Starting phenix.real_space_refine on Sat Jul 26 15:13:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b03_11955/07_2025/7b03_11955.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b03_11955/07_2025/7b03_11955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b03_11955/07_2025/7b03_11955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b03_11955/07_2025/7b03_11955.map" model { file = "/net/cci-nas-00/data/ceres_data/7b03_11955/07_2025/7b03_11955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b03_11955/07_2025/7b03_11955.cif" } resolution = 2.93 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 ------------------------------------------------------------------------------- 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= 0.442 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5855 2.51 5 N 1290 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8670 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1714 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 5, 'TRANS': 211} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Restraints were copied for chains: C, B, E, D Time building chain proxies: 3.45, per 1000 atoms: 0.40 Number of scatterers: 8670 At special positions: 0 Unit cell: (103.2, 100.62, 67.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1470 8.00 N 1290 7.00 C 5855 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 - 3.00 Amino acid : True - 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 955.3 milliseconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 0 sheets defined 89.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 30 through 53 removed outlier: 3.784A pdb=" N ARG A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASP A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 87 removed outlier: 3.670A pdb=" N TYR A 79 " --> pdb=" O TRP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 118 Proline residue: A 104 - end of helix removed outlier: 4.214A pdb=" N PHE A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 144 Processing helix chain 'A' and resid 148 through 177 removed outlier: 3.824A pdb=" N GLY A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLU A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 208 removed outlier: 3.945A pdb=" N TRP A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N TYR A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 219 through 249 removed outlier: 3.516A pdb=" N LEU A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N PHE A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 53 removed outlier: 3.783A pdb=" N ARG B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASP B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 87 removed outlier: 3.671A pdb=" N TYR B 79 " --> pdb=" O TRP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 118 Proline residue: B 104 - end of helix removed outlier: 4.214A pdb=" N PHE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 144 Processing helix chain 'B' and resid 148 through 177 removed outlier: 3.823A pdb=" N GLY B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY B 172 " --> pdb=" O TRP B 168 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 208 removed outlier: 3.945A pdb=" N TRP B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE B 200 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 219 through 249 removed outlier: 3.516A pdb=" N LEU B 234 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N PHE B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 53 removed outlier: 3.783A pdb=" N ARG C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASP C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 87 removed outlier: 3.670A pdb=" N TYR C 79 " --> pdb=" O TRP C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 118 Proline residue: C 104 - end of helix removed outlier: 4.214A pdb=" N PHE C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 144 Processing helix chain 'C' and resid 148 through 177 removed outlier: 3.824A pdb=" N GLY C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLU C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY C 172 " --> pdb=" O TRP C 168 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 208 removed outlier: 3.945A pdb=" N TRP C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE C 200 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Proline residue: C 202 - end of helix Processing helix chain 'C' and resid 219 through 249 removed outlier: 3.515A pdb=" N LEU C 234 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N PHE C 235 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY C 236 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 53 removed outlier: 3.784A pdb=" N ARG D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASP D 53 " --> pdb=" O PHE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 87 removed outlier: 3.669A pdb=" N TYR D 79 " --> pdb=" O TRP D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 