Starting phenix.real_space_refine on Fri Dec 8 22:57:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4l_31715/12_2023/7v4l_31715.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4l_31715/12_2023/7v4l_31715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4l_31715/12_2023/7v4l_31715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4l_31715/12_2023/7v4l_31715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4l_31715/12_2023/7v4l_31715.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4l_31715/12_2023/7v4l_31715.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.017 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 5980 2.51 5 N 1530 2.21 5 O 1780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 80": "OD1" <-> "OD2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "D ASP 339": "OD1" <-> "OD2" Residue "E PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "E TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 258": "NH1" <-> "NH2" Residue "E ASP 339": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9345 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 16, 'TRANS': 221} Chain breaks: 6 Chain: "B" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 16, 'TRANS': 221} Chain breaks: 6 Chain: "C" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 16, 'TRANS': 221} Chain breaks: 6 Chain: "D" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 16, 'TRANS': 221} Chain breaks: 6 Chain: "E" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 16, 'TRANS': 221} Chain breaks: 6 Time building chain proxies: 5.21, per 1000 atoms: 0.56 Number of scatterers: 9345 At special positions: 0 Unit cell: (117.665, 120.19, 61.61, 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 1780 8.00 N 1530 7.00 C 5980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.6 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 19 sheets defined 23.9% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 169 through 183 removed outlier: 3.706A pdb=" N GLY A 183 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 215 through 228 removed outlier: 4.460A pdb=" N LEU A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 350 removed outlier: 3.913A pdb=" N ALA A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 168 through 183 removed outlier: 3.516A pdb=" N GLY B 183 " --> pdb=" O CYS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 removed outlier: 3.559A pdb=" N ASP B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 228 removed outlier: 3.976A pdb=" N LEU B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.588A pdb=" N VAL C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 183 " --> pdb=" O CYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 228 removed outlier: 3.559A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY C 211 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG C 223 " --> pdb=" O TYR C 219 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 350 removed outlier: 3.712A pdb=" N THR C 350 " --> pdb=" O MET C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.710A pdb=" N VAL D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY D 183 " --> pdb=" O CYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 4.180A pdb=" N GLY D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG D 223 " --> pdb=" O TYR D 219 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 228 " --> pdb=" O ILE D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 350 removed outlier: 3.718A pdb=" N THR D 350 " --> pdb=" O MET D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 168 through 183 removed outlier: 3.636A pdb=" N VAL E 172 " --> pdb=" O GLY E 168 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY E 183 " --> pdb=" O CYS E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 228 removed outlier: 4.180A pdb=" N GLY E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU E 222 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG E 223 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA E 228 " --> pdb=" O ILE E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 350 removed outlier: 3.526A pdb=" N THR E 350 " --> pdb=" O MET E 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36 removed outlier: 3.803A pdb=" N ALA A 76 " --> pdb=" O MET A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 126 removed outlier: 4.071A pdb=" N SER A 205 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.860A pdb=" N GLN A 130 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 136 Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.605A pdb=" N ALA B 76 " --> pdb=" O MET B 91 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU B 22 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG B 38 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP B 32 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N SER B 35 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY E 191 