Starting phenix.real_space_refine on Tue Feb 13 11:08:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/02_2024/8cth_26990_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/02_2024/8cth_26990.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/02_2024/8cth_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_26990/02_2024/8cth_26990_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/02_2024/8cth_26990_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/02_2024/8cth_26990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/02_2024/8cth_26990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/02_2024/8cth_26990_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cth_26990/02_2024/8cth_26990_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.077 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-dev-5238/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: 4.03, per 1000 atoms: 0.73 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: 3.10 Conformation dependent library (CDL) restraints added in 729.8 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: 2.66 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: 1.68 Time building geometry restraints manager: 3.27 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 - 19.48: 2977 19.48 - 38.95: 315 38.95 - 58.42: 122 58.42 - 77.90: 74 77.90 - 97.37: 11 Dihedral angle restraints: 3499 sinusoidal: 2070 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=" O2P PSU C 39 " pdb=" P PSU C 39 " pdb=" O5* PSU C 39 " pdb=" C5* PSU C 39 " ideal model delta sinusoidal sigma weight residual 86.61 -176.02 -97.37 1 3.00e+01 1.11e-03 1.20e+01 dihedral pdb=" O2P PSU C 55 " pdb=" P PSU C 55 " pdb=" O5* PSU C 55 " pdb=" C5* PSU C 55 " ideal model delta sinusoidal sigma weight residual 86.61 179.26 -92.65 1 3.00e+01 1.11e-03 1.12e+01 ... (remaining 3496 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: 0.950 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: 3.780 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.290 Find NCS groups from input model: 0.120 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.320 ------------------------------------------------------------------------------- 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 : 20.241 97.372 2573 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 % Allowed : 22.93 % Favored : 77.07 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 206 HIS 0.003 0.001 HIS A 210 PHE 0.008 0.001 PHE A 159 TYR 0.014 0.002 TYR A 115 ARG 0.004 0.000 ARG A 124 *********************** 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 : 0.481 Fit side-chains REVERT: A 30 MET cc_start: 0.5957 (mpp) cc_final: 0.5019 (mtt) REVERT: B 157 ASP cc_start: 0.6945 (m-30) cc_final: 0.6048 (m-30) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1987 time to fit residues: 13.1183 Evaluate side-chains 46 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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: 0.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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: 0.6529 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5830 Z= 0.205 Angle : 1.295 14.329 8268 Z= 0.800 Chirality : 0.042 0.271 927 Planarity : 0.014 0.125 784 Dihedral : 21.709 169.209 1659 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.26 % Allowed : 18.68 % Favored : 77.07 % 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: 1.08 (0.65), residues: 64 sheet: -0.58 (0.44), residues: 155 loop : -1.30 (0.32), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 216 HIS 0.002 0.001 HIS A 233 PHE 0.010 0.001 PHE B 183 TYR 0.011 0.001 TYR B 282 ARG 0.002 0.000 ARG A 124 *********************** 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 73 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 55 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: B 117 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8751 (p) REVERT: B 269 TYR cc_start: 0.6528 (m-10) cc_final: 0.6109 (m-10) outliers start: 18 outliers final: 10 residues processed: 66 average time/residue: 0.1650 time to fit residues: 14.6107 Evaluate side-chains 57 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 207 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 50 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 overall best weight: 0.7786 ------------------------------------------------------------------------------- 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: 0.6601 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5830 Z= 0.217 Angle : 1.266 13.759 8268 Z= 0.789 Chirality : 0.041 0.213 927 Planarity : 0.014 0.125 784 Dihedral : 21.511 169.523 1659 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.73 % Allowed : 19.15 % Favored : 76.12 % 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: -1.06 (0.36), residues: 482 helix: 1.77 (0.68), residues: 59 sheet: -0.58 (0.42), residues: 160 loop : -1.36 (0.32), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 216 HIS 0.002 0.001 HIS A 33 PHE 0.011 0.001 PHE B 183 TYR 0.011 0.001 TYR A 115 ARG 0.002 0.000 ARG B 103 *********************** 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 71 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 51 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 115 TYR cc_start: 0.4652 (t80) cc_final: 0.4148 (t80) REVERT: A 124 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6589 (mpt-90) REVERT: A 142 MET cc_start: 0.7639 (mmm) cc_final: 0.7136 (mmm) REVERT: A 173 TRP cc_start: 0.8111 (m-10) cc_final: 0.7909 (m-10) REVERT: A 211 PHE cc_start: 0.4003 (OUTLIER) cc_final: 0.3615 (m-80) REVERT: B 117 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8812 (p) REVERT: B 157 ASP cc_start: 0.6887 (m-30) cc_final: 0.6144 (m-30) REVERT: B 164 ASP cc_start: 0.7444 (t70) cc_final: 0.7207 (t70) REVERT: B 269 TYR cc_start: 0.6509 (m-10) cc_final: 0.6253 (m-10) outliers start: 20 outliers final: 14 residues processed: 64 average time/residue: 0.1789 time to fit residues: 14.9589 Evaluate side-chains 66 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 49 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 258 VAL 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: 2.9990 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.0010 chunk 33 optimal weight: 0.0980 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.4586 ------------------------------------------------------------------------------- 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: 0.6534 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5830 Z= 0.165 Angle : 1.246 14.244 8268 Z= 0.784 Chirality : 0.039 0.215 927 Planarity : 0.014 0.122 784 Dihedral : 21.263 172.382 1659 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.49 % Allowed : 19.86 % Favored : 75.65 % 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: -0.84 (0.37), residues: 482 helix: 2.12 (0.69), residues: 59 sheet: -0.47 (0.42), residues: 160 loop : -1.25 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.002 0.001 HIS A 165 PHE 0.010 0.001 PHE A 131 TYR 0.009 0.001 TYR B 218 ARG 0.004 0.000 ARG B 283 *********************** 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 70 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 51 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 115 TYR cc_start: 0.4740 (t80) cc_final: 0.4410 (t80) REVERT: A 199 ASP cc_start: 0.6683 (t70) cc_final: 0.6458 (t70) REVERT: B 117 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8740 (p) REVERT: B 133 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7022 (tm-30) outliers start: 19 outliers final: 13 residues processed: 63 average time/residue: 0.2146 time to fit residues: 17.1878 Evaluate side-chains 61 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 279 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5830 Z= 0.207 Angle : 1.253 14.326 8268 Z= 0.785 Chirality : 0.040 0.234 927 Planarity : 0.014 0.124 784 Dihedral : 21.312 172.201 1659 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.49 % Allowed : 19.15 % Favored : 76.36 % 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: -0.93 (0.36), residues: 482 helix: 2.07 (0.68), residues: 60 sheet: -0.44 (0.43), residues: 149 loop : -1.37 (0.32), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.003 0.001 HIS A 204 PHE 0.017 0.001 PHE A 211 TYR 0.010 0.001 TYR A 115 ARG 0.002 0.000 ARG A 168 *********************** 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 71 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 52 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 115 TYR cc_start: 0.4962 (t80) cc_final: 0.4443 (t80) REVERT: A 142 MET cc_start: 0.7727 (mmm) cc_final: 0.7139 (mtp) REVERT: B 117 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8799 (p) outliers start: 19 outliers final: 13 residues processed: 66 average time/residue: 0.1830 time to fit residues: 15.7969 Evaluate side-chains 61 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 258 VAL 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: 0.7980 chunk 31 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 0.0030 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.0570 chunk 27 optimal weight: 0.0070 chunk 51 optimal weight: 20.0000 overall best weight: 0.3326 ------------------------------------------------------------------------------- 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: 0.6536 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5830 Z= 0.155 Angle : 1.247 14.335 8268 Z= 0.783 Chirality : 0.039 0.213 927 Planarity : 0.014 0.121 784 Dihedral : 21.266 174.824 1659 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.49 % Allowed : 20.33 % Favored : 75.18 % 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: -0.73 (0.37), residues: 482 helix: 2.35 (0.68), residues: 60 sheet: -0.34 (0.42), residues: 161 loop : -1.27 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 216 HIS 0.002 0.000 HIS A 33 PHE 0.010 0.001 PHE A 211 TYR 0.008 0.001 TYR B 218 ARG 0.002 0.000 ARG B 219 *********************** 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 65 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 46 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 115 TYR cc_start: 0.4811 (t80) cc_final: 0.4500 (t80) REVERT: A 142 MET cc_start: 0.7744 (mmm) cc_final: 0.7191 (mtp) REVERT: B 117 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8696 (p) REVERT: B 133 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7023 (tm-30) outliers start: 19 outliers final: 16 residues processed: 59 average time/residue: 0.1877 time to fit residues: 14.4247 Evaluate side-chains 62 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 45 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.0070 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 0.0370 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- 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: 0.6565 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 : 0.003 0.028 5830 Z= 0.165 Angle : 1.246 14.270 8268 Z= 0.783 Chirality : 0.039 0.209 927 Planarity : 0.014 0.121 784 Dihedral : 21.334 177.411 1659 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.49 % Allowed : 20.33 % Favored : 75.18 % 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: -0.62 (0.36), residues: 482 helix: 2.40 (0.68), residues: 60 sheet: -0.29 (0.41), residues: 159 loop : -1.17 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 216 HIS 0.002 0.000 HIS A 33 PHE 0.010 0.001 PHE A 159 TYR 0.010 0.001 TYR B 282 ARG 0.002 0.000 ARG A 168 *********************** 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 68 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 49 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 115 TYR cc_start: 