118 Proline residue: D 104 - end of helix removed outlier: 4.214A pdb=" N PHE D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 144 Processing helix chain 'D' and resid 148 through 177 removed outlier: 3.824A pdb=" N GLY D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLU D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS D 173 " --> pdb=" O ALA D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 208 removed outlier: 3.945A pdb=" N TRP D 198 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE D 200 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR D 201 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Proline residue: D 202 - end of helix Processing helix chain 'D' and resid 219 through 249 removed outlier: 3.516A pdb=" N LEU D 234 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N PHE D 235 " --> pdb=" O ASN D 231 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY D 236 " --> pdb=" O LYS D 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 53 removed outlier: 3.783A pdb=" N ARG E 52 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASP E 53 " --> pdb=" O PHE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 87 removed outlier: 3.670A pdb=" N TYR E 79 " --> pdb=" O TRP E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 118 Proline residue: E 104 - end of helix removed outlier: 4.214A pdb=" N PHE E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 144 Processing helix chain 'E' and resid 148 through 177 removed outlier: 3.824A pdb=" N GLY E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLU E 171 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY E 172 " --> pdb=" O TRP E 168 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS E 173 " --> pdb=" O ALA E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 208 removed outlier: 3.945A pdb=" N TRP E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 199 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE E 200 " --> pdb=" O PHE E 196 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Proline residue: E 202 - end of helix Processing helix chain 'E' and resid 219 through 249 removed outlier: 3.516A pdb=" N LEU E 234 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N PHE E 235 " --> pdb=" O ASN E 231 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY E 236 " --> pdb=" O LYS E 232 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1288 1.32 - 1.44: 2758 1.44 - 1.57: 4789 1.57 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 8930 Sorted by residual: bond pdb=" C TRP B 75 " pdb=" O TRP B 75 " ideal model delta sigma weight residual 1.236 1.198 0.039 1.15e-02 7.56e+03 1.12e+01 bond pdb=" C TRP A 75 " pdb=" O TRP A 75 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.15e-02 7.56e+03 1.10e+01 bond pdb=" C TRP D 75 " pdb=" O TRP D 75 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.15e-02 7.56e+03 1.09e+01 bond pdb=" C TRP C 75 " pdb=" O TRP C 75 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.15e-02 7.56e+03 1.09e+01 bond pdb=" C TRP E 75 " pdb=" O TRP E 75 " ideal model delta sigma weight residual 1.236 1.199 0.038 1.15e-02 7.56e+03 1.07e+01 ... (remaining 8925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 12120 3.75 - 7.51: 50 7.51 - 11.26: 10 11.26 - 15.01: 5 15.01 - 18.77: 10 Bond angle restraints: 12195 Sorted by residual: angle pdb=" C16 RET D 301 " pdb=" C1 RET D 301 " pdb=" C2 RET D 301 " ideal model delta sigma weight residual 105.80 124.57 -18.77 3.00e+00 1.11e-01 3.91e+01 angle pdb=" C16 RET B 301 " pdb=" C1 RET B 301 " pdb=" C2 RET B 301 " ideal model delta sigma weight residual 105.80 124.55 -18.75 3.00e+00 1.11e-01 3.91e+01 angle pdb=" C16 RET A 301 " pdb=" C1 RET A 301 " pdb=" C2 RET A 301 " ideal model delta sigma weight residual 105.80 124.53 -18.73 3.00e+00 1.11e-01 3.90e+01 angle pdb=" C16 RET E 301 " pdb=" C1 RET E 301 " pdb=" C2 RET E 301 " ideal model delta sigma weight residual 105.80 124.51 -18.71 3.00e+00 1.11e-01 3.89e+01 angle pdb=" C16 RET C 301 " pdb=" C1 RET C 301 " pdb=" C2 RET C 301 " ideal model delta sigma weight residual 105.80 124.51 -18.71 3.00e+00 1.11e-01 3.89e+01 ... (remaining 12190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.03: 4795 22.03 - 44.05: 115 44.05 - 66.08: 20 66.08 - 88.11: 10 88.11 - 110.13: 10 Dihedral angle restraints: 4950 sinusoidal: 1805 harmonic: 3145 Sorted by residual: dihedral pdb=" C2 RET E 301 " pdb=" C3 RET E 301 " pdb=" C4 RET E 301 " pdb=" C5 RET E 301 " ideal model delta sinusoidal sigma weight residual 42.40 -67.73 110.13 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C2 RET A 301 " pdb=" C3 RET A 301 " pdb=" C4 RET A 301 " pdb=" C5 RET A 301 " ideal model delta sinusoidal sigma weight residual 42.40 -67.71 110.11 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C2 RET D 301 " pdb=" C3 RET D 301 " pdb=" C4 RET D 301 " pdb=" C5 RET D 301 " ideal model delta sinusoidal sigma weight residual 42.40 -67.70 110.10 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 