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY E 188 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN E 130 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR E 126 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER E 205 " --> pdb=" O TYR E 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.605A pdb=" N ALA B 76 " --> pdb=" O MET B 91 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU B 22 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG B 38 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP B 32 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N SER B 35 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY E 191 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY E 188 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN E 130 " --> pdb=" O PHE E 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 201 removed outlier: 3.534A pdb=" N TYR B 132 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN B 130 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 133 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 33 through 40 removed outlier: 6.320A pdb=" N ILE C 20 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL C 90 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLU C 22 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB3, first strand: chain 'C' and resid 188 through 191 removed outlier: 3.695A pdb=" N GLY C 188 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 132 " --> pdb=" O TRP C 198 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 130 " --> pdb=" O PHE C 200 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 188 through 191 removed outlier: 3.695A pdb=" N GLY C 188 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 132 " --> pdb=" O TRP C 198 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 130 " --> pdb=" O PHE C 200 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 33 through 40 removed outlier: 6.190A pdb=" N ILE D 20 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL D 90 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLU D 22 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB7, first strand: chain 'D' and resid 188 through 191 removed outlier: 3.725A pdb=" N TYR D 132 " --> pdb=" O TRP D 198 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR D 126 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 188 through 191 removed outlier: 3.725A pdb=" N TYR D 132 " --> pdb=" O TRP D 198 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR D 126 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 34 through 39 removed outlier: 6.085A pdb=" N ILE E 20 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL E 90 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLU E 22 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N CYS E 92 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE E 24 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA E 94 " --> pdb=" O ILE E 24 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASP E 93 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR E 95 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU E 72 " --> pdb=" O TYR E 95 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 133 through 136 323 hydrogen bonds defined for protein. 903 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: 2.43 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1677 1.33 - 1.45: 2459 1.45 - 1.57: 5334 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 9560 Sorted by residual: bond pdb=" C ASP C 339 " pdb=" N PRO C 340 " ideal model delta sigma weight residual 1.336 1.376 -0.040 1.08e-02 8.57e+03 1.36e+01 bond pdb=" C ASP E 339 " pdb=" N PRO E 340 " ideal model delta sigma weight residual 1.336 1.374 -0.039 1.08e-02 8.57e+03 1.27e+01 bond pdb=" CA ASP C 339 " pdb=" C ASP C 339 " ideal model delta sigma weight residual 1.522 1.564 -0.043 1.22e-02 6.72e+03 1.23e+01 bond pdb=" CA ASP B 339 " pdb=" C ASP B 339 " ideal model delta sigma weight residual 1.521 1.558 -0.037 1.32e-02 5.74e+03 8.06e+00 bond pdb=" C ASP B 339 " pdb=" O ASP B 339 " ideal model delta sigma weight residual 1.246 1.221 0.025 9.20e-03 1.18e+04 7.67e+00 ... (remaining 9555 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.31: 359 106.31 - 113.29: 5037 113.29 - 120.27: 3459 120.27 - 127.26: 3977 127.26 - 134.24: 123 Bond angle restraints: 12955 Sorted by residual: angle pdb=" N LYS E 255 " pdb=" CA LYS E 255 " pdb=" C LYS E 255 " ideal model delta sigma weight residual 112.23 103.05 9.18 1.26e+00 6.30e-01 5.31e+01 angle pdb=" N LYS D 255 " pdb=" CA LYS D 255 " pdb=" C LYS D 255 " ideal model delta sigma weight residual 112.23 104.18 8.05 1.26e+00 6.30e-01 4.08e+01 angle pdb=" N ASN B 349 " pdb=" CA ASN B 349 " pdb=" C ASN B 349 " ideal model delta sigma weight residual 110.55 102.31 8.24 1.35e+00 5.49e-01 3.73e+01 angle pdb=" N ALA B 348 " pdb=" CA ALA B 348 " pdb=" C ALA B 348 " ideal model delta sigma weight residual 113.28 