Starting phenix.real_space_refine on Thu Mar 13 06:00:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b03_11955/03_2025/7b03_11955.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b03_11955/03_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_11955/03_2025/7b03_11955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b03_11955/03_2025/7b03_11955.map" model { file = "/net/cci-nas-00/data/ceres_data/7b03_11955/03_2025/7b03_11955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b03_11955/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.66, per 1000 atoms: 0.54 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: 2.84 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.71 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: 2.44 Time building geometry restraints manager: 3.28 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.370 Find NCS groups from input model: 0.180 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:22.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.210 ------------------------------------------------------------------------------- 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 : 0.005 0.048 8930 Z= 0.333 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 *********************** 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 : 0.895 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: 0.7136 time to fit residues: 168.3987 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 : 0.904 ------------------------------------------------------------------------------- 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: 3.9990 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: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.159644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.133975 restraints weight = 9292.526| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.41 r_work: 0.3198 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8930 Z= 0.264 Angle : 0.549 8.192 12195 Z= 0.286 Chirality : 0.039 0.121 1370 Planarity : 0.004 0.031 1450 Dihedral : 10.581 111.329 1217 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.36 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: 1.87 (0.25), residues: 1065 helix: 1.67 (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 0.014 0.002 PHE C 138 TYR 0.015 0.001 TYR A 187 ARG 0.005 0.001 ARG A 54 *********************** 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 222 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.939 Fit side-chains REVERT: A 34 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.6946 (t80) REVERT: A 53 ASP cc_start: 0.8140 (m-30) cc_final: 0.7893 (m-30) REVERT: B 34 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7045 (t80) REVERT: B 100 LEU cc_start: 0.9117 (tp) cc_final: 0.8832 (mt) REVERT: B 125 PHE cc_start: 0.8558 (t80) cc_final: 0.8339 (t80) REVERT: B 138 PHE cc_start: 0.8740 (m-80) cc_final: 0.8538 (OUTLIER) REVERT: C 80 MET cc_start: 0.6997 (mtm) cc_final: 0.6653 (mtm) REVERT: C 147 MET cc_start: 0.7201 (ttt) cc_final: 0.6825 (ttm) REVERT: C 163 MET cc_start: 0.8362 (mtp) cc_final: 0.7879 (mtp) REVERT: C 191 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8300 (ttm) REVERT: C 192 TYR cc_start: 0.8570 (m-80) cc_final: 0.8144 (m-80) REVERT: C 206 PHE cc_start: 0.8416 (t80) cc_final: 0.8187 (t80) REVERT: D 138 PHE cc_start: 0.8583 (m-80) cc_final: 0.8334 (m-80) REVERT: D 171 GLU cc_start: 0.7983 (tt0) cc_final: 0.7597 (tt0) REVERT: D 185 SER cc_start: 0.8701 (m) cc_final: 0.8499 (t) REVERT: D 187 TYR cc_start: 0.8525 (t80) cc_final: 0.8299 (t80) REVERT: D 192 TYR cc_start: 0.8213 (m-80) cc_final: 0.7863 (m-80) REVERT: E 35 TRP cc_start: 0.8027 (m100) cc_final: 0.7738 (m100) REVERT: E 80 MET cc_start: 0.6784 (mtm) cc_final: 0.6475 (mtp) REVERT: E 141 MET cc_start: 0.8250 (mtp) cc_final: 0.7950 (ttm) REVERT: E 191 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8377 (ttm) outliers start: 27 outliers final: 17 residues processed: 210 average time/residue: 0.7153 time to fit residues: 168.1913 Evaluate side-chains 201 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 2 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.163420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.138841 restraints weight = 