4947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 699 0.026 - 0.051: 402 0.051 - 0.077: 200 0.077 - 0.102: 50 0.102 - 0.128: 19 Chirality restraints: 1370 Sorted by residual: chirality pdb=" CA TYR E 201 " pdb=" N TYR E 201 " pdb=" C TYR E 201 " pdb=" CB TYR E 201 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA TYR D 201 " pdb=" N TYR D 201 " pdb=" C TYR D 201 " pdb=" CB TYR D 201 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA TYR A 201 " pdb=" N TYR A 201 " pdb=" C TYR A 201 " pdb=" CB TYR A 201 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 1367 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 229 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C PHE E 229 " 0.020 2.00e-02 2.50e+03 pdb=" O PHE E 229 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL E 230 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 229 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" C PHE B 229 " -0.020 2.00e-02 2.50e+03 pdb=" O PHE B 229 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL B 230 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 229 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C PHE A 229 " -0.020 2.00e-02 2.50e+03 pdb=" O PHE A 229 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL A 230 " 0.007 2.00e-02 2.50e+03 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 548 2.73 - 3.27: 9312 3.27 - 3.82: 15340 3.82 - 4.36: 17990 4.36 - 4.90: 31016 Nonbonded interactions: 74206 Sorted by model distance: nonbonded pdb=" OH TYR E 77 " pdb=" OD2 ASP E 228 " model vdw 2.190 3.040 nonbonded pdb=" OH TYR C 77 " pdb=" OD2 ASP C 228 " model vdw 2.190 3.040 nonbonded pdb=" OH TYR B 77 " pdb=" OD2 ASP B 228 " model vdw 2.190 3.040 nonbonded pdb=" OH TYR A 77 " pdb=" OD2 ASP A 228 " model vdw 2.191 3.040 nonbonded pdb=" OH TYR D 77 " pdb=" OD2 ASP D 228 " model vdw 2.191 3.040 ... (remaining 74201 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.210 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 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:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.006 0.087 8935 Z= 0.343 Angle : 0.896 18.768 12195 Z= 0.411 Chirality : 0.039 0.128 1370 Planarity : 0.004 0.026 1450 Dihedral : 13.223 110.134 2950 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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: 1.34 (0.24), residues: 1065 helix: 1.33 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -2.49 (0.37), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 168 HIS 0.001 0.001 HIS E 76 PHE 0.012 0.002 PHE E 235 TYR 0.009 0.001 TYR E 187 ARG 0.003 0.001 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.08731 ( 720) hydrogen bonds : angle 4.76206 ( 2160) covalent geometry : bond 0.00527 ( 8930) covalent geometry : angle 0.89638 (12195) Misc. bond : bond 0.08707 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.903 Fit side-chains REVERT: A 53 ASP cc_start: 0.6808 (m-30) cc_final: 0.6579 (m-30) REVERT: A 163 MET cc_start: 0.8067 (mtp) cc_final: 0.7710 (mtp) REVERT: A 192 TYR cc_start: 0.7791 (m-80) cc_final: 0.7449 (m-80) REVERT: B 125 PHE cc_start: 0.8641 (t80) cc_final: 0.8388 (t80) REVERT: B 163 MET cc_start: 0.8195 (mtp) cc_final: 0.7972 (mtp) REVERT: B 191 MET cc_start: 0.8375 (ttm) cc_final: 0.8061 (ttp) REVERT: C 80 MET cc_start: 0.6001 (mtm) cc_final: 0.5701 (mtm) REVERT: C 147 MET cc_start: 0.6964 (ttt) cc_final: 0.6645 (ttm) REVERT: C 163 MET cc_start: 0.8090 (mtp) cc_final: 0.7610 (mtp) REVERT: C 206 PHE cc_start: 0.8079 (t80) cc_final: 0.7810 (t80) REVERT: D 141 MET cc_start: 0.8032 (mtp) cc_final: 0.7829 (ttm) REVERT: E 80 MET cc_start: 0.6062 (mtm) cc_final: 0.5771 (mtp) REVERT: E 141 MET cc_start: 0.8051 (mtp) cc_final: 0.7676 (mtm) REVERT: E 192 TYR cc_start: 0.7434 (m-80) cc_final: 0.7090 (m-80) outliers start: 0 outliers final: 1 residues processed: 209 average time/residue: 0.6215 time to fit residues: 146.1620 Evaluate side-chains 180 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 200 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 40.0000 chunk 53 optimal weight: 9.9990 chunk 42 optimal weight: 40.0000 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 225 ASN B 241 ASN C 177 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.159280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.133653 restraints weight = 9285.000| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.40 r_work: 0.3193 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8935 Z= 0.191 Angle : 0.560 8.723 12195 Z= 0.291 Chirality : 0.039 0.123 1370 Planarity : 0.004 0.031 1450 Dihedral : 10.467 110.924 1217 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.05 % Allowed : 9.15 % Favored : 87.80 % 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: 1.83 (0.25), residues: 1065 helix: 1.64 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -2.11 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 75 HIS 0.003 0.002 HIS D 