Starting phenix.real_space_refine on Tue Sep 24 18:54:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/09_2024/7b03_11955.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/09_2024/7b03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/09_2024/7b03_11955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/09_2024/7b03_11955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/09_2024/7b03_11955.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b03_11955/09_2024/7b03_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-5461/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: 3.76, per 1000 atoms: 0.43 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: 2.45 Conformation dependent library (CDL) restraints added in 1.1 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: 0.80 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: 2.83 Time building geometry restraints manager: 2.78 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.840 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.720 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 0.820 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: 0.5983 time to fit residues: 140.8485 Evaluate side-chains 180 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 fitting. rotamer outliers: 27 poor density : 195 time to evaluate : 0.822 Fit side-chains REVERT: A 34 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7009 (t80) REVERT: A 53 ASP cc_start: 0.6826 (m-30) cc_final: 0.6589 (m-30) REVERT: B 34 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7086 (t80) REVERT: B 100 LEU cc_start: 0.8911 (tp) cc_final: 0.8590 (mt) REVERT: B 125 PHE cc_start: 0.8596 (t80) cc_final: 0.8349 (t80) REVERT: C 80 MET cc_start: 0.6068 (mtm) cc_final: 0.5758 (mtm) REVERT: C 147 MET cc_start: 0.6976 (ttt) cc_final: 0.6712 (ttm) REVERT: C 163 MET cc_start: 0.8133 (mtp) cc_final: 0.7684 (mtp) REVERT: C 191 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7960 (ttm) REVERT: C 192 TYR cc_start: 0.7787 (m-80) cc_final: 0.7315 (m-80) REVERT: C 206 PHE cc_start: 0.8219 (t80) cc_final: 0.8013 (t80) REVERT: D 138 PHE cc_start: 0.8453 (m-80) cc_final: 0.8171 (m-80) REVERT: D 187 TYR cc_start: 0.8248 (t80) cc_final: 0.8014 (t80) REVERT: D 192 TYR cc_start: 0.7454 (m-80) cc_final: 0.7077 (m-80) REVERT: E 141 MET cc_start: 0.7846 (mtp) cc_final: 0.7502 (ttm) REVERT: E 191 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7984 (ttm) outliers start: 27 outliers final: 17 residues processed: 210 average time/residue: 0.5963 time to fit residues: 140.7048 Evaluate side-chains 202 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 181 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 52 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 76 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8930 Z= 0.277 Angle : 0.542 7.179 12195 Z= 0.285 Chirality : 0.039 0.116 1370 Planarity : 0.004 0.032 1450 Dihedral : 9.744 109.954 1215 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.50 % Allowed : 12.32 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.25), residues: 1065 helix: 1.68 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.84 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 35 HIS 0.003 0.002 HIS D 76 PHE 0.016 0.002 PHE C 138 TYR 0.016 0.001 TYR A 187 ARG 0.004 0.001 ARG A 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 213 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 182 time to evaluate : 0.792 Fit side-chains REVERT: A 34 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.6886 (t80) REVERT: B 34 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7138 (t80) REVERT: B 100 LEU cc_start: 0.8909 (tp) cc_final: 0.8619 (mt) REVERT: B 125 PHE cc_start: 0.8631 (t80) cc_final: 0.8420 (t80) REVERT: B 191 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8198 (ttm) REVERT: C 80 MET cc_start: 0.6050 (mtm) cc_final: 0.5724 (mtm) REVERT: C 140 TYR cc_start: 0.7746 (t80) cc_final: 0.7371 (t80) REVERT: C 147 MET cc_start: 0.6886 (ttt) cc_final: 0.6615 (ttm) REVERT: C 163 MET cc_start: 0.8172 (mtp) cc_final: 0.7764 (mtp) REVERT: C 191 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7926 (ttm) REVERT: C 192 TYR cc_start: 0.7697 (m-80) cc_final: 0.7335 (m-80) REVERT: C 206 PHE cc_start: 0.8209 (t80) cc_final: 0.8006 (t80) REVERT: D 187 TYR cc_start: 0.8225 (t80) cc_final: 0.8002 (t80) REVERT: D 192 TYR cc_start: 0.7429 (m-80) cc_final: 0.7120 (m-80) REVERT: E 138 PHE cc_start: 0.8335 (m-80) cc_final: 0.8119 (OUTLIER) REVERT: E 141 MET cc_start: 0.7754 (mtp) cc_final: 0.7490 (ttm) REVERT: E 185 SER cc_start: 0.8209 (m) cc_final: 0.7942 (m) REVERT: E 191 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7964 (ttm) outliers start: 31 outliers final: 20 residues processed: 199 average time/residue: 0.6194 time to fit residues: 137.9648 Evaluate side-chains 199 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 D residue 203 VAL 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 94 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 50.0000 chunk 27 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8930 