Starting phenix.real_space_refine on Mon Mar 11 09:39:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0s_23102/03_2024/7l0s_23102.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0s_23102/03_2024/7l0s_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_23102/03_2024/7l0s_23102.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0s_23102/03_2024/7l0s_23102.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0s_23102/03_2024/7l0s_23102.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0s_23102/03_2024/7l0s_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-dev-5265/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: 5.92, per 1000 atoms: 0.75 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: 3.06 Conformation dependent library (CDL) restraints added in 1.9 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: 0.76 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: 2.14 Time building geometry restraints manager: 3.33 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.950 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.160 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.110 ------------------------------------------------------------------------------- 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 : 0.904 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 REVERT: C 66 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7195 (pp) REVERT: C 87 PHE cc_start: 0.5700 (t80) cc_final: 0.5394 (m-10) REVERT: C 105 TYR cc_start: 0.7591 (m-80) cc_final: 0.7375 (m-80) REVERT: C 153 THR cc_start: 0.7532 (m) cc_final: 0.7254 (m) REVERT: C 169 LEU cc_start: 0.8763 (tp) cc_final: 0.8547 (tp) REVERT: C 242 THR cc_start: 0.8417 (t) cc_final: 0.8115 (t) REVERT: C 325 HIS cc_start: 0.7032 (m-70) cc_final: 0.5956 (m-70) REVERT: C 376 PHE cc_start: 0.5539 (t80) cc_final: 0.4751 (t80) REVERT: A 28 GLU cc_start: 0.8284 (tt0) cc_final: 0.7792 (tm-30) REVERT: B 79 LEU cc_start: 0.9083 (pt) cc_final: 0.8600 (pp) REVERT: B 149 CYS cc_start: 0.7744 (p) cc_final: 0.7450 (m) REVERT: B 233 CYS cc_start: 0.7340 (p) cc_final: 0.7044 (p) REVERT: B 275 SER cc_start: 0.9186 (t) cc_final: 0.8629 (m) REVERT: B 276 VAL cc_start: 0.8726 (m) cc_final: 0.8477 (m) REVERT: B 329 THR cc_start: 0.8680 (t) cc_final: 0.8475 (t) REVERT: B 337 LYS cc_start: 0.8774 (mttm) cc_final: 0.8372 (mptt) REVERT: G 32 LEU cc_start: 0.8607 (tp) cc_final: 0.8281 (tp) REVERT: G 37 CYS cc_start: 0.7880 (p) cc_final: 0.6775 (p) REVERT: G 46 GLU cc_start: 0.8395 (tt0) cc_final: 0.7607 (tm-30) outliers start: 11 outliers final: 3 residues processed: 322 average time/residue: 0.2302 time to fit residues: 95.1361 Evaluate side-chains 216 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 212 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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: 7.9990 chunk 40 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN C 132 HIS 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8063 Z= 0.271 Angle : 0.717 9.188 10926 Z= 0.386 Chirality : 0.044 0.161 1252 Planarity : 0.005 0.042 1384 Dihedral : 5.232 32.255 1092 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.35 % Allowed : 3.95 % Favored : 95.70 % 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: -1.50 (0.25), residues: 992 helix: -0.14 (0.22), residues: 459 sheet: -1.83 (0.36), residues: 176 loop : -1.49 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 339 HIS 0.006 0.001 HIS B 266 PHE 0.025 0.002 PHE A 199 TYR 0.018 0.002 TYR B 264 ARG 0.005 0.001 ARG B 137 *********************** 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 245 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 242 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 PHE cc_start: 0.6023 (t80) cc_final: 0.5475 (m-80) REVERT: C 119 LEU cc_start: 0.8288 (mt) cc_final: 0.8056 (tt) REVERT: C 166 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8321 (tm-30) REVERT: C 168 TYR cc_start: 0.7008 (t80) cc_final: 0.6085 (t80) REVERT: C 169 LEU cc_start: 0.8277 (tp) cc_final: 0.7854 (tp) REVERT: C 187 LYS cc_start: 0.8002 (mtpt) cc_final: 0.7550 (mttp) REVERT: C 190 ILE cc_start: 0.8017 (pt) cc_final: 0.7780 (pt) REVERT: C 330 MET cc_start: 0.7058 (tpp) cc_final: 0.6809 (ttp) REVERT: C 352 MET cc_start: 0.7333 (mmp) cc_final: 0.7118 (tpp) REVERT: A 196 PHE cc_start: 0.8151 (m-80) cc_final: 0.7910 (m-80) REVERT: A 209 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8658 (ttpp) REVERT: A 248 LYS cc_start: 0.8546 (ptpp) cc_final: 0.8269 (ptpp) REVERT: B 57 LYS cc_start: 0.8854 (mttt) cc_final: 0.8642 (mtmt) REVERT: B 146 LEU cc_start: 0.9073 (mp) cc_final: 0.8822 (mt) REVERT: B 190 LEU cc_start: 0.9320 (tt) cc_final: 0.8943 (tt) REVERT: B 233 CYS cc_start: 0.7906 (p) cc_final: 0.7507 (p) REVERT: B 246 ASP cc_start: 0.7992 (m-30) cc_final: 0.7720 (m-30) REVERT: B 337 LYS cc_start: 0.9003 (mttm) cc_final: 0.8614 (mptt) REVERT: G 37 CYS cc_start: 0.8092 (p) cc_final: 0.7323 (p) REVERT: G 38 GLU cc_start: 0.8673 (mp0) cc_final: 0.8321 (mm-30) outliers start: 3 outliers final: 0 residues processed: 243 average time/residue: 0.1948 time to fit residues: 63.7284 Evaluate side-chains 176 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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: 6.9990 chunk 27 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 95 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8063 Z= 0.237 Angle : 0.673 8.055 10926 Z= 0.361 Chirality : 0.044 0.256 1252 Planarity : 0.004 0.044 1384 Dihedral : 4.873 25.211 1092 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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: -0.72 (0.26), residues: 992 helix: 0.48 (0.23), residues: 465 sheet: -1.38 (0.36), residues: 191 loop : -1.09 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 339 HIS 0.005 0.001 HIS B 266 PHE 0.025 0.002 PHE A 108 TYR 0.027 0.002 TYR C 168 ARG 0.007 0.001 ARG C 149 *********************** 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 242 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.910 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: C 119 LEU cc_start: 0.8317 (mt) cc_final: 0.8105 (tt) REVERT: C 244 MET cc_start: 0.8214 (ppp) cc_final: 0.7455 (ppp) REVERT: C 330 MET cc_start: 0.7068 (tpp) cc_final: 0.6686 (ttp) REVERT: C 359 TYR cc_start: 0.6819 (m-10) cc_final: 0.6463 (m-80) REVERT: A 18 MET cc_start: 0.8770 (tmm) cc_final: 0.8376 (tmm) REVERT: A 209 LYS cc_start: 0.8995 (mtmt) cc_final: 0.8663 (ttpp) REVERT: A 248 LYS cc_start: 0.8513 (ptpp) cc_final: 0.8234 (ptpp) REVERT: A 265 ILE cc_start: 0.8734 (mt) cc_final: 0.8419 (mm) REVERT: B 57 LYS cc_start: 0.8939 (mttt) cc_final: 0.8578 (mtmt) REVERT: B 114 CYS cc_start: 0.6671 (p) cc_final: 0.6321 (m) REVERT: B 246 ASP cc_start: 0.8205 (m-30) cc_final: 0.7762 (m-30) REVERT: G 37 CYS cc_start: 0.8135 (p) cc_final: 0.7654 (p) REVERT: G 38 GLU cc_start: 0.8658 (mp0) cc_final: 0.8452 (mm-30) REVERT: G 45 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8508 (pt0) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1978 time to fit residues: 65.0793 Evaluate side-chains 177 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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: 4.9990 chunk 66 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 ASN 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8063 Z= 0.298 Angle : 0.714 7.661 10926 Z= 0.384 Chirality : 0.045 0.220 1252 Planarity : 0.004 0.045 1384 Dihedral : 5.036 22.752 1092 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.35 % Allowed : 4.53 % Favored : 95.12 % 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: -0.47 (0.27), residues: 992 helix: 0.61 (0.24), residues: 456 sheet: -0.76 (0.40), residues: 171 loop : -1.15 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 339 HIS 0.007 0.001 HIS B 91 PHE 0.018 0.002 PHE C 344 TYR 0.025 0.002 TYR B 124 ARG 0.006 0.001 ARG C 149 *********************** 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 219 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 