76 PHE 0.015 0.002 PHE C 138 TYR 0.015 0.001 TYR A 187 ARG 0.005 0.001 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.05386 ( 720) hydrogen bonds : angle 3.89513 ( 2160) covalent geometry : bond 0.00434 ( 8930) covalent geometry : angle 0.56003 (12195) Misc. bond : bond 0.00019 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.930 Fit side-chains REVERT: A 34 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.6893 (t80) REVERT: A 53 ASP cc_start: 0.7596 (m-30) cc_final: 0.7350 (m-30) REVERT: B 34 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.6994 (t80) REVERT: B 100 LEU cc_start: 0.9048 (tp) cc_final: 0.8752 (mt) REVERT: B 125 PHE cc_start: 0.8533 (t80) cc_final: 0.8317 (t80) REVERT: C 80 MET cc_start: 0.6614 (mtm) cc_final: 0.6257 (mtm) REVERT: C 147 MET cc_start: 0.7132 (ttt) cc_final: 0.6777 (ttm) REVERT: C 163 MET cc_start: 0.8276 (mtp) cc_final: 0.7816 (mtp) REVERT: C 191 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8182 (ttm) REVERT: C 192 TYR cc_start: 0.8367 (m-80) cc_final: 0.7900 (m-80) REVERT: C 206 PHE cc_start: 0.8320 (t80) cc_final: 0.8076 (t80) REVERT: D 138 PHE cc_start: 0.8546 (m-80) cc_final: 0.8302 (m-80) REVERT: D 171 GLU cc_start: 0.7826 (tt0) cc_final: 0.7499 (tt0) REVERT: D 187 TYR cc_start: 0.8398 (t80) cc_final: 0.8160 (t80) REVERT: D 192 TYR cc_start: 0.7968 (m-80) cc_final: 0.7589 (m-80) REVERT: E 35 TRP cc_start: 0.7910 (m100) cc_final: 0.7610 (m100) REVERT: E 80 MET cc_start: 0.6453 (mtm) cc_final: 0.6192 (mtp) REVERT: E 141 MET cc_start: 0.8129 (mtp) cc_final: 0.7847 (ttm) REVERT: E 191 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8252 (ttm) outliers start: 27 outliers final: 17 residues processed: 211 average time/residue: 0.6390 time to fit residues: 151.2105 Evaluate side-chains 202 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 191 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 7 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 225 ASN B 241 ASN C 177 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.160680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.136507 restraints weight = 9200.576| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.16 r_work: 0.3244 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8935 Z= 0.158 Angle : 0.503 7.234 12195 Z= 0.266 Chirality : 0.037 0.111 1370 Planarity : 0.004 0.030 1450 Dihedral : 9.745 111.234 1215 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.39 % Allowed : 12.09 % Favored : 84.52 % 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: 2.10 (0.25), residues: 1065 helix: 1.79 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.73 (0.50), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 75 HIS 0.003 0.002 HIS D 76 PHE 0.015 0.002 PHE C 138 TYR 0.014 0.001 TYR A 187 ARG 0.004 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.05021 ( 720) hydrogen bonds : angle 3.72428 ( 2160) covalent geometry : bond 0.00350 ( 8930) covalent geometry : angle 0.50290 (12195) Misc. bond : bond 0.00048 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.900 Fit side-chains REVERT: A 34 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.6882 (t80) REVERT: A 53 ASP cc_start: 0.8063 (m-30) cc_final: 0.7850 (m-30) REVERT: B 34 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.7112 (t80) REVERT: B 100 LEU cc_start: 0.9088 (tp) cc_final: 0.8792 (mt) REVERT: B 125 PHE cc_start: 0.8559 (t80) cc_final: 0.8349 (t80) REVERT: B 191 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8484 (ttm) REVERT: C 80 MET cc_start: 0.6855 (mtm) cc_final: 0.6504 (mtm) REVERT: C 140 TYR cc_start: 0.8108 (t80) cc_final: 0.7717 (t80) REVERT: C 147 MET cc_start: 0.7114 (ttt) cc_final: 0.6729 (ttm) REVERT: C 163 MET cc_start: 0.8320 (mtp) cc_final: 0.7859 (mtp) REVERT: C 191 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8202 (ttm) REVERT: C 192 TYR cc_start: 0.8390 (m-80) cc_final: 0.8067 (m-80) REVERT: C 206 PHE cc_start: 0.8407 (t80) cc_final: 0.8138 (t80) REVERT: D 171 GLU cc_start: 0.7877 (tt0) cc_final: 0.7547 (tt0) REVERT: D 192 TYR cc_start: 0.8162 (m-80) cc_final: 0.7895 (m-80) REVERT: D 205 TYR cc_start: 0.8105 (t80) cc_final: 0.7896 (t80) REVERT: E 35 TRP cc_start: 0.8021 (m100) cc_final: 0.7718 (m100) REVERT: E 80 MET cc_start: 0.6557 (mtm) cc_final: 0.6308 (mtp) REVERT: E 138 PHE cc_start: 0.8411 (m-80) cc_final: 0.8164 (m-80) REVERT: E 141 MET cc_start: 0.8196 (mtp) cc_final: 0.7938 (ttm) REVERT: E 191 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8207 (ttm) outliers start: 30 outliers final: 18 residues processed: 205 average time/residue: 0.6326 time to fit residues: 145.2976 Evaluate side-chains 200 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 191 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 55 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.160792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.136541 restraints weight = 9231.461| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.17 r_work: 