (0.31), residues: 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.423 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.1565 time to fit residues: 10.6114 Evaluate side-chains 46 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.517 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0541 time to fit residues: 1.0657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.6587 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 5830 Z= 0.183 Angle : 1.250 14.263 8268 Z= 0.785 Chirality : 0.039 0.216 927 Planarity : 0.014 0.123 784 Dihedral : 15.850 179.252 1421 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.36), residues: 482 helix: 1.76 (0.68), residues: 67 sheet: -0.45 (0.43), residues: 152 loop : -1.51 (0.32), residues: 263 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.553 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.1643 time to fit residues: 11.3726 Evaluate side-chains 47 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0523 time to fit residues: 1.1164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.6651 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 5830 Z= 0.232 Angle : 1.264 14.199 8268 Z= 0.791 Chirality : 0.040 0.229 927 Planarity : 0.014 0.124 784 Dihedral : 15.975 179.277 1421 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 0.95 % 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: -1.12 (0.36), residues: 482 helix: 1.75 (0.68), residues: 66 sheet: -0.47 (0.44), residues: 145 loop : -1.58 (0.31), residues: 271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.514 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 49 average time/residue: 0.1613 time to fit residues: 10.9683 Evaluate side-chains 44 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.493 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0885 time to fit residues: 0.8463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 0.0970 chunk 52 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.6638 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 5830 Z= 0.214 Angle : 1.262 14.118 8268 Z= 0.790 Chirality : 0.040 0.228 927 Planarity : 0.014 0.123 784 Dihedral : 16.005 179.897 1421 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.36), residues: 482 helix: 1.64 (0.68), residues: 66 sheet: -0.52 (0.44), residues: 147 loop : -1.48 (0.32), residues: 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.512 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 50 average time/residue: 0.1655 time to fit residues: 11.4143 Evaluate side-chains 46 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.530 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0574 time to fit residues: 0.9815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.6620 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 : 0.003 0.036 5830 Z= 0.196 Angle : 1.258 13.965 8268 Z= 0.789 Chirality : 0.039 0.218 927 Planarity : 0.014 0.122 784 Dihedral : 15.970 176.671 1421 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.24 % 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: -1.01 (0.36), residues: 482 helix: 1.49 (0.67), residues: 67 sheet: -0.30 (0.45), residues: 144 loop : -1.48 (0.32), residues: 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.516 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.1719 time to fit residues: 10.4095 Evaluate side-chains 43 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.500 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0546 time to fit residues: 0.7651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.258977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.220226 restraints weight = 7167.803| |-----------------------------------------------------------------------------| r_work (start): 0.4655 rms_B_bonded: 1.76 r_work: 0.4429 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 5830 Z= 0.200 Angle : 1.258 13.793 8268 Z= 0.789 Chirality : 0.039 0.214 927 Planarity : 0.014 0.122 784 Dihedral : 15.951 175.549 1421 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % 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: -1.02 (0.37), residues: 482 helix: 1.50 (0.67), residues: 67 sheet: -0.32 (0.46), residues: 144 loop : -1.48 (0.32), residues: 271 =============================================================================== Job complete usr+sys time: 1356.80 seconds wall clock time: 25 minutes 16.01 seconds (1516.01 seconds total)