Starting phenix.real_space_refine on Tue Jul 23 13:45:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psx_17864/07_2024/8psx_17864_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psx_17864/07_2024/8psx_17864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psx_17864/07_2024/8psx_17864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psx_17864/07_2024/8psx_17864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psx_17864/07_2024/8psx_17864_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psx_17864/07_2024/8psx_17864_neut_trim.cif" } resolution = 2.96 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: 8 Type Number sf(0) Gaussians Zn 3 6.06 5 P 37 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 7046 2.51 5 N 2010 2.21 5 O 2239 1.98 5 H 11003 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C GLU 396": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 22403 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6652 Classifications: {'peptide': 417} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 394} Chain: "B" Number of atoms: 7958 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 513, 7925 Classifications: {'peptide': 513} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 513, 7925 Classifications: {'peptide': 513} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 1 bond proxies already assigned to first conformer: 7960 Chain: "C" Number of atoms: 6676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6676 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 22, 'TRANS': 403} Chain breaks: 1 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: "V" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 250 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 3} Chain: "S" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 422 Classifications: {'RNA': 13} Modifications used: {'3*END': 1, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna3p': 12} Chain: "P" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 411 Classifications: {'RNA': 13} Modifications used: {'3*END': 1, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 12} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, 'A0I': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2585 SG CYS A 161 45.999 46.033 18.402 1.00 25.04 S ATOM 4473 SG CYS A 282 43.659 44.596 15.566 1.00 19.11 S ATOM 18214 SG CYS C 233 23.303 55.910 108.964 1.00 84.75 S ATOM 18238 SG CYS C 235 23.645 57.568 105.415 1.00 85.78 S ATOM 16880 SG CYS C 146 12.277 64.309 89.727 1.00 78.45 S ATOM 17068 SG CYS C 159 11.918 67.914 91.277 1.00 82.86 S ATOM 17124 SG CYS C 163 14.801 65.538 91.727 1.00 75.36 S ATOM 17134 SG CYS C 164 14.321 67.369 88.371 1.00 76.72 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AASP B 213 " occ=0.50 ... (22 atoms not shown) pdb=" HB3BASP B 213 " occ=0.50 residue: pdb=" N ATYR B 393 " occ=0.60 ... (40 atoms not shown) pdb=" HH BTYR B 393 " occ=0.40 Time building chain proxies: 13.61, per 1000 atoms: 0.61 Number of scatterers: 22403 At special positions: 0 Unit cell: (91.56, 103.32, 126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 S 63 16.00 P 37 15.00 Mg 2 11.99 O 2239 8.00 N 2010 7.00 C 7046 6.00 H 11003 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.55 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 296 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 284 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 282 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 161 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 191 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 184 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 233 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 235 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 163 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 146 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 159 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 164 " Number of angles added : 8 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2550 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 16 sheets defined 42.1% alpha, 14.2% beta 9 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 12.38 Creating SS restraints... Processing helix chain 'A' and resid 2 through 4 No H-bonds generated for 'chain 'A' and resid 2 through 4' Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.559A pdb=" N ILE A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 312 through 323 removed outlier: 4.422A pdb=" N ASP A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.640A pdb=" N VAL A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.897A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.681A