0.3237 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8935 Z= 0.155 Angle : 0.503 6.854 12195 Z= 0.265 Chirality : 0.037 0.110 1370 Planarity : 0.004 0.030 1450 Dihedral : 9.600 110.607 1215 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.95 % Allowed : 13.33 % Favored : 82.71 % 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: 2.20 (0.25), residues: 1065 helix: 1.84 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.55 (0.52), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 75 HIS 0.003 0.002 HIS D 76 PHE 0.019 0.002 PHE D 125 TYR 0.015 0.001 TYR A 187 ARG 0.003 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04954 ( 720) hydrogen bonds : angle 3.66922 ( 2160) covalent geometry : bond 0.00343 ( 8930) covalent geometry : angle 0.50318 (12195) Misc. bond : bond 0.00059 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.818 Fit side-chains REVERT: A 34 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.6916 (t80) REVERT: B 34 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7117 (t80) REVERT: B 100 LEU cc_start: 0.9073 (tp) cc_final: 0.8788 (mt) REVERT: B 191 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8485 (ttm) REVERT: B 205 TYR cc_start: 0.8197 (t80) cc_final: 0.7996 (t80) REVERT: C 80 MET cc_start: 0.6842 (mtm) cc_final: 0.6518 (mtm) REVERT: C 140 TYR cc_start: 0.8100 (t80) cc_final: 0.7729 (t80) REVERT: C 147 MET cc_start: 0.7113 (ttt) cc_final: 0.6737 (ttm) REVERT: C 163 MET cc_start: 0.8349 (mtp) cc_final: 0.7928 (mtp) REVERT: C 191 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8190 (ttm) REVERT: C 192 TYR cc_start: 0.8399 (m-80) cc_final: 0.8103 (m-80) REVERT: C 206 PHE cc_start: 0.8400 (t80) cc_final: 0.8162 (t80) REVERT: D 171 GLU cc_start: 0.7915 (tt0) cc_final: 0.7552 (tt0) REVERT: D 192 TYR cc_start: 0.8207 (m-80) cc_final: 0.7990 (m-80) REVERT: D 205 TYR cc_start: 0.8054 (t80) cc_final: 0.7620 (t80) REVERT: E 34 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.6921 (t80) REVERT: E 35 TRP cc_start: 0.8023 (m100) cc_final: 0.7731 (m100) REVERT: E 80 MET cc_start: 0.6635 (mtm) cc_final: 0.6357 (mtp) REVERT: E 141 MET cc_start: 0.8245 (mtp) cc_final: 0.8000 (ttm) REVERT: E 191 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8127 (ttm) outliers start: 35 outliers final: 19 residues processed: 217 average time/residue: 0.6013 time to fit residues: 146.7210 Evaluate side-chains 207 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 191 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 72 optimal weight: 0.0370 chunk 103 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 overall best weight: 4.8066 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.161243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.137178 restraints weight = 9238.778| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.17 r_work: 0.3247 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8935 Z= 0.157 Angle : 0.514 6.916 12195 Z= 0.269 Chirality : 0.037 0.115 1370 Planarity : 0.004 0.030 1450 Dihedral : 9.609 111.126 1215 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.50 % Allowed : 14.92 % Favored : 81.58 % 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: 2.23 (0.25), residues: 1065 helix: 1.85 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.47 (0.53), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 75 HIS 0.003 0.001 HIS D 76 PHE 0.013 0.001 PHE B 138 TYR 0.015 0.001 TYR A 187 ARG 0.003 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04945 ( 720) hydrogen bonds : angle 3.67208 ( 2160) covalent geometry : bond 0.00349 ( 8930) covalent geometry : angle 0.51352 (12195) Misc. bond : bond 0.00058 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.849 Fit side-chains REVERT: A 34 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.6941 (t80) REVERT: B 34 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7117 (t80) REVERT: B 100 LEU cc_start: 0.9085 (tp) cc_final: 0.8798 (mt) REVERT: B 191 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8487 (ttm) REVERT: B 205 TYR cc_start: 0.8159 (t80) cc_final: 0.7904 (t80) REVERT: C 80 MET cc_start: 0.6980 (mtm) cc_final: 0.6705 (mtm) REVERT: C 140 TYR cc_start: 0.8099 (t80) cc_final: 0.7718 (t80) REVERT: C 147 MET cc_start: 0.7073 (ttt) cc_final: 0.6689 (ttm) REVERT: C 163 MET cc_start: 0.8531 (mtp) cc_final: 0.8116 (mtp) REVERT: C 192 TYR cc_start: 0.8383 (m-80) cc_final: 0.8109 (m-80) REVERT: C 206 PHE cc_start: 0.8267 (t80) cc_final: 0.8023 (t80) REVERT: D 171 GLU cc_start: 0.7908 (tt0) cc_final: 0.7557 (tt0) REVERT: D 205 TYR cc_start: 0.8063 (t80) cc_final: 0.7680 (t80) REVERT: E 34 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.6928 (t80) REVERT: E 35 TRP cc_start: 0.8031 (m100) cc_final: 0.7720 (m100) REVERT: E 80 MET cc_start: 0.6542 (mtm) cc_final: 0.6282 (mtp) REVERT: E 141 MET cc_start: 0.8193 (mtp) cc_final: 0.7946 (ttm) REVERT: E 191 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8168 (ttm) outliers start: 31 