216 time to evaluate : 0.892 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: C 121 MET cc_start: 0.8174 (tpt) cc_final: 0.7599 (tpt) REVERT: C 244 MET cc_start: 0.8222 (ppp) cc_final: 0.7567 (ppp) REVERT: C 359 TYR cc_start: 0.6827 (m-10) cc_final: 0.6553 (m-80) REVERT: D 12 ILE cc_start: 0.8084 (mp) cc_final: 0.7850 (mp) REVERT: A 18 MET cc_start: 0.8838 (tmm) cc_final: 0.8388 (tmm) REVERT: A 19 ILE cc_start: 0.9150 (tt) cc_final: 0.8760 (tt) REVERT: A 28 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8792 (mm-30) REVERT: A 209 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8626 (ttpp) REVERT: A 248 LYS cc_start: 0.8603 (ptpp) cc_final: 0.8307 (ptpp) REVERT: A 347 ASN cc_start: 0.8385 (m-40) cc_final: 0.8168 (m-40) REVERT: B 85 TYR cc_start: 0.8795 (m-80) cc_final: 0.8574 (m-80) REVERT: B 111 TYR cc_start: 0.7701 (m-80) cc_final: 0.7274 (m-80) REVERT: B 246 ASP cc_start: 0.8121 (m-30) cc_final: 0.7916 (m-30) REVERT: B 297 TRP cc_start: 0.6320 (m100) cc_final: 0.5722 (m-10) REVERT: G 31 MET cc_start: 0.3478 (ptp) cc_final: 0.3250 (ptt) REVERT: G 37 CYS cc_start: 0.8140 (p) cc_final: 0.7551 (p) REVERT: G 38 GLU cc_start: 0.8763 (mp0) cc_final: 0.8460 (mm-30) REVERT: G 45 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8617 (pt0) outliers start: 3 outliers final: 1 residues processed: 219 average time/residue: 0.1694 time to fit residues: 51.8107 Evaluate side-chains 169 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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: 0.6980 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 ASN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 GLN ** 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** B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.5462 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= 0.220 Angle : 0.664 7.341 10926 Z= 0.351 Chirality : 0.045 0.223 1252 Planarity : 0.004 0.044 1384 Dihedral : 4.823 20.157 1092 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.12 % Allowed : 3.02 % 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: -0.26 (0.27), residues: 992 helix: 0.74 (0.24), residues: 463 sheet: -0.65 (0.40), residues: 166 loop : -1.01 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 339 HIS 0.006 0.001 HIS A 195 PHE 0.036 0.002 PHE A 108 TYR 0.027 0.002 TYR B 124 ARG 0.003 0.000 ARG C 327 *********************** 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 229 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 0.948 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: C 121 MET cc_start: 0.8233 (tpt) cc_final: 0.7821 (tpt) REVERT: C 168 TYR cc_start: 0.7035 (t80) cc_final: 0.6565 (t80) REVERT: C 359 TYR cc_start: 0.6978 (m-10) cc_final: 0.6595 (m-10) REVERT: A 18 MET cc_start: 0.8802 (tmm) cc_final: 0.8338 (tmm) REVERT: A 19 ILE cc_start: 0.9133 (tt) cc_final: 0.8864 (tt) REVERT: A 28 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8787 (mm-30) REVERT: A 209 LYS cc_start: 0.8890 (mtmt) cc_final: 0.8611 (ttpp) REVERT: A 248 LYS cc_start: 0.8562 (ptpp) cc_final: 0.8190 (ptpp) REVERT: A 347 ASN cc_start: 0.8322 (m-40) cc_final: 0.8110 (m-40) REVERT: B 61 MET cc_start: 0.8041 (ppp) cc_final: 0.7796 (ppp) REVERT: B 246 ASP cc_start: 0.8301 (m-30) cc_final: 0.7828 (m-30) REVERT: G 35 LYS cc_start: 0.9121 (pttt) cc_final: 0.8761 (ptmt) REVERT: G 37 CYS cc_start: 0.7862 (p) cc_final: 0.7519 (p) REVERT: G 38 GLU cc_start: 0.8742 (mp0) cc_final: 0.8055 (mp0) REVERT: G 45 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8608 (pt0) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.1849 time to fit residues: 57.7168 Evaluate side-chains 178 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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: 0.9980 chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 0.0970 chunk 7 optimal weight: 0.0070 chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 257 ASN ** C 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN ** 