pdb=" N ILE A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.608A pdb=" N GLN B 5 " --> pdb=" O TRP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 40 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.658A pdb=" N TYR B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 161 through 183 removed outlier: 3.525A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.568A pdb=" N GLY B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 removed outlier: 3.702A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 354 through 372 removed outlier: 4.154A pdb=" N LEU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 396 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.596A pdb=" N GLY B 413 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 429 through 435 removed outlier: 3.985A pdb=" N GLN B 434 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 Processing helix chain 'B' and resid 479 through 497 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 16 through 23 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 42 through 54 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.577A pdb=" N VAL C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 219 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 281 through 289 Processing helix chain 'C' and resid 303 through 317 removed outlier: 4.084A pdb=" N ARG C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 334 Processing helix chain 'C' and resid 350 through 356 Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'C' and resid 421 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.741A pdb=" N TRP A 52 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS A 71 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA A 54 " --> pdb=" O CYS A 71 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU A 73 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLU A 56 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.622A pdb=" N PHE B 291 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.285A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.285A pdb=" N TRP A 198 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER A 248 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU A 277 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 9 removed outlier: 7.231A pdb=" N VAL B 8 " --> pdb=" O GLY B 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA9, first strand: chain 'B' and resid 155 through 159 removed outlier: 7.100A pdb=" N PHE B 140 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AB2, first strand: chain 'B' and resid 477 through 478 Processing sheet with id=AB3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB4, first strand: chain 'C' and resid 77 through 83 Processing sheet with id=AB5, first strand: chain 'C' and resid 221 through 224 removed outlier: 6.876A pdb=" N GLY C 262 " --> pdb=" O PHE C 258 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 300 through 301 removed outlier: 4.831A pdb=" N THR C 362 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 383 through 388 removed outlier: 6.543A pdb=" N MET C 415 " --> pdb=" O LEU C 387 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1342 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 8.90 Time building geometry restraints manager: 19.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10971 1.03 - 1.23: 49 1.23 - 1.42: 4962 1.42 - 1.62: 6634 1.62 - 1.81: 89 Bond restraints: 22705 Sorted by residual: bond pdb=" O7 A0I B 601 " pdb=" P3 A0I B 601 " ideal model delta sigma weight residual 1.731 1.619 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" N4 A0I B 601 " pdb=" P2 A0I B 601 " ideal model delta sigma weight residual 1.701 1.639 0.062 2.00e-02 2.50e+03 9.53e+00 bond pdb=" O3 A0I B 601 " pdb=" P1 A0I B 601 " ideal model delta sigma weight residual 1.662 1.602 0.060 2.00e-02 2.50e+03 9.15e+00 bond pdb=" N4 A0I B 601 " pdb=" P1 A0I B 601 " ideal model delta sigma weight residual 1.691 1.640 0.051 2.00e-02 2.50e+03 6.46e+00 bond pdb=" C7 A0I B 601 " pdb=" O12 A0I B 601 " ideal model delta sigma weight residual 1.383 1.422 -0.039 2.00e-02 2.50e+03 3.87e+00 ... (remaining 22700 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.14: 442 106.14 - 113.09: 26327 113.09 - 120.05: 6975 120.05 - 127.01: 7052 127.01 - 133.97: 199 Bond angle restraints: 40995 Sorted by residual: angle pdb=" C LYS A 163 " pdb=" CA LYS A 163 " pdb=" CB LYS A 163 " ideal model delta sigma weight residual 116.54 111.92 4.62 1.15e+00 7.56e-01 1.61e+01 angle pdb=" CA PRO A 132 " pdb=" N PRO A 132 " pdb=" CD PRO A 132 " ideal model delta sigma weight residual 112.00 106.90 