Z= 0.264 Angle : 0.537 7.016 12195 Z= 0.282 Chirality : 0.038 0.115 1370 Planarity : 0.004 0.031 1450 Dihedral : 9.596 110.372 1215 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.41 % Allowed : 12.88 % 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: 1.96 (0.25), residues: 1065 helix: 1.68 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.65 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 84 HIS 0.003 0.002 HIS D 76 PHE 0.017 0.002 PHE C 138 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 228 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 0.879 Fit side-chains REVERT: A 34 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.6883 (t80) REVERT: B 34 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7140 (t80) REVERT: B 100 LEU cc_start: 0.8921 (tp) cc_final: 0.8617 (mt) REVERT: B 125 PHE cc_start: 0.8632 (t80) cc_final: 0.8417 (t80) REVERT: B 191 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8319 (ttm) REVERT: C 80 MET cc_start: 0.6251 (mtm) cc_final: 0.5979 (mtm) REVERT: C 147 MET cc_start: 0.6853 (ttt) cc_final: 0.6591 (ttm) REVERT: C 163 MET cc_start: 0.8365 (mtp) cc_final: 0.7946 (mtp) REVERT: C 191 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7917 (ttm) REVERT: C 192 TYR cc_start: 0.7677 (m-80) cc_final: 0.7375 (m-80) REVERT: D 187 TYR cc_start: 0.8247 (t80) cc_final: 0.8040 (t80) REVERT: D 192 TYR cc_start: 0.7458 (m-80) cc_final: 0.7166 (m-80) REVERT: E 141 MET cc_start: 0.7812 (mtp) cc_final: 0.7553 (ttm) REVERT: E 185 SER cc_start: 0.8238 (m) cc_final: 0.7964 (m) REVERT: E 191 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7857 (ttm) outliers start: 39 outliers final: 22 residues processed: 208 average time/residue: 0.5866 time to fit residues: 137.6077 Evaluate side-chains 206 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 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 84 optimal weight: 30.0000 chunk 57 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 51 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8930 Z= 0.209 Angle : 0.504 6.945 12195 Z= 0.266 Chirality : 0.037 0.117 1370 Planarity : 0.004 0.030 1450 Dihedral : 9.628 111.570 1215 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.62 % Allowed : 15.14 % 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: 2.16 (0.25), residues: 1065 helix: 1.81 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.48 (0.54), 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 0.018 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 224 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 0.899 Fit side-chains REVERT: A 34 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.6945 (t80) REVERT: B 34 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7156 (t80) REVERT: B 100 LEU cc_start: 0.8884 (tp) cc_final: 0.8573 (mt) REVERT: B 125 PHE cc_start: 0.8602 (t80) cc_final: 0.8400 (t80) REVERT: B 132 SER cc_start: 0.8547 (p) cc_final: 0.8271 (p) REVERT: B 191 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8143 (ttm) REVERT: B 203 VAL cc_start: 0.8033 (t) cc_final: 0.7830 (t) REVERT: C 80 MET cc_start: 0.6169 (mtm) cc_final: 0.5957 (mtm) REVERT: C 163 MET cc_start: 0.8337 (mtp) cc_final: 0.7983 (mtp) REVERT: C 192 TYR cc_start: 0.7678 (m-80) cc_final: 0.7370 (m-80) REVERT: D 192 TYR cc_start: 0.7345 (m-80) cc_final: 0.7124 (m-80) REVERT: E 35 TRP cc_start: 0.7583 (m100) cc_final: 0.7301 (m100) REVERT: E 141 MET cc_start: 0.7751 (mtp) cc_final: 0.7505 (ttm) REVERT: E 185 SER cc_start: 0.8164 (m) cc_final: 0.7948 (m) REVERT: E 191 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7760 (ttm) outliers start: 32 outliers final: 20 residues processed: 209 average time/residue: 0.6036 time to fit residues: 141.8359 Evaluate side-chains 209 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 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 34 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 chunk 53 optimal weight: 20.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8930 Z= 0.194 Angle : 0.492 6.848 12195 Z= 0.260 Chirality : 0.037 0.126 1370 Planarity : 0.003 0.030 1450 Dihedral : 9.633 111.398 1215 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.84 % Allowed : 15.25 % 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: 2.34 (0.25), residues: 1065 helix: 1.92 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.35 (0.56), 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 138 TYR 0.014 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 227 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 193 time to evaluate : 0.835 Fit side-chains REVERT: A 34 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.6944 (t80) REVERT: B 34 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7158 (t80) REVERT: B 100 LEU cc_start: 0.8876 (tp) cc_final: 0.8555 (mt) REVERT: B 125 PHE cc_start: 0.8598 (t80) cc_final: 0.8367 (t80) REVERT: B 132 SER cc_start: 0.8388 (p) cc_final: 0.8152 (p) REVERT: B 191 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8138 (ttm) REVERT: C 80 MET cc_start: 0.6219 (mtm) cc_final: 0.5968 (mtm) REVERT: C 191 