Starting phenix.real_space_refine on Fri Dec 8 08:58:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0s_23102/12_2023/7l0s_23102.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0s_23102/12_2023/7l0s_23102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0s_23102/12_2023/7l0s_23102.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0s_23102/12_2023/7l0s_23102.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0s_23102/12_2023/7l0s_23102.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0s_23102/12_2023/7l0s_23102.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 57 5.16 5 C 5034 2.51 5 N 1343 2.21 5 O 1472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 8": "NH1" <-> "NH2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G GLU 45": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7906 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2424 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 297} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "A" Number of atoms: 2729 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2694 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 4, 'TRANS': 332} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 337, 2694 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 4, 'TRANS': 332} Chain breaks: 3 bond proxies already assigned to first conformer: 2697 Chain: "B" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2385 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 305} Chain: "G" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 310 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AASP A 97 " occ=0.56 ... (14 atoms not shown) pdb=" OD2BASP A 97 " occ=0.44 residue: pdb=" N AARG A 105 " occ=0.68 ... (20 atoms not shown) pdb=" NH2BARG A 105 " occ=0.32 residue: pdb=" N AASP A 158 " occ=0.51 ... (14 atoms not shown) pdb=" OD2BASP A 158 " occ=0.49 residue: pdb=" N AASP A 160 " occ=0.44 ... (14 atoms not shown) pdb=" OD2BASP A 160 " occ=0.56 Time building chain proxies: 5.69, per 1000 atoms: 0.72 Number of scatterers: 7906 At special positions: 0 Unit cell: (88.275, 117.15, 121.275, 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 57 16.00 O 1472 8.00 N 1343 7.00 C 5034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 225 " distance=2.03 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: 3.09 Conformation dependent library (CDL) restraints added in 1.8 seconds 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 48.2% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'C' and resid 60 through 91 Processing helix chain 'C' and resid 100 through 129 Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 137 through 173 Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 182 through 202 Processing helix chain 'C' and resid 202 through 207 removed outlier: 3.519A pdb=" N THR C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 270 Proline residue: C 249 - end of helix Processing helix chain 'C' and resid 300 through 334 Proline residue: C 323 - end of helix removed outlier: 3.533A pdb=" N ILE C 334 " --> pdb=" O MET C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 371 Proline residue: C 366 - end of helix Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.507A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 65 through 68 Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.598A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.851A pdb=" N ASP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 133 Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.541A pdb=" N AASP A 158 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.781A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.404A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'G' and resid 32 through 48 Processing sheet with id=AA1, first strand: chain 'C' and resid 208 through 212 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 6.527A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.895A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.837A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.974A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.399A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.062A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.903A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1234 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: 2.39 Time building geometry restraints manager: 3.35 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: 1635 1.33 - 1.45: 1967 1.45 - 1.57: 4376 1.57 - 1.69: 2 1.69 - 1.82: 83 Bond restraints: 8063 Sorted by residual: bond pdb=" C HIS C 133 " pdb=" N PRO C 134 " ideal model delta sigma weight residual 1.331 1.385 -0.054 1.28e-02 6.10e+03 1.76e+01 bond pdb=" N LEU B 95 " pdb=" CA LEU B 95 