106.87 6.41 1.22e+00 6.72e-01 2.76e+01 angle pdb=" N ILE A 352 " pdb=" CA ILE A 352 " pdb=" C ILE A 352 " ideal model delta sigma weight residual 109.37 116.17 -6.80 1.35e+00 5.49e-01 2.54e+01 ... (remaining 12950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 4994 16.73 - 33.47: 544 33.47 - 50.20: 120 50.20 - 66.94: 37 66.94 - 83.67: 5 Dihedral angle restraints: 5700 sinusoidal: 2275 harmonic: 3425 Sorted by residual: dihedral pdb=" C ILE A 352 " pdb=" N ILE A 352 " pdb=" CA ILE A 352 " pdb=" CB ILE A 352 " ideal model delta harmonic sigma weight residual -122.00 -133.91 11.91 0 2.50e+00 1.60e-01 2.27e+01 dihedral pdb=" CA ARG A 38 " pdb=" C ARG A 38 " pdb=" N THR A 39 " pdb=" CA THR A 39 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" N ILE A 352 " pdb=" C ILE A 352 " pdb=" CA ILE A 352 " pdb=" CB ILE A 352 " ideal model delta harmonic sigma weight residual 123.40 132.55 -9.15 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 5697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1162 0.068 - 0.136: 208 0.136 - 0.204: 34 0.204 - 0.272: 4 0.272 - 0.340: 2 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CA THR C 351 " pdb=" N THR C 351 " pdb=" C THR C 351 " pdb=" CB THR C 351 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA ILE A 352 " pdb=" N ILE A 352 " pdb=" C ILE A 352 " pdb=" CB ILE A 352 " both_signs ideal model delta sigma weight residual False 2.43 2.10 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA ARG B 258 " pdb=" N ARG B 258 " pdb=" C ARG B 258 " pdb=" CB ARG B 258 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1407 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 339 " 0.074 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO A 340 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 340 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 340 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 102 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO A 103 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 194 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO A 195 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 195 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 195 " 0.032 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 197 2.66 - 3.22: 9031 3.22 - 3.78: 14294 3.78 - 4.34: 18893 4.34 - 4.90: 31070 Nonbonded interactions: 73485 Sorted by model distance: nonbonded pdb=" NH1 ARG B 169 " pdb=" OD1 ASP B 173 " model vdw 2.102 2.520 nonbonded pdb=" NH1 ARG C 169 " pdb=" OD1 ASP C 173 " model vdw 2.104 2.520 nonbonded pdb=" OE2 GLU D 22 " pdb=" OG SER D 35 " model vdw 2.148 2.440 nonbonded pdb=" OE2 GLU B 22 " pdb=" OG SER B 35 " model vdw 2.154 2.440 nonbonded pdb=" OE2 GLU C 22 " pdb=" OG SER C 35 " model vdw 2.180 2.440 ... (remaining 73480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 7.620 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: 27.280 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 26.110 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5318 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 0.049 9560 Z= 0.295 Angle : 0.817 9.185 12955 Z= 0.475 Chirality : 0.056 0.340 1410 Planarity : 0.007 0.114 1640 Dihedral : 15.200 83.670 3500 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.84 % Favored : 90.62 % Rotamer: Outliers : 3.71 % Allowed : 1.56 % Favored : 94.73 % Cbeta Deviations : 0.09 % 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: -2.60 (0.25), residues: 1120 helix: -0.22 (0.32), residues: 253 sheet: -2.45 (0.25), residues: 359 loop : -1.82 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 53 HIS 0.004 0.001 HIS C 175 PHE 0.014 0.002 PHE C 200 TYR 0.021 0.002 TYR A 132 ARG 0.009 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 167 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 5 residues processed: 196 average time/residue: 0.1996 time to fit residues: 55.4207 Evaluate side-chains 153 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0925 time to fit residues: 2.3547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 chunk 90 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 ASN D 190 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5389 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9560 Z= 0.286 Angle : 0.726 7.904 12955 Z= 0.381 Chirality : 0.050 0.174 1410 Planarity : 0.006 0.062 1640 Dihedral : 5.037 22.437 1270 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.48 % Favored : 91.43 % Rotamer: Outliers : 1.85 % Allowed : 12.68 % Favored : 85.46 % 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: -2.69 (0.24), residues: 1120 helix: -0.10 (0.32), residues: 268 sheet: -2.51 (0.24), residues: 367 loop : -2.03 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 53 HIS 0.005 0.002 HIS C 175 PHE 0.020 0.002 PHE D 200 TYR 0.026 0.002 TYR D 73 ARG 0.008 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 1.413 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 