9174.914| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.19 r_work: 0.3281 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8930 Z= 0.174 Angle : 0.464 5.974 12195 Z= 0.248 Chirality : 0.036 0.105 1370 Planarity : 0.003 0.028 1450 Dihedral : 9.822 112.240 1215 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.50 % Allowed : 11.30 % Favored : 85.20 % 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: 2.29 (0.25), residues: 1065 helix: 1.91 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.65 (0.50), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 75 HIS 0.003 0.001 HIS C 76 PHE 0.017 0.002 PHE D 125 TYR 0.012 0.001 TYR A 187 ARG 0.003 0.001 ARG E 52 *********************** 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 229 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.930 Fit side-chains REVERT: A 34 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.6915 (t80) REVERT: A 53 ASP cc_start: 0.8060 (m-30) cc_final: 0.7829 (m-30) REVERT: B 34 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.6933 (t80) REVERT: B 100 LEU cc_start: 0.9040 (tp) cc_final: 0.8726 (mt) REVERT: B 125 PHE cc_start: 0.8449 (t80) cc_final: 0.8224 (t80) REVERT: B 191 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8435 (ttm) REVERT: B 205 TYR cc_start: 0.8122 (t80) cc_final: 0.7823 (t80) REVERT: C 80 MET cc_start: 0.6726 (mtm) cc_final: 0.6392 (mtm) REVERT: C 140 TYR cc_start: 0.7996 (t80) cc_final: 0.7641 (t80) REVERT: C 147 MET cc_start: 0.7013 (ttt) cc_final: 0.6708 (ttm) REVERT: C 163 MET cc_start: 0.8243 (mtp) cc_final: 0.7765 (mtp) REVERT: C 191 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8230 (ttm) REVERT: C 192 TYR cc_start: 0.8301 (m-80) cc_final: 0.8007 (m-80) REVERT: C 206 PHE cc_start: 0.8330 (t80) cc_final: 0.8099 (t80) REVERT: D 171 GLU cc_start: 0.7793 (tt0) cc_final: 0.7452 (tt0) REVERT: D 192 TYR cc_start: 0.8069 (m-80) cc_final: 0.7814 (m-80) REVERT: D 205 TYR cc_start: 0.8007 (t80) cc_final: 0.7653 (t80) REVERT: E 34 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.6835 (t80) REVERT: E 35 TRP cc_start: 0.7897 (m100) cc_final: 0.7599 (m100) REVERT: E 80 MET cc_start: 0.6409 (mtm) cc_final: 0.6141 (mtp) REVERT: E 138 PHE cc_start: 0.8354 (m-80) cc_final: 0.8099 (m-80) REVERT: E 141 MET cc_start: 0.8250 (mtp) cc_final: 0.8006 (ttm) REVERT: E 191 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8152 (ttm) outliers start: 31 outliers final: 19 residues processed: 213 average time/residue: 0.6063 time to fit residues: 145.2239 Evaluate side-chains 209 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 158 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 55 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.160394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.136305 restraints weight = 9262.958| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.17 r_work: 0.3232 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8930 Z= 0.246 Angle : 0.522 7.032 12195 Z= 0.273 Chirality : 0.038 0.113 1370 Planarity : 0.004 0.030 1450 Dihedral : 9.581 109.604 1215 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.73 % Allowed : 12.88 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.25), residues: 1065 helix: 1.83 (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 0.012 0.002 PHE B 206 TYR 0.016 0.001 TYR A 187 ARG 0.004 0.001 ARG A 52 *********************** 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 226 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.856 Fit side-chains REVERT: A 34 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.6995 (t80) REVERT: B 34 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7089 (t80) REVERT: B 100 LEU cc_start: 0.9073 (tp) cc_final: 0.8798 (mt) REVERT: B 125 PHE cc_start: 0.8538 (t80) cc_final: 0.8329 (t80) REVERT: B 191 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8504 (ttm) REVERT: B 205 TYR cc_start: 0.8157 (t80) cc_final: 0.7887 (t80) REVERT: C 80 MET cc_start: 0.6845 (mtm) cc_final: 0.6508 (mtm) REVERT: C 140 TYR cc_start: 0.8102 (t80) cc_final: 0.7727 (t80) REVERT: C 147 MET cc_start: 0.7070 (ttt) cc_final: 0.6681 (ttm) REVERT: C 163 MET cc_start: 0.8328 (mtp) cc_final: 0.7866 (mtp) REVERT: C 191 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8189 (ttm) REVERT: C 192 TYR cc_start: 0.8385 (m-80) cc_final: 0.8097 (m-80) REVERT: C 206 PHE cc_start: 0.8401 (t80) cc_final: 0.8174 (t80) REVERT: D 171 GLU cc_start: 0.7922 (tt0) cc_final: 0.7558 (tt0) REVERT: D 192 TYR cc_start: 0.8198 (m-80) cc_final: 0.7937 (m-80) REVERT: D 205 TYR cc_start: 0.8059 (t80) cc_final: 0.7594 (t80) REVERT: E 35 TRP cc_start: 0.8024 (m100) cc_final: 0.7718 (m100) REVERT: E 80 MET cc_start: 0.6634 (mtm) cc_final: 0.6418 (mtp) REVERT: E 141 MET cc_start: 0.8228 (mtp) cc_final: 0.7970 (ttm) REVERT: E 191 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8290 (ttm) outliers start: 33 outliers final: 22 residues processed: 211 average time/residue: 0.6009 time to fit residues: 142.4451 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 : 0.849 ------------------------------------------------------------------------------- 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 138 PHE Chi-restraints excluded: chain B residue 158 LEU 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 36 LEU 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 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: 6.9990 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.161003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.136931 restraints weight = 9250.833| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.17 r_work: 0.3254 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8930 Z= 0.220 Angle : 0.505 6.907 12195 Z= 0.265 Chirality : 0.037 0.116 1370 Planarity : 0.004 0.029 1450 Dihedral : 9.589 111.611 1215 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 4.07 % Allowed : 14.12 % Favored : 81.81 % 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: 2.27 (0.25), residues: 1065 helix: 1.87 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.45 (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 0.021 0.002 PHE D 125 TYR 0.015 0.001 TYR A 187 ARG 0.003 0.001 ARG A 52 *********************** 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 228 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.847 Fit side-chains REVERT: A 34 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.6933 (t80) REVERT: B 34 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7101 (t80) REVERT: B 100 LEU cc_start: 0.9070 (tp) cc_final: 0.8781 (mt) REVERT: B 125 PHE cc_start: 0.8536 (t80) cc_final: 0.8329 (t80) REVERT: B 191 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8480 (ttm) REVERT: B 203 VAL cc_start: 0.8192 (t) cc_final: 0.7958 (t) REVERT: C 80 MET cc_start: 0.6982 (mtm) cc_final: 0.6663 (mtm) REVERT: C 140 TYR cc_start: 0.8073 (t80) cc_final: 0.7729 (t80) REVERT: C 147 MET cc_start: 0.7075 (ttt) cc_final: 0.6707 (ttm) REVERT: C 163 MET cc_start: 0.8507 (mtp) cc_final: 0.8098 (mtp) REVERT: C 191 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8371 (ttm) REVERT: C 192 TYR cc_start: 0.8412 (m-80) cc_final: 0.8158 (m-80) REVERT: C 206 PHE cc_start: 0.8255 (t80) cc_final: 0.8020 (t80) REVERT: D 171 GLU cc_start: 0.7919 (tt0) cc_final: 0.7567 (tt0) REVERT: D 205 TYR cc_start: 0.8083 (t80) cc_final: 0.7693 (t80) REVERT: E 34 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.6940 (t80) REVERT: E 35 TRP cc_start: 0.8033 (m100) cc_final: 0.7724 (m100) REVERT: E 80 MET cc_start: 0.6612 (mtm) cc_final: 0.6407 (mtp) REVERT: E 141 MET cc_start: 0.8178 (mtp) cc_final: 0.7934 (ttm) REVERT: E 191 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7991 (ttm) outliers start: 36 outliers final: 23 residues processed: 211 average time/residue: 0.6204 time to fit residues: 146.9748 Evaluate side-chains 213 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 138 PHE Chi-restraints excluded: chain B residue 158 LEU 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 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 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: 7.9990 chunk 76 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.163035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.139124 restraints weight = 9180.775| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.16 r_work: 0.3265 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8930 Z= 0.177 Angle : 0.483 6.846 12195 Z= 0.254 Chirality : 0.036 0.114 1370 Planarity : 0.003 0.028 1450 