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.73e+00 bond pdb=" CA ILE A 81 " pdb=" CB ILE A 81 " ideal model delta sigma weight residual 1.540 1.572 -0.032 1.29e-02 6.01e+03 6.26e+00 bond pdb=" N ASP A 309 " pdb=" CA ASP A 309 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.23e+00 bond pdb=" N LEU C 256 " pdb=" CA LEU C 256 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 6.21e+00 ... (remaining 8058 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.07: 145 106.07 - 113.10: 4219 113.10 - 120.13: 3237 120.13 - 127.16: 3236 127.16 - 134.19: 89 Bond angle restraints: 10926 Sorted by residual: angle pdb=" N PHE C 376 " pdb=" CA PHE C 376 " pdb=" C PHE C 376 " ideal model delta sigma weight residual 112.54 105.52 7.02 1.22e+00 6.72e-01 3.31e+01 angle pdb=" N VAL C 131 " pdb=" CA VAL C 131 " pdb=" C VAL C 131 " ideal model delta sigma weight residual 107.51 99.04 8.47 1.49e+00 4.50e-01 3.23e+01 angle pdb=" N LYS A 46 " pdb=" CA LYS A 46 " pdb=" C LYS A 46 " ideal model delta sigma weight residual 111.28 105.15 6.13 1.09e+00 8.42e-01 3.16e+01 angle pdb=" N GLY B 141 " pdb=" CA GLY B 141 " pdb=" C GLY B 141 " ideal model delta sigma weight residual 113.18 101.68 11.50 2.37e+00 1.78e-01 2.35e+01 angle pdb=" C SER B 227 " pdb=" N ASP B 228 " pdb=" CA ASP B 228 " ideal model delta sigma weight residual 120.82 127.94 -7.12 1.47e+00 4.63e-01 2.35e+01 ... (remaining 10921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 4300 15.98 - 31.97: 369 31.97 - 47.95: 86 47.95 - 63.93: 30 63.93 - 79.91: 4 Dihedral angle restraints: 4789 sinusoidal: 1862 harmonic: 2927 Sorted by residual: dihedral pdb=" CB CYS C 142 " pdb=" SG CYS C 142 " pdb=" SG CYS C 225 " pdb=" CB CYS C 225 " ideal model delta sinusoidal sigma weight residual -86.00 -165.91 79.91 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CA PHE G 64 " pdb=" C PHE G 64 " pdb=" N LYS G 65 " pdb=" CA LYS G 65 " ideal model delta harmonic sigma weight residual 180.00 153.93 26.07 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 4786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 932 0.082 - 0.164: 261 0.164 - 0.246: 45 0.246 - 0.328: 13 0.328 - 0.410: 1 Chirality restraints: 1252 Sorted by residual: chirality pdb=" CA HIS C 133 " pdb=" N HIS C 133 " pdb=" C HIS C 133 " pdb=" CB HIS C 133 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB VAL C 266 " pdb=" CA VAL C 266 " pdb=" CG1 VAL C 266 " pdb=" CG2 VAL C 266 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 1249 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 374 " 0.027 2.00e-02 2.50e+03 5.29e-02 2.80e+01 pdb=" C ALA C 374 " -0.091 2.00e-02 2.50e+03 pdb=" O ALA C 374 " 0.034 2.00e-02 2.50e+03 pdb=" N ASN C 375 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 49 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ARG B 49 " 0.059 2.00e-02 2.50e+03 pdb=" O ARG B 49 " -0.022 2.00e-02 2.50e+03 pdb=" N THR B 50 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 191 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C SER B 191 " 0.055 2.00e-02 2.50e+03 pdb=" O SER B 191 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 192 " -0.019 2.00e-02 2.50e+03 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 221 2.67 - 3.22: 7554 3.22 - 3.78: 13158 3.78 - 4.34: 16982 4.34 - 4.90: 27714 Nonbonded interactions: 65629 Sorted by model distance: nonbonded pdb=" OH TYR C 146 " pdb=" OXT LEU D 13 " model vdw 2.107 2.440 nonbonded pdb=" NZ LYS A 128 " pdb=" OD1AASP A 160 " model vdw 2.197 2.520 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.233 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.279 2.440 nonbonded pdb=" N GLU A 43 " pdb=" OE1 GLU A 43 " model vdw 2.286 2.520 ... (remaining 65624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.32 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.070 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 26.550 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 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 : 0.008 0.081 8063 Z= 0.524 Angle : 1.345 11.500 10926 Z= 0.786 Chirality : 0.079 0.410 1252 Planarity : 0.008 0.061 1384 Dihedral : 13.518 70.452 2896 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.39 % Allowed : 10.80 % Favored : 87.80 % Cbeta Deviations : 0.21 % 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: -3.19 (0.22), residues: 992 helix: -1.81 (0.19), residues: 461 sheet: -2.25 (0.36), residues: 173 loop : -2.15 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP B 297 HIS 0.008 0.003 HIS B 54 PHE 0.038 0.004 PHE C 376 TYR 0.029 0.004 TYR C 349 ARG 0.013 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 316 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 322 average time/residue: 0.2352 time to fit residues: 97.2922 Evaluate side-chains 