outliers final: 21 residues processed: 209 average time/residue: 0.6060 time to fit residues: 142.0777 Evaluate side-chains 210 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 191 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 78 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 54 optimal weight: 0.0370 chunk 58 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 overall best weight: 3.8064 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.163373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.139399 restraints weight = 9136.645| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.16 r_work: 0.3256 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8935 Z= 0.138 Angle : 0.489 6.967 12195 Z= 0.258 Chirality : 0.037 0.115 1370 Planarity : 0.003 0.028 1450 Dihedral : 9.602 111.417 1215 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.84 % Allowed : 14.80 % Favored : 81.36 % 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: 2.38 (0.25), residues: 1065 helix: 1.94 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.32 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 75 HIS 0.003 0.001 HIS D 76 PHE 0.023 0.001 PHE D 125 TYR 0.014 0.001 TYR A 187 ARG 0.002 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04681 ( 720) hydrogen bonds : angle 3.58195 ( 2160) covalent geometry : bond 0.00297 ( 8930) covalent geometry : angle 0.48932 (12195) Misc. bond : bond 0.00051 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.952 Fit side-chains REVERT: A 34 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.6980 (t80) REVERT: B 34 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7121 (t80) REVERT: B 100 LEU cc_start: 0.9065 (tp) cc_final: 0.8746 (mt) REVERT: B 132 SER cc_start: 0.8447 (p) cc_final: 0.8091 (p) REVERT: B 191 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8480 (ttm) REVERT: B 203 VAL cc_start: 0.8132 (t) cc_final: 0.7916 (t) REVERT: C 80 MET cc_start: 0.6968 (mtm) cc_final: 0.6655 (mtm) REVERT: C 140 TYR cc_start: 0.8026 (t80) cc_final: 0.7697 (t80) REVERT: C 147 MET cc_start: 0.6942 (ttt) cc_final: 0.6632 (ttm) REVERT: C 191 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8025 (ttm) REVERT: C 192 TYR cc_start: 0.8314 (m-80) cc_final: 0.8100 (m-80) REVERT: C 206 PHE cc_start: 0.8251 (t80) cc_final: 0.7993 (t80) REVERT: D 171 GLU cc_start: 0.7897 (tt0) cc_final: 0.7547 (tt0) REVERT: D 205 TYR cc_start: 0.8054 (t80) cc_final: 0.7682 (t80) REVERT: E 34 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.6965 (t80) REVERT: E 80 MET cc_start: 0.6544 (mtm) cc_final: 0.6278 (mtp) REVERT: E 141 MET cc_start: 0.8175 (mtp) cc_final: 0.7914 (ttm) REVERT: E 191 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7979 (ttm) outliers start: 34 outliers final: 22 residues processed: 209 average time/residue: 0.6131 time to fit residues: 143.9644 Evaluate side-chains 210 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 191 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 61 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.160104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.136062 restraints weight = 9356.467| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.17 r_work: 0.3233 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8935 Z= 0.172 Angle : 0.538 8.544 12195 Z= 0.280 Chirality : 0.038 0.118 1370 Planarity : 0.004 0.030 1450 Dihedral : 9.499 109.811 1215 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.62 % Allowed : 14.80 % Favored : 81.58 % 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: 2.19 (0.25), residues: 1065 helix: 1.81 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.38 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 84 HIS 0.003 0.002 HIS D 76 PHE 0.014 0.002 PHE B 138 TYR 0.017 0.001 TYR A 187 ARG 0.003 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.05086 ( 720) hydrogen bonds : angle 3.68005 ( 2160) covalent geometry : bond 0.00387 ( 8930) covalent geometry : angle 0.53788 (12195) Misc. bond : bond 0.00066 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 1.040 Fit side-chains REVERT: A 34 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.6888 (t80) REVERT: A 141 MET cc_start: 0.8253 (mtp) cc_final: 0.7900 (mtp) REVERT: B 34 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7086 (t80) REVERT: B 100 LEU cc_start: 0.9092 (tp) cc_final: 0.8796 (mt) REVERT: B 132 SER cc_start: 0.8453 (p) cc_final: 0.8065 (p) REVERT: B 191 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8510 (ttm) REVERT: B 203 VAL cc_start: 0.8177 (t) cc_final: 0.7958 (t) REVERT: C 80 MET cc_start: 0.7024 (mtm) cc_final: 0.6750 (mtm) REVERT: C 140 TYR cc_start: 0.8116 (t80) cc_final: 0.7727 (t80) REVERT: C 147 MET cc_start: 0.6919 (ttt) cc_final: 0.6565 (ttm) REVERT: C 191 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8057 (ttm) REVERT: C 192 TYR cc_start: 0.8425 (m-80) cc_final: 0.8169 (m-80) REVERT: C 206 PHE cc_start: 0.8283 (t80) cc_final: 0.8037 (t80) REVERT: D 171 GLU cc_start: 0.7931 (tt0) cc_final: 0.7579 (tt0) REVERT: D 205 TYR cc_start: 0.8054 (t80) cc_final: 0.7836 (t80) REVERT: D 222 LEU cc_start: 0.8719 (tp) cc_final: 0.8507 (tp) REVERT: E 34 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.6887 (t80) REVERT: E 35 TRP cc_start: 0.8061 (m100) cc_final: 0.7722 (m100) REVERT: E 80 MET cc_start: 0.6574 (mtm) cc_final: 0.6316 (mtp) REVERT: E 141 MET cc_start: 0.8212 (mtp) cc_final: 0.7962 (ttm) REVERT: E 191 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8126 (ttm) outliers start: 32 outliers final: 21 residues processed: 203 average time/residue: 0.6660 time to fit residues: 151.0806 Evaluate side-chains 208 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 191 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 9 optimal weight: 0.0050 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 overall best weight: 5.0002 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.160778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.136915 restraints weight = 9341.941| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.16 r_work: 0.3241 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8935 Z= 0.161 Angle : 0.532 10.369 12195 Z= 0.276 Chirality : 0.038 0.120 1370 Planarity : 0.004 0.029 1450 Dihedral : 9.347 110.684 1215 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.16 % Allowed : 15.59 % Favored : 81.24 % 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: 2.24 (0.25), residues: 1065 helix: 1.84 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.32 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 84 HIS 0.003 0.002 HIS D 76 PHE 0.021 0.002 PHE D 125 TYR 0.016 0.001 TYR A 187 ARG 0.003 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04929 ( 720) hydrogen bonds : angle 3.66012 ( 2160) covalent geometry : bond 0.00359 ( 8930) covalent geometry : angle 0.53215 (12195) Misc. bond : bond 0.00063 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.923 Fit side-chains REVERT: A 34 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.6899 (t80) REVERT: A 141 MET cc_start: 0.8255 (mtp) cc_final: 0.7917 (mtp) REVERT: B 34 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7087 (t80) REVERT: B 100 LEU cc_start: 0.9082 (tp) cc_final: 0.8785 (mt) REVERT: B 132 SER cc_start: 0.8390 (p) cc_final: 0.8035 (p) REVERT: B 191 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8502 (ttm) REVERT: B 203 VAL cc_start: 0.8173 (t) cc_final: 0.7948 (t) REVERT: C 80 MET cc_start: 0.7027 (mtm) cc_final: 0.6766 (mtm) REVERT: C 140 TYR cc_start: 0.8101 (t80) cc_final: 0.7730 (t80) REVERT: C 163 MET cc_start: 0.8528 (mtp) cc_final: 0.8147 (mtp) REVERT: C 191 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8021 (ttm) REVERT: C 192 TYR cc_start: 0.8360 (m-80) cc_final: 0.8115 (m-80) REVERT: C 206 PHE cc_start: 0.8278 (t80) cc_final: 0.8010 (t80) REVERT: D 171 GLU cc_start: 0.7920 (tt0) cc_final: 0.7564 (tt0) REVERT: E 34 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.6923 (t80) REVERT: E 80 MET cc_start: 0.6600 (mtm) cc_final: 0.6340 (mtp) REVERT: E 141 MET cc_start: 0.8207 (mtp) cc_final: 0.7950 (ttm) REVERT: E 191 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8053 (ttm) outliers start: 28 outliers final: 20 residues processed: 202 average time/residue: 0.6633 time to fit residues: 149.7756 Evaluate side-chains 208 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 191 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 38 optimal weight: 0.0010 chunk 63 optimal weight: 50.0000 chunk 3 optimal weight: 6.9990 chunk 42 optimal weight: 40.0000 chunk 102 optimal weight: 9.9990 chunk 48 optimal weight: 40.0000 chunk 57 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 overall best weight: 4.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.161398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.136083 restraints weight = 9317.043| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.44 r_work: 0.3255 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8935 Z= 0.147 Angle : 0.518 11.683 12195 Z= 0.271 Chirality : 0.037 0.138 1370 Planarity : 0.004 0.030 1450 Dihedral : 8.677 110.008 1215 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.62 % Allowed : 15.82 % Favored : 80.56 % 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: 2.32 (0.25), residues: 1065 helix: 1.89 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.26 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 75 HIS 0.003 0.002 HIS D 76 PHE 0.015 0.002 PHE B 206 TYR 0.015 0.001 TYR A 187 ARG 0.003 0.001 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.04778 ( 720) hydrogen bonds : angle 3.62687 ( 2160) covalent geometry : bond 0.00320 ( 8930) covalent geometry : angle 0.51848 (12195) Misc. bond : bond 0.00056 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.832 Fit side-chains REVERT: A 34 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.6823 (t80) REVERT: A 141 MET cc_start: 0.8195 (mtp) cc_final: 0.7834 (mtp) REVERT: B 34 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.6986 (t80) REVERT: B 100 LEU cc_start: 0.9078 (tp) cc_final: 0.8777 (mt) REVERT: B 132 SER cc_start: 0.8371 (p) cc_final: 0.8009 (p) REVERT: B 191 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8462 (ttm) REVERT: C 80 MET cc_start: 0.6930 (mtm) cc_final: 0.6618 (mtm) REVERT: C 140 TYR cc_start: 0.8083 (t80) cc_final: 0.7740 (t80) REVERT: C 147 MET cc_start: 0.7289 (ttp) cc_final: 0.6963 (ttm) REVERT: C 191 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8049 (ttm) REVERT: C 192 TYR cc_start: 0.8281 (m-80) cc_final: 0.8072 (m-80) REVERT: C 206 PHE cc_start: 0.8230 (t80) cc_final: 0.7960 (t80) REVERT: D 171 GLU cc_start: 0.7845 (tt0) cc_final: 0.7490 (tt0) REVERT: E 34 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.6872 (t80) REVERT: E 80 MET cc_start: 0.6456 (mtm) cc_final: 0.6208 (mtp) REVERT: E 141 MET cc_start: 0.8138 (mtp) cc_final: 0.7881 (ttm) REVERT: E 191 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7964 (ttm) outliers start: 32 outliers final: 21 residues processed: 202 average time/residue: 0.6539 time to fit residues: 147.7303 Evaluate side-chains 206 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 191 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 101 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.162051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.138360 restraints weight = 9273.743| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.16 r_work: 0.3260 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8935 Z= 0.145 Angle : 0.518 9.881 12195 Z= 0.272 Chirality : 0.037 0.129 1370 Planarity : 0.003 0.030 1450 Dihedral : 8.566 109.408 1215 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.05 % Allowed : 16.38 % Favored : 80.56 % 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: 2.34 (0.25), residues: 1065 helix: 1.90 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.23 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 75 HIS 0.003 0.002 HIS D 76 PHE 0.023 0.002 PHE D 125 TYR 0.015 0.001 TYR C 111 ARG 0.003 0.001 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.04717 ( 720) hydrogen bonds : angle 3.62075 ( 2160) covalent geometry : bond 0.00317 ( 8930) covalent geometry : angle 0.51795 (12195) Misc. bond : bond 0.00054 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.834 Fit side-chains REVERT: A 34 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.6956 (t80) REVERT: A 141 MET cc_start: 0.8251 (mtp) cc_final: 0.7895 (mtp) REVERT: B 34 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7014 (t80) REVERT: B 100 LEU cc_start: 0.9078 (tp) cc_final: 0.8774 (mt) REVERT: B 132 SER cc_start: 0.8484 (p) cc_final: 0.8096 (p) REVERT: B 191 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8461 (ttm) REVERT: C 80 MET cc_start: 0.7033 (mtm) cc_final: 0.6709 (mtm) REVERT: C 140 TYR cc_start: 0.8013 (t80) cc_final: 0.7723 (t80) REVERT: C 191 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8031 (ttm) REVERT: C 206 PHE cc_start: 0.8267 (t80) cc_final: 0.8031 (t80) REVERT: D 171 GLU cc_start: 0.7897 (tt0) cc_final: 0.7549 (tt0) REVERT: E 34 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.6968 (t80) REVERT: E 80 MET cc_start: 0.6520 (mtm) cc_final: 0.6264 (mtp) REVERT: E 141 MET cc_start: 0.8178 (mtp) cc_final: 0.7908 (ttm) REVERT: E 191 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7980 (ttm) outliers start: 27 outliers final: 21 residues processed: 200 average time/residue: 0.6167 time to fit residues: 138.1522 Evaluate side-chains 209 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 191 MET Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain E residue 34 PHE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 191 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.162555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.138880 restraints weight = 9299.445| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.17 r_work: 0.3276 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8935 Z= 0.139 Angle : 0.510 10.105 12195 Z= 0.269 Chirality : 0.037 0.122 1370 Planarity : 0.003 0.030 1450 Dihedral : 8.547 108.744 1215 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.28 % Allowed : 16.27 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.25), residues: 1065 helix: 1.94 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.20 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 75 HIS 0.003 0.002 HIS D 76 PHE 0.016 0.002 PHE B 206 TYR 0.015 0.001 TYR A 187 ARG 0.003 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04622 ( 720) hydrogen bonds : angle 3.59152 ( 2160) covalent geometry : bond 0.00303 ( 8930) covalent geometry : angle 0.51042 (12195) Misc. bond : bond 0.00053 ( 5) =============================================================================== Job complete usr+sys time: 5152.35 seconds wall clock time: 88 minutes 42.07 seconds (5322.07 seconds total)