Dihedral : 9.579 111.532 1215 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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: 2.47 (0.25), residues: 1065 helix: 2.00 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.31 (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 0.012 0.001 PHE B 206 TYR 0.013 0.001 TYR A 187 ARG 0.003 0.000 ARG A 52 *********************** 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 229 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.857 Fit side-chains REVERT: A 34 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.6948 (t80) REVERT: B 34 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7040 (t80) REVERT: B 132 SER cc_start: 0.8470 (p) cc_final: 0.8131 (p) REVERT: B 191 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8457 (ttm) REVERT: B 203 VAL cc_start: 0.8152 (t) cc_final: 0.7932 (t) REVERT: C 80 MET cc_start: 0.6980 (mtm) cc_final: 0.6662 (mtm) REVERT: C 140 TYR cc_start: 0.8012 (t80) cc_final: 0.7688 (t80) REVERT: C 163 MET cc_start: 0.8474 (mtp) cc_final: 0.8149 (mtp) REVERT: C 191 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8242 (ttt) REVERT: C 192 TYR cc_start: 0.8323 (m-80) cc_final: 0.8067 (m-80) REVERT: C 206 PHE cc_start: 0.8235 (t80) cc_final: 0.8005 (t80) REVERT: D 171 GLU cc_start: 0.7894 (tt0) cc_final: 0.7529 (tt0) REVERT: D 205 TYR cc_start: 0.8025 (t80) cc_final: 0.7641 (t80) REVERT: E 34 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.6949 (t80) REVERT: E 141 MET cc_start: 0.8123 (mtp) cc_final: 0.7857 (ttm) REVERT: E 191 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7947 (ttm) outliers start: 32 outliers final: 21 residues processed: 214 average time/residue: 0.6361 time to fit residues: 152.6998 Evaluate side-chains 214 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 138 PHE Chi-restraints excluded: chain B residue 158 LEU 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 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 191 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 61 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.160357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.136227 restraints weight = 9326.751| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.17 r_work: 0.3236 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8930 Z= 0.258 Angle : 0.542 7.781 12195 Z= 0.282 Chirality : 0.039 0.125 1370 Planarity : 0.004 0.031 1450 Dihedral : 9.417 109.445 1215 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.39 % Allowed : 15.59 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.25), residues: 1065 helix: 1.85 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.39 (0.55), 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 0.027 0.002 PHE B 125 TYR 0.017 0.001 TYR A 187 ARG 0.003 0.001 ARG A 52 *********************** 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 216 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.866 Fit side-chains REVERT: A 34 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.6789 (t80) REVERT: B 34 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7058 (t80) REVERT: B 100 LEU cc_start: 0.9081 (tp) cc_final: 0.8802 (mt) REVERT: B 132 SER cc_start: 0.8448 (p) cc_final: 0.8099 (p) REVERT: B 184 GLN cc_start: 0.8700 (mt0) cc_final: 0.8454 (mt0) REVERT: B 191 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8503 (ttm) REVERT: B 203 VAL cc_start: 0.8222 (t) cc_final: 0.7989 (t) REVERT: C 80 MET cc_start: 0.7015 (mtm) cc_final: 0.6733 (mtm) REVERT: C 140 TYR cc_start: 0.8124 (t80) cc_final: 0.7761 (t80) REVERT: C 147 MET cc_start: 0.7264 (ttp) cc_final: 0.6923 (ttm) REVERT: C 191 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8187 (ttm) REVERT: C 192 TYR cc_start: 0.8339 (m-80) cc_final: 0.8101 (m-80) REVERT: C 206 PHE cc_start: 0.8266 (t80) cc_final: 0.8026 (t80) REVERT: D 171 GLU cc_start: 0.7938 (tt0) cc_final: 0.7577 (tt0) REVERT: D 205 TYR cc_start: 0.8054 (t80) cc_final: 0.7829 (t80) REVERT: E 34 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.6874 (t80) REVERT: E 35 TRP cc_start: 0.8059 (m100) cc_final: 0.7729 (m100) REVERT: E 141 MET cc_start: 0.8210 (mtp) cc_final: 0.7960 (ttm) REVERT: E 185 SER cc_start: 0.8566 (m) cc_final: 0.8352 (m) REVERT: E 191 