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7752 (ttm) REVERT: C 192 TYR cc_start: 0.7592 (m-80) cc_final: 0.7345 (m-80) REVERT: E 35 TRP cc_start: 0.7610 (m100) cc_final: 0.7339 (m100) REVERT: E 141 MET cc_start: 0.7719 (mtp) cc_final: 0.7439 (ttm) REVERT: E 191 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7613 (ttm) outliers start: 34 outliers final: 21 residues processed: 212 average time/residue: 0.6020 time to fit residues: 143.5019 Evaluate side-chains 209 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 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 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 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 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 92 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 97 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 63 optimal weight: 50.0000 chunk 61 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8930 Z= 0.234 Angle : 0.529 7.631 12195 Z= 0.276 Chirality : 0.038 0.121 1370 Planarity : 0.004 0.030 1450 Dihedral : 9.546 110.012 1215 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.28 % Allowed : 15.71 % 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: 2.19 (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 0.009 0.001 TRP E 84 HIS 0.003 0.002 HIS D 76 PHE 0.019 0.002 PHE D 125 TYR 0.016 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 fitting. rotamer outliers: 29 poor density : 187 time to evaluate : 0.827 Fit side-chains REVERT: A 34 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.6922 (t80) REVERT: B 34 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7131 (t80) REVERT: B 100 LEU cc_start: 0.8911 (tp) cc_final: 0.8601 (mt) REVERT: B 125 PHE cc_start: 0.8631 (t80) cc_final: 0.8384 (t80) REVERT: B 132 SER cc_start: 0.8318 (p) cc_final: 0.8061 (p) REVERT: B 191 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8151 (ttm) REVERT: C 80 MET cc_start: 0.6226 (mtm) cc_final: 0.5984 (mtm) REVERT: C 191 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7758 (ttm) REVERT: C 192 TYR cc_start: 0.7623 (m-80) cc_final: 0.7358 (m-80) REVERT: D 222 LEU cc_start: 0.8750 (tp) cc_final: 0.8523 (tp) REVERT: E 35 TRP cc_start: 0.7685 (m100) cc_final: 0.7406 (m100) REVERT: E 141 MET cc_start: 0.7800 (mtp) cc_final: 0.7515 (ttm) REVERT: E 185 SER cc_start: 0.8116 (m) cc_final: 0.7889 (m) REVERT: E 191 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7697 (ttm) outliers start: 29 outliers final: 20 residues processed: 203 average time/residue: 0.6241 time to fit residues: 141.9397 Evaluate side-chains 206 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 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 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 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 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 158 LEU 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 40 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8930 Z= 0.241 Angle : 0.539 9.405 12195 Z= 0.281 Chirality : 0.038 0.120 1370 Planarity : 0.004 0.030 1450 Dihedral : 9.396 110.181 1215 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.50 % Allowed : 16.05 % 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: 2.18 (0.25), residues: 1065 helix: 1.80 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.35 (0.57), 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 0.013 0.002 PHE B 138 TYR 0.017 0.001 TYR A 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 224 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 193 time to evaluate : 0.885 Fit side-chains REVERT: A 34 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.6879 (t80) REVERT: B 34 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7142 (t80) REVERT: B 100 LEU cc_start: 0.8897 (tp) cc_final: 0.8594 (mt) REVERT: B 125 PHE cc_start: 0.8628 (t80) cc_final: 0.8411 (t80) REVERT: B 132 SER cc_start: 0.8372 (p) cc_final: 0.8116 (p) REVERT: B 191 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8151 (ttm) REVERT: C 80 MET cc_start: 0.6223 (mtm) cc_final: 0.5988 (mtm) REVERT: C 191 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7826 (ttm) REVERT: C 192 TYR cc_start: 0.7625 (m-80) cc_final: 0.7393 (m-80) REVERT: E 35 TRP cc_start: 0.7691 (m100) cc_final: 0.7399 (m100) REVERT: E 141 MET cc_start: 0.7805 (mtp) cc_final: 0.7522 (ttm) REVERT: E 185 SER cc_start: 0.8119 (m) cc_final: 0.7892 (m) REVERT: E 191 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7813 (ttm) outliers start: 31 outliers final: 22 residues processed: 209 average time/residue: 0.6352 time to fit residues: 149.0051 Evaluate side-chains 210 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 183 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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 177 ASN Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 158 LEU 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 88 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 0.0670 chunk 61 optimal weight: 0.