17 residues processed: 169 average time/residue: 0.1768 time to fit residues: 44.7308 Evaluate side-chains 159 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0976 time to fit residues: 4.5136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 104 optimal weight: 0.0070 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5376 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9560 Z= 0.243 Angle : 0.652 8.416 12955 Z= 0.342 Chirality : 0.048 0.186 1410 Planarity : 0.006 0.060 1640 Dihedral : 4.737 20.756 1270 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.86 % Favored : 92.05 % Rotamer: Outliers : 1.56 % Allowed : 15.02 % Favored : 83.41 % 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: -2.66 (0.24), residues: 1120 helix: 0.07 (0.32), residues: 264 sheet: -2.57 (0.24), residues: 377 loop : -1.98 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 53 HIS 0.004 0.001 HIS C 175 PHE 0.017 0.002 PHE A 200 TYR 0.019 0.002 TYR B 55 ARG 0.003 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 166 average time/residue: 0.1754 time to fit residues: 43.6171 Evaluate side-chains 154 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1275 time to fit residues: 3.2652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5381 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9560 Z= 0.227 Angle : 0.635 8.514 12955 Z= 0.330 Chirality : 0.047 0.187 1410 Planarity : 0.006 0.059 1640 Dihedral : 4.666 26.285 1270 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.86 % Favored : 92.05 % Rotamer: Outliers : 2.44 % Allowed : 15.90 % Favored : 81.66 % 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: -2.62 (0.24), residues: 1120 helix: 0.05 (0.31), residues: 264 sheet: -2.54 (0.24), residues: 370 loop : -1.95 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 53 HIS 0.004 0.001 HIS C 175 PHE 0.017 0.002 PHE A 200 TYR 0.019 0.002 TYR E 126 ARG 0.004 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 152 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 167 average time/residue: 0.1682 time to fit residues: 42.3507 Evaluate side-chains 161 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 1.062 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1083 time to fit residues: 3.8483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN D 9 ASN D 190 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5444 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9560 Z= 0.271 Angle : 0.695 11.702 12955 Z= 0.359 Chirality : 0.050 0.187 1410 Planarity : 0.006 0.058 1640 Dihedral : 4.841 18.555 1270 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.02 % Favored : 90.89 % Rotamer: Outliers : 2.15 % Allowed : 17.76 % Favored : 80.10 % 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: -2.78 (0.24), residues: 1120 helix: -0.17 (0.32), residues: 263 sheet: -2.60 (0.24), residues: 370 loop : -2.02 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 53 HIS 0.005 0.001 HIS C 175 PHE 0.017 0.002 PHE C 200 TYR 0.019 0.002 TYR A 132 ARG 0.004 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.034 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 176 average time/residue: 0.1832 time to fit residues: 47.6601 Evaluate side-chains 161 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0925 time to fit residues: 2.6236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.9980 chunk 21 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 58 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN C 9 ASN D 9 ASN D 190 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5360 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9560 Z= 0.206 Angle : 0.663 10.466 12955 Z= 0.336 Chirality : 0.047 0.185 1410 Planarity : 0.006 0.058 1640 Dihedral : 4.503 17.312 1270 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.34 % Favored : 93.57 % Rotamer: Outliers : 2.44 % Allowed : 18.83 % Favored : 78.73 % 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: -2.55 (0.24), residues: 1120 helix: 0.02 (0.31), residues: 263 sheet: -2.46 (0.24), residues: 369 loop : -1.89 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 53 HIS 0.004 0.001 HIS D 175 PHE 0.016 0.001 PHE D 200 TYR 0.017 0.002 TYR E 55 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 173 average time/residue: 0.1886 time to fit residues: 48.3199 Evaluate side-chains 168 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0921 time to fit residues: 3.7802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 0.0770 chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 67 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5368 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9560 Z= 0.217 Angle : 0.664 9.418 12955 Z= 0.339 Chirality : 0.047 0.194 1410 Planarity : 0.006 0.060 1640 Dihedral : 4.471 16.319 1270 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.86 % Favored : 92.05 % Rotamer: Outliers : 1.27 % Allowed : 19.71 % Favored : 79.02 % 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: -2.52 (0.24), residues: 1120 helix: 0.05 (0.31), residues: 264 sheet: -2.39 (0.24), residues: 369 loop : -1.91 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 53 HIS 0.004 0.001 HIS C 175 PHE 0.015 0.001 PHE D 200 TYR 0.019 0.002 TYR D 55 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 1.056 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 161 average time/residue: 0.1843 time to fit residues: 44.6162 Evaluate side-chains 157 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 151 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1719 time to fit residues: 2.8968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 0.2980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN E 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5508 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9560 Z= 0.338 Angle : 0.773 11.287 12955 Z= 0.396 Chirality : 0.051 0.206 1410 Planarity : 0.007 0.061 1640 Dihedral : 5.125 18.120 1270 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.91 % Favored : 90.00 % Rotamer: Outliers : 1.95 % Allowed : 21.17 % Favored : 76.88 % 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: -2.94 (0.24), residues: 1120 helix: -0.48 (0.31), residues: 267 sheet: -2.58 (0.24), residues: 369 loop : -2.13 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 53 HIS 0.006 0.002 HIS C 175 PHE 0.016 0.002 PHE A 200 TYR 0.025 0.003 TYR E 126 ARG 0.005 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 1.050 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 162 average time/residue: 0.1857 time to fit residues: 44.2205 Evaluate side-chains 156 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 1.081 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0958 time to fit residues: 3.2350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5459 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9560 Z= 0.275 Angle : 0.728 10.239 12955 Z= 0.375 Chirality : 0.049 0.202 1410 Planarity : 0.006 0.061 1640 Dihedral : 4.935 17.456 1270 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.39 % Favored : 91.52 % Rotamer: Outliers : 0.88 % Allowed : 22.24 % Favored : 76.88 % 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: -2.87 (0.24), residues: 1120 helix: -0.47 (0.31), residues: 266 sheet: -2.43 (0.25), residues: 360 loop : -2.18 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 53 HIS 0.005 0.001 HIS C 175 PHE 0.015 0.002 PHE E 200 TYR 0.020 0.002 TYR D 55 ARG 0.004 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 1.081 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 154 average time/residue: 0.1965 time to fit residues: 44.9884 Evaluate side-chains 156 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1120 time to fit residues: 3.2420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 91 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5374 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9560 Z= 0.218 Angle : 0.693 12.022 12955 Z= 0.350 Chirality : 0.047 0.199 1410 Planarity : 0.006 0.064 1640 Dihedral : 4.586 16.594 1270 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.88 % Favored : 93.04 % Rotamer: Outliers : 0.20 % Allowed : 23.12 % Favored : 76.68 % 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: -2.65 (0.24), residues: 1120 helix: -0.25 (0.31), residues: 265 sheet: -2.31 (0.25), residues: 360 loop : -2.05 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 53 HIS 0.004 0.001 HIS C 175 PHE 0.014 0.001 PHE D 200 TYR 0.019 0.002 TYR D 55 ARG 0.004 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 1.032 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 149 average time/residue: 0.1809 time to fit residues: 40.1028 Evaluate side-chains 144 residues out of total 1025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0814 time to fit residues: 1.7152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5033 r_free = 0.5033 target = 0.213951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.155740 restraints weight = 9365.053| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 3.42 r_work: 0.4149 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9560 Z= 0.210 Angle : 0.676 10.777 12955 Z= 0.343 Chirality : 0.047 0.192 1410 Planarity : 0.006 0.065 1640 Dihedral : 4.455 15.529 1270 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.70 % Favored : 93.21 % Rotamer: Outliers : 0.29 % Allowed : 23.32 % Favored : 76.39 % 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: -2.54 (0.24), residues: 1120 helix: -0.14 (0.30), residues: 267 sheet: -2.25 (0.25), residues: 360 loop : -2.00 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 53 HIS 0.004 0.001 HIS C 175 PHE 0.014 0.001 PHE D 200 TYR 0.019 0.002 TYR B 55 ARG 0.005 0.000 ARG A 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2805.65 seconds wall clock time: 51 minutes 36.85 seconds (3096.85 seconds total)