5.10 1.40e+00 5.10e-01 1.33e+01 angle pdb=" CA PRO C 84 " pdb=" N PRO C 84 " pdb=" CD PRO C 84 " ideal model delta sigma weight residual 112.00 107.89 4.11 1.40e+00 5.10e-01 8.61e+00 angle pdb=" N GLY C 405 " pdb=" CA GLY C 405 " pdb=" C GLY C 405 " ideal model delta sigma weight residual 110.56 114.32 -3.76 1.36e+00 5.41e-01 7.66e+00 angle pdb=" N PRO A 132 " pdb=" CD PRO A 132 " pdb=" CG PRO A 132 " ideal model delta sigma weight residual 103.20 99.18 4.02 1.50e+00 4.44e-01 7.18e+00 ... (remaining 40990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 9449 17.70 - 35.41: 832 35.41 - 53.11: 324 53.11 - 70.82: 95 70.82 - 88.52: 27 Dihedral angle restraints: 10727 sinusoidal: 6131 harmonic: 4596 Sorted by residual: dihedral pdb=" CA ALA A 77 " pdb=" C ALA A 77 " pdb=" N THR A 78 " pdb=" CA THR A 78 " ideal model delta harmonic sigma weight residual -180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA ARG B 394 " pdb=" C ARG B 394 " pdb=" N TYR B 395 " pdb=" CA TYR B 395 " ideal model delta harmonic sigma weight residual -180.00 -160.10 -19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LEU B 265 " pdb=" C LEU B 265 " pdb=" N MET B 266 " pdb=" CA MET B 266 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 10724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1489 0.042 - 0.084: 223 0.084 - 0.126: 92 0.126 - 0.168: 2 0.168 - 0.210: 1 Chirality restraints: 1807 Sorted by residual: chirality pdb=" C7 A0I B 601 " pdb=" C6 A0I B 601 " pdb=" C8 A0I B 601 " pdb=" O12 A0I B 601 " both_signs ideal model delta sigma weight residual False -2.37 -2.58 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA VAL C 195 " pdb=" N VAL C 195 " pdb=" C VAL C 195 " pdb=" CB VAL C 195 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA VAL A 252 " pdb=" N VAL A 252 " pdb=" C VAL A 252 " pdb=" CB VAL A 252 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1804 not shown) Planarity restraints: 3245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 83 " 0.076 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO C 84 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO C 84 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 84 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 427 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C ASP B 427 " -0.034 2.00e-02 2.50e+03 pdb=" O ASP B 427 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS B 428 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 131 " 0.033 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 132 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 132 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 132 " 0.027 5.00e-02 4.00e+02 ... (remaining 3242 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1910 2.21 - 2.81: 45994 2.81 - 3.41: 60929 3.41 - 4.00: 84242 4.00 - 4.60: 126377 Nonbonded interactions: 319452 Sorted by model distance: nonbonded pdb=" O SER A 128 " pdb="HD22 ASN B 44 " model vdw 1.618 1.850 nonbonded pdb="HH22 ARG A 201 " pdb=" O LYS A 263 " model vdw 1.622 1.850 nonbonded pdb="HE22 GLN B 57 " pdb=" OP1 U P 5 " model vdw 1.632 1.850 nonbonded pdb=" OE2 GLU B 148 " pdb=" HE ARG B 155 " model vdw 1.646 1.850 nonbonded pdb=" O LEU C 80 " pdb=" HZ1 LYS C 126 " model vdw 1.654 1.850 ... (remaining 319447 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.340 Extract box with map and model: 0.920 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 93.270 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.110 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:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 : 0.003 0.112 11702 Z= 0.199 Angle : 0.516 8.006 15982 Z= 0.270 Chirality : 0.037 0.210 1807 Planarity : 0.004 0.114 1934 Dihedral : 17.612 88.522 4590 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.71 % Allowed : 19.19 % Favored : 79.09 % 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 (0.23), residues: 1352 helix: 1.62 (0.23), residues: 534 sheet: -0.70 (0.37), residues: 163 loop : 0.08 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 HIS 0.004 0.001 HIS B 174 PHE 0.012 0.001 PHE C 82 TYR 0.010 0.001 TYR A 403 ARG 0.002 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 18 residues processed: 151 average time/residue: 3.0143 time to fit residues: 489.0253 Evaluate side-chains 143 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 346 LYS Chi-restraints excluded: chain C residue 388 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11702 Z= 0.368 Angle : 0.589 5.545 15982 Z= 0.311 Chirality : 0.041 0.140 1807 Planarity : 0.005 0.072 1934 Dihedral : 11.472 73.488 2045 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.77 % Allowed : 17.22 % Favored : 79.01 % 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: 0.39 (0.22), residues: 1352 helix: 1.24 (0.22), residues: 535 sheet: -0.80 (0.36), residues: 156 loop : -0.19 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 77 HIS 0.007 0.001 HIS B 378 PHE 0.018 0.002 PHE B 4 TYR 0.015 0.002 TYR C 315 ARG 0.004 0.000 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 126 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: A 83 GLU cc_start: 0.5238 (OUTLIER) cc_final: 0.4908 (mm-30) REVERT: B 59 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7208 (pp20) REVERT: C 115 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7250 (mm-30) REVERT: C 317 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.7066 (ptt180) REVERT: C 396 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6775 (mt-10) outliers start: 44 outliers final: 21 residues processed: 159 average time/residue: 2.9612 time to fit residues: 506.2159 Evaluate side-chains 153 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 123 optimal weight: 0.0270 chunk 133 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11702 Z= 0.227 Angle : 0.511 4.881 15982 Z= 0.269 Chirality : 0.038 0.148 1807 Planarity : 0.004 0.062 1934 Dihedral : 11.111 73.489 2032 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.49 % Allowed : 18.25 % Favored : 79.26 % 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: 0.54 (0.22), residues: 1352 helix: 1.44 (0.23), residues: 535 sheet: -0.79 (0.36), residues: 156 loop : -0.16 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 HIS 0.004 0.001 HIS B 378 PHE 0.011 0.001 PHE B 4 TYR 0.013 0.001 TYR A 403 ARG 0.002 0.000 ARG B 302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: A 83 GLU cc_start: 0.5080 (OUTLIER) cc_final: 0.4829 (mm-30) REVERT: B 427 ASP cc_start: 0.7789 (t0) cc_final: 0.7267 (t0) REVERT: B 467 ASP cc_start: 0.7627 (t0) cc_final: 0.7375 (t70) REVERT: C 115 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7296 (mm-30) outliers start: 29 outliers final: 17 residues processed: 150 average time/residue: 2.9441 time to fit residues: 474.9147 Evaluate side-chains 144 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 325 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 0.0170 chunk 117 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.2424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11702 Z= 0.220 Angle : 0.499 4.734 15982 Z= 0.261 Chirality : 0.038 0.150 1807 Planarity : 0.004 0.055 1934 Dihedral : 10.811 73.451 2029 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.17 % Allowed : 17.31 % Favored : 79.52 % 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: 0.63 (0.22), residues: 1352 helix: 1.53 (0.23), residues: 535 sheet: -0.76 (0.37), residues: 156 loop : -0.12 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 239 HIS 0.004 0.001 HIS B 378 PHE 0.011 0.001 PHE B 4 TYR 0.012 0.001 TYR A 403 ARG 0.003 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8359 (m) REVERT: B 59 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7166 (pp20) REVERT: B 427 ASP cc_start: 0.7784 (t0) cc_final: 0.7182 (t0) REVERT: B 467 ASP cc_start: 0.7615 (t0) cc_final: 0.7406 (t0) REVERT: C 115 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7247 (mm-30) REVERT: C 396 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6729 (mt-10) outliers start: 37 outliers final: 19 residues processed: 159 average time/residue: 2.9786 time to fit residues: 512.5973 Evaluate side-chains 146 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11702 Z= 0.261 Angle : 0.519 5.028 15982 Z= 0.273 Chirality : 0.038 0.151 1807 Planarity : 0.004 0.053 1934 Dihedral : 10.907 73.436 2027 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.17 % Allowed : 17.65 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1352 helix: 1.39 (0.22), residues: 535 sheet: -0.76 (0.37), residues: 152 loop : -0.17 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 HIS 0.005 0.001 HIS B 378 PHE 0.013 0.001 PHE B 4 TYR 0.013 0.002 TYR A 403 ARG 0.003 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 126 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8378 (m) REVERT: B 59 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7172 (pp20) REVERT: B 427 ASP cc_start: 0.7752 (t0) cc_final: 0.7150 (t0) REVERT: B 467 ASP cc_start: 0.7698 (t0) cc_final: 0.7442 (t70) REVERT: C 115 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7154 (mm-30) REVERT: C 396 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6776 (mt-10) outliers start: 37 outliers final: 21 residues processed: 156 average time/residue: 3.0174 time to fit