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8930 Z= 0.195 Angle : 0.515 10.710 12195 Z= 0.268 Chirality : 0.037 0.132 1370 Planarity : 0.004 0.031 1450 Dihedral : 9.081 109.739 1215 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.05 % Allowed : 16.50 % 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: 2.36 (0.25), residues: 1065 helix: 1.92 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.24 (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 0.020 0.002 PHE D 125 TYR 0.015 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 217 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 190 time to evaluate : 0.941 Fit side-chains REVERT: A 34 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.6804 (t80) REVERT: A 147 MET cc_start: 0.6620 (ttm) cc_final: 0.6383 (ttm) REVERT: B 34 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7159 (t80) REVERT: B 100 LEU cc_start: 0.8885 (tp) cc_final: 0.8578 (mt) REVERT: B 125 PHE cc_start: 0.8614 (t80) cc_final: 0.8379 (t80) REVERT: B 132 SER cc_start: 0.8357 (p) cc_final: 0.8113 (p) REVERT: B 191 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8129 (ttm) REVERT: C 80 MET cc_start: 0.6220 (mtm) cc_final: 0.5981 (mtm) REVERT: C 191 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7762 (ttm) REVERT: C 192 TYR cc_start: 0.7609 (m-80) cc_final: 0.7389 (m-80) REVERT: E 35 TRP cc_start: 0.7649 (m100) cc_final: 0.7362 (m100) REVERT: E 141 MET cc_start: 0.7768 (mtp) cc_final: 0.7473 (ttm) REVERT: E 185 SER cc_start: 0.8126 (m) cc_final: 0.7902 (m) REVERT: E 191 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7710 (ttm) outliers start: 27 outliers final: 20 residues processed: 205 average time/residue: 0.5726 time to fit residues: 131.7698 Evaluate side-chains 210 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 185 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 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 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 177 ASN Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 158 LEU 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 99 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8930 Z= 0.213 Angle : 0.523 9.929 12195 Z= 0.275 Chirality : 0.038 0.122 1370 Planarity : 0.004 0.031 1450 Dihedral : 8.526 108.870 1215 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.94 % Allowed : 16.84 % Favored : 80.23 % 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: 2.31 (0.25), residues: 1065 helix: 1.89 (0.16), residues: 945 sheet: None (None), residues: 0 loop : -1.27 (0.58), 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 138 TYR 0.016 0.001 TYR A 187 ARG 0.003 0.001 ARG A 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 213 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 0.661 Fit side-chains REVERT: A 34 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.6904 (t80) REVERT: B 34 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7133 (t80) REVERT: B 100 LEU cc_start: 0.8892 (tp) cc_final: 0.8590 (mt) REVERT: B 125 PHE cc_start: 0.8632 (t80) cc_final: 0.8395 (t80) REVERT: B 132 SER cc_start: 0.8307 (p) cc_final: 0.8064 (p) REVERT: B 191 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8155 (ttm) REVERT: C 80 MET cc_start: 0.6220 (mtm) cc_final: 0.5973 (mtm) REVERT: C 191 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7769 (ttm) REVERT: C 192 TYR cc_start: 0.7608 (m-80) cc_final: 0.7384 (m-80) REVERT: E 35 TRP cc_start: 0.7661 (m100) cc_final: 0.7372 (m100) REVERT: E 141 MET cc_start: 0.7823 (mtp) cc_final: 0.7528 (ttm) REVERT: E 185 SER cc_start: 0.8144 (m) cc_final: 0.7919 (m) REVERT: E 191 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7622 (ttm) outliers start: 26 outliers final: 22 residues processed: 201 average time/residue: 0.6243 time to fit residues: 141.0285 Evaluate side-chains 211 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 184 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 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 177 ASN Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 135 MET Chi-restraints excluded: chain E residue 158 LEU 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 88 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.162282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.137296 restraints weight = 9215.144| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.36 r_work: 0.3288 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8930 Z= 0.195 Angle : 0.512 9.997 12195 Z= 0.269 Chirality : 0.037 0.122 1370 Planarity : 0.004 0.031 1450 Dihedral : 8.473 108.372 1215 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.62 % Allowed : 16.27 % Favored : 80.11 % 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: 2.39 (0.25), residues: 1065 helix: 1.93 (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 0.010 0.001 TRP D 75 HIS 0.003 0.002 HIS D 76 PHE 0.022 0.002 PHE D 125 TYR 0.015 0.001 TYR A 187 ARG 0.003 0.001 ARG A 52 =============================================================================== Job complete usr+sys time: 2576.70 seconds wall clock time: 51 minutes 0.33 seconds (3060.33 seconds total)