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8119 (ttm) outliers start: 30 outliers final: 21 residues processed: 203 average time/residue: 0.6408 time to fit residues: 145.3247 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 : 0.853 ------------------------------------------------------------------------------- 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 138 PHE 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 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: 4.9990 chunk 101 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.162222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.137408 restraints weight = 9332.278| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.33 r_work: 0.3272 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8930 Z= 0.195 Angle : 0.503 9.270 12195 Z= 0.262 Chirality : 0.037 0.129 1370 Planarity : 0.003 0.028 1450 Dihedral : 8.999 111.050 1215 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.16 % Allowed : 15.93 % Favored : 80.90 % 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 : -1.29 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 75 HIS 0.003 0.002 HIS C 76 PHE 0.024 0.002 PHE B 125 TYR 0.015 0.001 TYR C 187 ARG 0.003 0.001 ARG A 52 *********************** 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: 0.7968 (OUTLIER) cc_final: 0.6892 (t80) REVERT: B 34 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.6975 (t80) REVERT: B 100 LEU cc_start: 0.9051 (tp) cc_final: 0.8780 (mt) REVERT: B 163 MET cc_start: 0.8435 (mtp) cc_final: 0.8164 (mtp) REVERT: B 184 GLN cc_start: 0.8648 (mt0) cc_final: 0.8384 (mt0) REVERT: B 191 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8458 (ttm) REVERT: C 80 MET cc_start: 0.6855 (mtm) cc_final: 0.6539 (mtm) REVERT: C 140 TYR cc_start: 0.8022 (t80) cc_final: 0.7705 (t80) REVERT: C 192 TYR cc_start: 0.8285 (m-80) cc_final: 0.8026 (m-80) REVERT: C 206 PHE cc_start: 0.8204 (t80) cc_final: 0.7961 (t80) REVERT: D 171 GLU cc_start: 0.7855 (tt0) cc_final: 0.7490 (tt0) REVERT: D 205 TYR cc_start: 0.7983 (t80) cc_final: 0.7733 (t80) REVERT: E 34 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.6854 (t80) REVERT: E 141 MET cc_start: 0.8145 (mtp) cc_final: 0.7885 (ttm) REVERT: E 185 SER cc_start: 0.8566 (m) cc_final: 0.8341 (m) REVERT: E 191 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7949 (ttm) outliers start: 28 outliers final: 18 residues processed: 203 average time/residue: 0.7430 time to fit residues: 169.1489 Evaluate side-chains 207 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 138 PHE 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 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 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: 0.9990 chunk 63 optimal weight: 50.0000 chunk 3 optimal weight: 6.9990 chunk 42 optimal weight: 50.0000 chunk 102 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.160993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.137241 restraints weight = 9317.075| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.16 r_work: 0.3246 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8930 Z= 0.248 Angle : 0.536 10.806 12195 Z= 0.281 Chirality : 0.038 0.127 1370 Planarity : 0.004 0.030 1450 Dihedral : 8.556 110.004 1215 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.16 % Allowed : 15.71 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.25), residues: 1065 helix: 1.86 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.29 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 35 HIS 0.003 0.002 HIS D 76 PHE 0.023 0.002 PHE B 125 TYR 0.017 0.001 TYR A 187 ARG 0.003 0.001 ARG A 52 *********************** 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 215 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.904 Fit side-chains REVERT: A 34 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.6984 (t80) REVERT: B 34 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7091 (t80) REVERT: B 100 LEU cc_start: 0.9065 (tp) cc_final: 0.8794 (mt) REVERT: B 163 MET cc_start: 0.8432 (mtp) cc_final: 0.8176 (mtt) REVERT: B 184 GLN cc_start: 0.8705 (mt0) cc_final: 0.8456 (mt0) REVERT: B 191 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8496 (ttm) REVERT: C 80 MET cc_start: 0.7008 (mtm) cc_final: 0.6738 (mtm) REVERT: C 140 TYR cc_start: 0.8043 (t80) cc_final: 0.7731 (t80) REVERT: C 206 PHE cc_start: 0.8262 (t80) cc_final: 0.8022 (t80) REVERT: D 171 GLU cc_start: 0.7916 (tt0) cc_final: 0.7565 (tt0) REVERT: E 34 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.6966 (t80) REVERT: E 35 TRP cc_start: 0.8058 (m100) cc_final: 0.7759 (m100) REVERT: E 141 MET cc_start: 0.8154 (mtp) cc_final: 0.7889 (ttm) REVERT: E 185 SER cc_start: 0.8596 (m) cc_final: 0.8385 (m) REVERT: E 191 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8110 (ttm) outliers start: 28 outliers final: 20 residues processed: 202 average time/residue: 0.6484 time to fit residues: 146.3651 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 : 0.900 ------------------------------------------------------------------------------- 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 138 PHE 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 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 191 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.163929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.139229 restraints weight = 9242.801| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.37 r_work: 0.3289 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8930 Z= 0.195 Angle : 0.504 11.854 12195 Z= 0.266 Chirality : 0.037 0.128 1370 Planarity : 0.003 0.029 1450 Dihedral : 8.561 110.223 1215 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.49 % Allowed : 16.95 % 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: 2.43 (0.25), residues: 1065 helix: 1.96 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.17 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 35 HIS 0.003 0.002 HIS D 76 PHE 0.023 0.002 PHE B 125 TYR 0.015 0.001 TYR C 111 ARG 0.003 0.000 ARG E 52 ********************** 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 207 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.989 Fit side-chains REVERT: A 34 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.6918 (t80) REVERT: B 34 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.6982 (t80) REVERT: B 75 TRP cc_start: 0.8672 (t-100) cc_final: 0.8162 (t60) REVERT: B 100 LEU cc_start: 0.9115 (tp) cc_final: 0.8844 (mt) REVERT: B 163 MET cc_start: 0.8428 (mtp) cc_final: 0.8178 (mtt) REVERT: B 184 GLN cc_start: 0.8650 (mt0) cc_final: 0.8386 (mt0) REVERT: B 191 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8460 (ttm) REVERT: B 203 VAL cc_start: 0.8169 (t) cc_final: 0.7956 (t) REVERT: C 80 MET cc_start: 0.6875 (mtm) cc_final: 0.6566 (mtm) REVERT: C 140 TYR cc_start: 0.7830 (t80) cc_final: 0.7606 (t80) REVERT: C 206 PHE cc_start: 0.8196 (t80) cc_final: 0.7921 (t80) REVERT: D 171 GLU cc_start: 0.7856 (tt0) cc_final: 0.7493 (tt0) REVERT: E 34 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.6899 (t80) REVERT: E 141 MET cc_start: 0.8080 (mtp) cc_final: 0.7828 (ttm) REVERT: E 191 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8048 (ttm) outliers start: 22 outliers final: 18 residues processed: 197 average time/residue: 0.6650 time to fit residues: 146.5444 Evaluate side-chains 202 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 138 PHE 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 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: 7.9990 chunk 96 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.167858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.143515 restraints weight = 9309.303| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.44 r_work: 0.3342 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8930 Z= 0.149 Angle : 0.466 11.848 12195 Z= 0.249 Chirality : 0.036 0.120 1370 Planarity : 0.003 0.030 1450 Dihedral : 8.673 110.436 1215 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.92 % Allowed : 17.63 % 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: 2.77 (0.26), residues: 1065 helix: 2.17 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -0.96 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 35 HIS 0.003 0.001 HIS D 76 PHE 0.024 0.002 PHE B 125 TYR 0.013 0.001 TYR C 111 ARG 0.002 0.000 ARG A 52 =============================================================================== Job complete usr+sys time: 5619.41 seconds wall clock time: 99 minutes 3.72 seconds (5943.72 seconds total)