0.4907 (t80) cc_final: 0.4614 (t80) REVERT: A 142 MET cc_start: 0.7638 (mmm) cc_final: 0.7161 (mtp) REVERT: B 117 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8736 (p) REVERT: B 133 GLU cc_start: 0.7365 (tm-30) cc_final: 0.7010 (tm-30) REVERT: B 164 ASP cc_start: 0.7629 (t70) cc_final: 0.7235 (t70) outliers start: 19 outliers final: 17 residues processed: 63 average time/residue: 0.1716 time to fit residues: 14.3787 Evaluate side-chains 65 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 47 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.6687 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5830 Z= 0.265 Angle : 1.285 14.158 8268 Z= 0.797 Chirality : 0.042 0.239 927 Planarity : 0.014 0.125 784 Dihedral : 21.462 174.269 1659 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.96 % Allowed : 21.28 % Favored : 73.76 % 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: -1.11 (0.35), residues: 482 helix: 2.02 (0.68), residues: 60 sheet: -0.54 (0.43), residues: 144 loop : -1.52 (0.31), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 216 HIS 0.003 0.001 HIS A 165 PHE 0.016 0.002 PHE A 159 TYR 0.013 0.002 TYR A 115 ARG 0.002 0.000 ARG B 103 *********************** 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 67 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 46 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 115 TYR cc_start: 0.5116 (t80) cc_final: 0.4513 (t80) REVERT: A 142 MET cc_start: 0.7816 (mmm) cc_final: 0.7423 (mtp) REVERT: B 117 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8867 (p) REVERT: B 164 ASP cc_start: 0.7534 (t70) cc_final: 0.7250 (t70) outliers start: 21 outliers final: 16 residues processed: 62 average time/residue: 0.2048 time to fit residues: 16.2975 Evaluate side-chains 61 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 44 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 258 VAL 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: 0.0170 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5830 Z= 0.316 Angle : 1.309 14.039 8268 Z= 0.808 Chirality : 0.044 0.265 927 Planarity : 0.014 0.126 784 Dihedral : 21.469 171.294 1659 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 4.02 % Allowed : 22.46 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.35), residues: 482 helix: 1.54 (0.69), residues: 60 sheet: -0.94 (0.43), residues: 145 loop : -1.70 (0.31), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 216 HIS 0.005 0.001 HIS A 165 PHE 0.017 0.002 PHE A 159 TYR 0.013 0.002 TYR A 115 ARG 0.003 0.001 ARG B 103 *********************** 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 59 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 42 time to evaluate : 0.524 Fit side-chains REVERT: A 115 TYR cc_start: 0.5315 (t80) cc_final: 0.4551 (t80) REVERT: A 142 MET cc_start: 0.7819 (mmm) cc_final: 0.7537 (mtp) REVERT: A 168 ARG cc_start: 0.7750 (tpt90) cc_final: 0.7438 (ttm110) REVERT: B 117 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8904 (p) REVERT: B 164 ASP cc_start: 0.7582 (t70) cc_final: 0.7322 (t70) outliers start: 17 outliers final: 14 residues processed: 56 average time/residue: 0.1836 time to fit residues: 13.5778 Evaluate side-chains 52 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 37 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 258 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.3980 chunk 36 optimal weight: 0.2980 chunk 54 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 46 optimal weight: 0.0470 chunk 13 optimal weight: 0.2980 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5830 Z= 0.156 Angle : 1.258 13.964 8268 Z= 0.788 Chirality : 0.039 0.233 927 Planarity : 0.014 0.121 784 Dihedral : 21.294 177.025 1659 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.31 % Allowed : 23.64 % Favored : 73.05 % 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 (0.36), residues: 482 helix: 2.11 (0.70), residues: 59 sheet: -0.49 (0.43), residues: 148 loop : -1.45 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.002 0.001 HIS B 187 PHE 0.009 0.001 PHE A 159 TYR 0.011 0.001 TYR A 150 ARG 0.002 0.000 ARG B 89 ********************** 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 57 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 43 time to evaluate : 0.398 Fit side-chains REVERT: A 115 TYR cc_start: 0.5103 (t80) cc_final: 0.4648 (t80) REVERT: A 142 MET cc_start: 0.7683 (mmm) cc_final: 0.7295 (mtp) REVERT: A 168 ARG cc_start: 0.7582 (tpt90) cc_final: 0.6994 (ttt-90) REVERT: B 164 ASP cc_start: 0.7622 (t70) cc_final: 0.7222 (t70) outliers start: 14 outliers final: 12 residues processed: 53 average time/residue: 0.1720 time to fit residues: 12.1413 Evaluate side-chains 51 residues out of total 424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 258 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 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 = 0.4984 r_free = 0.4984 target = 0.258220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.218762 restraints weight = 7160.522| |-----------------------------------------------------------------------------| r_work (start): 0.4641 rms_B_bonded: 1.76 r_work: 0.4440 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5830 Z= 0.192 Angle : 1.261 13.828 8268 Z= 0.789 Chirality : 0.040 0.226 927 Planarity : 0.014 0.122 784 Dihedral : 21.326 178.780 1659 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.84 % Allowed : 24.11 % Favored : 73.05 % 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: 1.96 (0.69), residues: 60 sheet: -0.46 (0.44), residues: 143 loop : -1.49 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 216 HIS 0.002 0.001 HIS A 204 PHE 0.012 0.001 PHE A 159 TYR 0.010 0.001 TYR A 115 ARG 0.001 0.000 ARG A 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1470.22 seconds wall clock time: 27 minutes 16.09 seconds (1636.09 seconds total)