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 239 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: 0.6748 moved from start: 0.5760 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= 0.194 Angle : 0.651 7.800 10926 Z= 0.340 Chirality : 0.044 0.229 1252 Planarity : 0.004 0.044 1384 Dihedral : 4.694 20.486 1092 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.35 % Allowed : 2.21 % Favored : 97.44 % 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: 0.02 (0.28), residues: 992 helix: 0.93 (0.24), residues: 457 sheet: 0.05 (0.41), residues: 173 loop : -1.12 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 339 HIS 0.006 0.001 HIS A 195 PHE 0.020 0.001 PHE B 241 TYR 0.019 0.001 TYR B 124 ARG 0.004 0.000 ARG A 208 *********************** 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 237 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 234 time to evaluate : 0.886 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: C 121 MET cc_start: 0.8029 (tpt) cc_final: 0.7728 (tpt) REVERT: C 168 TYR cc_start: 0.6920 (t80) cc_final: 0.6635 (t80) REVERT: C 352 MET cc_start: 0.7158 (mmt) cc_final: 0.6773 (mmp) REVERT: C 359 TYR cc_start: 0.6758 (m-10) cc_final: 0.6288 (m-10) REVERT: D 12 ILE cc_start: 0.7947 (mp) cc_final: 0.7491 (mt) REVERT: A 18 MET cc_start: 0.8752 (tmm) cc_final: 0.8243 (tmm) REVERT: A 21 ARG cc_start: 0.8694 (mpp80) cc_final: 0.8464 (mtt180) REVERT: A 25 GLU cc_start: 0.8451 (pt0) cc_final: 0.8237 (mm-30) REVERT: A 209 LYS cc_start: 0.8939 (mtmt) cc_final: 0.8590 (ttpp) REVERT: A 248 LYS cc_start: 0.8457 (ptpp) cc_final: 0.8062 (ptpp) REVERT: A 347 ASN cc_start: 0.8356 (m-40) cc_final: 0.8121 (m-40) REVERT: B 61 MET cc_start: 0.8060 (ppp) cc_final: 0.7758 (ppp) REVERT: B 85 TYR cc_start: 0.8791 (m-80) cc_final: 0.8498 (m-80) REVERT: B 111 TYR cc_start: 0.7415 (m-80) cc_final: 0.7153 (m-80) REVERT: B 246 ASP cc_start: 0.8349 (m-30) cc_final: 0.7972 (m-30) REVERT: B 308 LEU cc_start: 0.9039 (tp) cc_final: 0.8611 (tt) REVERT: G 38 GLU cc_start: 0.8783 (mp0) cc_final: 0.8575 (mm-30) REVERT: G 45 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8586 (pt0) outliers start: 3 outliers final: 1 residues processed: 236 average time/residue: 0.1830 time to fit residues: 59.1438 Evaluate side-chains 177 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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: 3.9990 chunk 53 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 58 optimal weight: 0.0980 chunk 56 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8063 Z= 0.182 Angle : 0.656 7.952 10926 Z= 0.345 Chirality : 0.044 0.226 1252 Planarity : 0.004 0.045 1384 Dihedral : 4.536 18.849 1092 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.12 % Allowed : 1.86 % Favored : 98.03 % 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: 1.00 (0.24), residues: 461 sheet: 0.08 (0.41), residues: 174 loop : -1.02 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 339 HIS 0.008 0.001 HIS A 195 PHE 0.036 0.002 PHE A 108 TYR 0.017 0.001 TYR B 124 ARG 0.007 0.000 ARG A 32 *********************** 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 224 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 0.921 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: C 121 MET cc_start: 0.8173 (tpt) cc_final: 0.7779 (tpt) REVERT: C 168 TYR cc_start: 0.6988 (t80) cc_final: 0.6492 (t80) REVERT: C 204 MET cc_start: 0.4441 (ttp) cc_final: 0.3478 (mmt) REVERT: C 352 MET cc_start: 0.7079 (mmt) cc_final: 0.6821 (mmp) REVERT: C 359 TYR cc_start: 0.6759 (m-10) cc_final: 0.6173 (m-10) REVERT: D 12 ILE cc_start: 0.7856 (mp) cc_final: 0.7288 (mt) REVERT: A 18 MET cc_start: 0.8706 (tmm) cc_final: 0.8208 (tmm) REVERT: A 209 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8555 (ttpp) REVERT: A 248 LYS cc_start: 0.8483 (ptpp) cc_final: 0.8076 (ptpp) REVERT: A 265 ILE cc_start: 0.8906 (mt) cc_final: 0.8553 (mm) REVERT: A 347 ASN cc_start: 0.8367 (m-40) cc_final: 0.8123 (m-40) REVERT: B 61 MET cc_start: 0.7972 (ppp) cc_final: 0.7705 (ppp) REVERT: B 246 ASP cc_start: 0.8435 (m-30) cc_final: 0.7983 (m-30) REVERT: G 45 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8593 (pt0) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.1720 time to fit residues: 53.4770 Evaluate side-chains 175 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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: 3.