209 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 206 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0809 time to fit residues: 1.6903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 25 optimal weight: 0.0570 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN C 159 ASN C 219 HIS C 262 ASN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 GLN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN B 75 GLN B 88 ASN B 142 HIS B 230 ASN B 259 GLN B 295 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8063 Z= 0.188 Angle : 0.680 8.625 10926 Z= 0.362 Chirality : 0.044 0.160 1252 Planarity : 0.005 0.042 1384 Dihedral : 5.079 31.539 1092 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.46 % Allowed : 2.90 % Favored : 96.63 % 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: -1.55 (0.25), residues: 992 helix: -0.11 (0.22), residues: 458 sheet: -1.62 (0.35), residues: 183 loop : -1.76 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 339 HIS 0.007 0.001 HIS B 266 PHE 0.023 0.002 PHE C 344 TYR 0.011 0.001 TYR G 43 ARG 0.005 0.001 ARG G 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 260 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 261 average time/residue: 0.1974 time to fit residues: 69.4589 Evaluate side-chains 189 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1022 time to fit residues: 1.2992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 HIS C 257 ASN ** C 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8063 Z= 0.251 Angle : 0.676 7.907 10926 Z= 0.362 Chirality : 0.043 0.140 1252 Planarity : 0.004 0.043 1384 Dihedral : 4.896 24.608 1092 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.26), residues: 992 helix: 0.47 (0.23), residues: 458 sheet: -1.29 (0.35), residues: 180 loop : -1.34 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 339 HIS 0.006 0.001 HIS A 195 PHE 0.022 0.002 PHE A 108 TYR 0.015 0.002 TYR C 154 ARG 0.006 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1977 time to fit residues: 62.1271 Evaluate side-chains 171 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.903 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 6.9990 chunk 66 optimal weight: 0.0470 chunk 45 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 292 ASN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8063 Z= 0.225 Angle : 0.654 7.510 10926 Z= 0.347 Chirality : 0.044 0.198 1252 Planarity : 0.004 0.044 1384 Dihedral : 4.788 21.406 1092 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.23 % Allowed : 3.14 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.27), residues: 992 helix: 0.84 (0.24), residues: 457 sheet: -0.91 (0.37), residues: 191 loop : -1.02 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 339 HIS 0.006 0.001 HIS A 195 PHE 0.013 0.002 PHE B 253 TYR 0.018 0.001 TYR B 59 ARG 0.003 0.000 ARG G 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 225 average time/residue: 0.1854 time to fit residues: 57.4880 Evaluate side-chains 165 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0728 time to fit residues: 1.2879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN C 257 ASN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8063 Z= 0.241 Angle : 0.667 7.946 10926 Z= 0.351 Chirality : 0.044 0.208 1252 Planarity : 0.004 0.044 1384 Dihedral : 4.770 20.233 1092 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.28), residues: 992 helix: 0.89 (0.25), residues: 461 sheet: -0.46 (0.40), residues: 177 loop : -1.11 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 339 HIS 0.006 0.001 HIS A 195 PHE 0.033 0.002 PHE A 108 TYR 0.015 0.001 TYR B 264 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1763 time to fit residues: 53.0018 Evaluate side-chains 162 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8063 Z= 0.231 Angle : 0.673 7.790 10926 Z= 0.357 Chirality : 0.045 0.262 1252 Planarity : 0.004 0.044 1384 Dihedral : 4.781 20.589 1092 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.28), residues: 992 helix: 0.88 (0.24), residues: 463 sheet: -0.37 (0.44), residues: 153 loop : -0.98 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 339 HIS 0.006 0.001 HIS A 195 PHE 0.028 0.002 PHE A 108 TYR 0.014 0.001 TYR C 333 ARG 0.002 0.000 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1737 time to fit residues: 52.6658 Evaluate side-chains 165 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN C 257 ASN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 195 HIS ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 230 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8063 Z= 0.255 Angle : 0.683 7.536 10926 Z= 0.362 Chirality : 0.045 0.245 1252 Planarity : 0.004 0.044 1384 Dihedral : 4.861 19.855 1092 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.23 % Allowed : 1.28 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.28), residues: 992 helix: 0.85 (0.24), residues: 464 sheet: -0.11 (0.43), residues: 164 loop : -1.06 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 339 HIS 0.004 0.001 HIS A 195 PHE 0.026 0.002 PHE A 108 TYR 0.022 0.001 TYR B 59 ARG 0.003 0.000 ARG G 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 206 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 208 average time/residue: 0.1750 time to fit residues: 50.8788 Evaluate side-chains 150 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0707 time to fit residues: 1.3051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.0870 chunk 28 optimal weight: 0.3980 chunk 18 optimal weight: 9.9990 chunk 59 optimal weight: 0.1980 chunk 63 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN C 241 ASN C 262 ASN A 172 GLN A 195 HIS ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8063 Z= 0.176 Angle : 0.669 8.689 10926 Z= 0.346 Chirality : 0.045 0.334 1252 Planarity : 0.004 0.047 1384 Dihedral : 4.568 19.535 1092 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.23 % Allowed : 1.86 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.28), residues: 992 helix: 1.17 (0.25), residues: 458 sheet: 0.08 (0.41), residues: 176 loop : -1.22 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP B 339 HIS 0.005 0.001 HIS A 195 PHE 0.031 0.001 PHE C 344 TYR 0.016 0.001 TYR B 289 ARG 0.010 0.000 ARG G 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 208 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 210 average time/residue: 0.1642 time to fit residues: 49.1286 Evaluate side-chains 159 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1024 time to fit residues: 1.4176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 68 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 257 ASN C 262 ASN A 195 HIS ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.6420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8063 Z= 0.268 Angle : 0.731 12.226 10926 Z= 0.383 Chirality : 0.047 0.271 1252 Planarity : 0.004 0.045 1384 Dihedral : 4.807 18.332 1092 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.12 % Allowed : 0.93 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.27), residues: 992 helix: 0.85 (0.24), residues: 463 sheet: -0.08 (0.40), residues: 178 loop : -1.24 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 339 HIS 0.008 0.001 HIS A 195 PHE 0.024 0.002 PHE A 108 TYR 0.016 0.002 TYR C 333 ARG 0.005 0.001 ARG C 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.1600 time to fit residues: 45.8799 Evaluate side-chains 153 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 0.0370 chunk 61 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 overall best weight: 2.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 GLN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8063 Z= 0.266 Angle : 0.729 10.026 10926 Z= 0.383 Chirality : 0.048 0.407 1252 Planarity : 0.004 0.045 1384 Dihedral : 4.892 23.404 1092 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.27), residues: 992 helix: 0.87 (0.24), residues: 458 sheet: -0.18 (0.40), residues: 179 loop : -1.31 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 297 HIS 0.037 0.003 HIS C 325 PHE 0.063 0.002 PHE C 246 TYR 0.014 0.002 TYR C 369 ARG 0.006 0.001 ARG C 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1984 Ramachandran restraints generated. 992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1653 time to fit residues: 46.4763 Evaluate side-chains 156 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 77 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 0.2980 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN C 239 GLN C 257 ASN A 195 HIS ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.110816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.083866 restraints weight = 85551.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.087338 restraints weight = 34015.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.090006 restraints weight = 18800.385| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.6633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8063 Z= 0.192 Angle : 0.703 12.466 10926 Z= 0.360 Chirality : 0.046 0.239 1252 Planarity : 0.004 0.047 1384 Dihedral : 4.663 21.826 1092 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.27), residues: 992 helix: 0.95 (0.24), residues: 460 sheet: -0.09 (0.40), residues: 176 loop : -1.23 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 339 HIS 0.007 0.001 HIS A 195 PHE 0.028 0.002 PHE A 108 TYR 0.014 0.001 TYR C 369 ARG 0.003 0.000 ARG C 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2033.71 seconds wall clock time: 37 minutes 56.05 seconds (2276.05 seconds total)