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** 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 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.6277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8063 Z= 0.291 Angle : 0.731 8.121 10926 Z= 0.385 Chirality : 0.046 0.171 1252 Planarity : 0.004 0.044 1384 Dihedral : 4.931 23.729 1092 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.27), residues: 992 helix: 0.87 (0.24), residues: 460 sheet: 0.01 (0.41), residues: 169 loop : -1.21 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP B 339 HIS 0.008 0.002 HIS A 195 PHE 0.027 0.002 PHE C 344 TYR 0.016 0.002 TYR C 333 ARG 0.007 0.001 ARG A 32 *********************** 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 206 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 MET cc_start: 0.8289 (tpt) cc_final: 0.7729 (tpt) REVERT: C 166 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8301 (tm-30) REVERT: C 168 TYR cc_start: 0.7069 (t80) cc_final: 0.6621 (t80) REVERT: C 352 MET cc_start: 0.7251 (mmt) cc_final: 0.6954 (mmp) REVERT: C 359 TYR cc_start: 0.7029 (m-10) cc_final: 0.6341 (m-10) REVERT: A 18 MET cc_start: 0.8703 (tmm) cc_final: 0.8212 (tmm) REVERT: A 198 MET cc_start: 0.7738 (tpp) cc_final: 0.7408 (tpt) REVERT: A 209 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8583 (ttpp) REVERT: A 248 LYS cc_start: 0.8596 (ptpp) cc_final: 0.8295 (ptpp) REVERT: A 347 ASN cc_start: 0.8383 (m-40) cc_final: 0.8080 (m-40) REVERT: B 61 MET cc_start: 0.7995 (ppp) cc_final: 0.7762 (ppp) REVERT: B 85 TYR cc_start: 0.9015 (m-80) cc_final: 0.8326 (m-80) REVERT: B 246 ASP cc_start: 0.8335 (m-30) cc_final: 0.8011 (m-30) REVERT: B 275 SER cc_start: 0.9285 (t) cc_final: 0.8811 (m) REVERT: G 38 GLU cc_start: 0.8878 (mp0) cc_final: 0.8165 (mp0) REVERT: G 45 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8611 (pt0) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1642 time to fit residues: 47.8779 Evaluate side-chains 156 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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: 0.9990 chunk 89 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 0.3980 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8063 Z= 0.186 Angle : 0.676 8.115 10926 Z= 0.352 Chirality : 0.044 0.185 1252 Planarity : 0.004 0.048 1384 Dihedral : 4.674 21.440 1092 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.28), residues: 992 helix: 0.94 (0.24), residues: 464 sheet: 0.01 (0.43), residues: 164 loop : -1.13 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 339 HIS 0.007 0.001 HIS A 195 PHE 0.025 0.002 PHE C 344 TYR 0.024 0.002 TYR C 145 ARG 0.007 0.000 ARG A 32 *********************** 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 213 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 0.962 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: C 121 MET cc_start: 0.8071 (tpt) cc_final: 0.7794 (tpt) REVERT: C 166 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8265 (tm-30) REVERT: C 168 TYR cc_start: 0.6961 (t80) cc_final: 0.6465 (t80) REVERT: C 204 MET cc_start: 0.4228 (tmm) cc_final: 0.3832 (mmt) REVERT: C 352 MET cc_start: 0.7162 (mmt) cc_final: 0.6961 (mmp) REVERT: D 12 ILE cc_start: 0.7973 (mp) cc_final: 0.7338 (mt) REVERT: A 18 MET cc_start: 0.8644 (tmm) cc_final: 0.8078 (tmm) REVERT: A 209 LYS cc_start: 0.8788 (mtmt) cc_final: 0.8566 (ttpp) REVERT: A 347 ASN cc_start: 0.8392 (m-40) cc_final: 0.8065 (m-40) REVERT: B 61 MET cc_start: 0.7952 (ppp) cc_final: 0.7691 (ppp) REVERT: B 85 TYR cc_start: 0.8870 (m-80) cc_final: 0.8331 (m-80) REVERT: B 111 TYR cc_start: 0.7473 (m-80) cc_final: 0.7132 (m-80) REVERT: B 190 LEU cc_start: 0.8958 (tt) cc_final: 0.8683 (tt) REVERT: B 246 ASP cc_start: 0.8422 (m-30) cc_final: 0.7959 (m-30) REVERT: B 253 PHE cc_start: 0.6827 (m-80) cc_final: 0.6385 (m-80) REVERT: B 275 SER cc_start: 0.9045 (t) cc_final: 0.8571 (m) REVERT: G 35 LYS cc_start: 0.9108 (pttt) cc_final: 0.8741 (pptt) REVERT: G 38 GLU cc_start: 0.8831 (mp0) cc_final: 0.8066 (mp0) REVERT: G 39 GLU cc_start: 0.9199 (pm20) cc_final: 0.8847 (pm20) REVERT: G 45 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8541 (pt0) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1731 time to fit residues: 51.5745 Evaluate side-chains 168 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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: 3.9990 chunk 43 optimal weight: 9.9990 chunk 64 optimal weight: 0.0270 chunk 96 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.0470 chunk 7 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 213 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.6565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8063 Z= 0.182 Angle : 0.687 8.315 10926 Z= 0.353 Chirality : 0.044 0.184 1252 Planarity : 0.004 0.050 1384 Dihedral : 4.621 20.037 1092 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: 0.01 (0.27), residues: 992 helix: 0.89 (0.24), residues: 465 sheet: -0.02 (0.42), residues: 168 loop : -1.06 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 339 HIS 0.007 0.001 HIS A 195 PHE 0.025 0.002 PHE B 241 TYR 0.016 0.001 TYR C 145 ARG 0.007 0.000 ARG A 32 ********************** 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 211 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 0.992 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: C 153 THR cc_start: 0.7030 (m) cc_final: 0.6418 (m) REVERT: C 166 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8226 (tm-30) REVERT: C 204 MET cc_start: 0.4054 (tmm) cc_final: 0.3781 (mmt) REVERT: C 256 LEU cc_start: 0.7281 (mt) cc_final: 0.7063 (mp) REVERT: C 293 MET cc_start: 0.4768 (pmm) cc_final: 0.4045 (ppp) REVERT: C 352 MET cc_start: 0.7200 (mmt) cc_final: 0.6915 (mmp) REVERT: C 359 TYR cc_start: 0.7003 (m-10) cc_final: 0.6306 (m-10) REVERT: D 12 ILE cc_start: 0.7970 (mp) cc_final: 0.7275 (mt) REVERT: A 18 MET cc_start: 0.8573 (tmm) cc_final: 0.8037 (tmm) REVERT: A 251 ASP cc_start: 0.8183 (t0) cc_final: 0.7887 (t0) REVERT: A 312 LYS cc_start: 0.8771 (mptt) cc_final: 0.8548 (mmtt) REVERT: A 347 ASN cc_start: 0.8401 (m-40) cc_final: 0.8111 (m-40) REVERT: B 85 TYR cc_start: 0.8821 (m-80) cc_final: 0.8483 (m-80) REVERT: B 246 ASP cc_start: 0.8413 (m-30) cc_final: 0.7931 (m-30) REVERT: G 38 GLU cc_start: 0.8818 (mp0) cc_final: 0.8030 (mp0) REVERT: G 45 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8523 (pt0) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1671 time to fit residues: 49.7441 Evaluate side-chains 164 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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: 0.9980 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN A 195 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.112419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.086427 restraints weight = 86633.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.089465 restraints weight = 33985.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.091669 restraints weight = 20178.131| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8063 Z= 0.213 Angle : 0.729 15.997 10926 Z= 0.375 Chirality : 0.045 0.313 1252 Planarity : 0.004 0.047 1384 Dihedral : 4.632 22.313 1092 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.01 (0.27), residues: 992 helix: 0.93 (0.24), residues: 464 sheet: 0.07 (0.43), residues: 156 loop : -1.20 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 339 HIS 0.008 0.001 HIS A 195 PHE 0.034 0.002 PHE A 108 TYR 0.015 0.001 TYR B 264 ARG 0.007 0.000 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2051.43 seconds wall clock time: 38 minutes 2.28 seconds (2282.28 seconds total)