residues: 505.5011 Evaluate side-chains 150 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 411 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 131 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11702 Z= 0.185 Angle : 0.478 4.543 15982 Z= 0.250 Chirality : 0.037 0.149 1807 Planarity : 0.004 0.051 1934 Dihedral : 10.613 73.490 2026 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.83 % Allowed : 17.65 % Favored : 79.52 % 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: 0.75 (0.22), residues: 1352 helix: 1.62 (0.23), residues: 535 sheet: -0.66 (0.39), residues: 149 loop : -0.06 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.009 0.001 PHE B 4 TYR 0.012 0.001 TYR A 403 ARG 0.002 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8409 (m) REVERT: B 59 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7132 (pp20) REVERT: B 427 ASP cc_start: 0.7765 (t0) cc_final: 0.7131 (t0) REVERT: B 467 ASP cc_start: 0.7589 (t0) cc_final: 0.7388 (t70) REVERT: C 115 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7269 (mm-30) REVERT: C 396 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6709 (mt-10) outliers start: 33 outliers final: 21 residues processed: 158 average time/residue: 2.9626 time to fit residues: 503.4509 Evaluate side-chains 152 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 411 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11702 Z= 0.170 Angle : 0.468 4.505 15982 Z= 0.244 Chirality : 0.037 0.149 1807 Planarity : 0.004 0.049 1934 Dihedral : 10.508 73.461 2026 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.14 % Allowed : 18.59 % Favored : 79.26 % 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: 0.92 (0.23), residues: 1352 helix: 1.79 (0.23), residues: 535 sheet: -0.57 (0.39), residues: 149 loop : -0.00 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.009 0.001 PHE B 158 TYR 0.010 0.001 TYR A 403 ARG 0.002 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8076 (mt-10) REVERT: B 427 ASP cc_start: 0.7735 (t0) cc_final: 0.7101 (t0) REVERT: C 115 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7266 (mm-30) REVERT: C 358 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: C 396 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6704 (mt-10) outliers start: 25 outliers final: 20 residues processed: 154 average time/residue: 3.1239 time to fit residues: 514.8425 Evaluate side-chains 150 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 411 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11702 Z= 0.258 Angle : 0.513 4.934 15982 Z= 0.269 Chirality : 0.038 0.151 1807 Planarity : 0.004 0.049 1934 Dihedral : 10.711 73.405 2024 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.08 % Allowed : 17.91 % Favored : 79.01 % 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: 0.67 (0.22), residues: 1352 helix: 1.54 (0.23), residues: 534 sheet: -0.69 (0.38), residues: 152 loop : -0.10 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 77 HIS 0.006 0.001 HIS B 378 PHE 0.013 0.001 PHE B 4 TYR 0.014 0.002 TYR A 403 ARG 0.005 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 127 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8403 (m) REVERT: B 59 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7099 (pp20) REVERT: B 84 ARG cc_start: 0.6412 (mtm110) cc_final: 0.6123 (mtm180) REVERT: B 427 ASP cc_start: 0.7763 (t0) cc_final: 0.7137 (t0) REVERT: C 32 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6343 (mt) REVERT: C 115 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6623 (mp0) REVERT: C 358 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: C 396 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6778 (mt-10) outliers start: 36 outliers final: 23 residues processed: 153 average time/residue: 2.8657 time to fit residues: 472.2869 Evaluate side-chains 155 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 411 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11702 Z= 0.159 Angle : 0.464 4.493 15982 Z= 0.241 Chirality : 0.037 0.150 1807 Planarity : 0.004 0.049 1934 Dihedral : 10.432 73.503 2024 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.89 % Allowed : 19.11 % Favored : 79.01 % 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: 0.98 (0.23), residues: 1352 helix: 1.85 (0.23), residues: 534 sheet: -0.56 (0.39), residues: 149 loop : 0.04 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.008 0.001 PHE C 175 TYR 0.010 0.001 TYR C 315 ARG 0.006 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8091 (mt-10) REVERT: B 427 ASP cc_start: 0.7730 (t0) cc_final: 0.7086 (t0) REVERT: C 32 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6440 (mt) REVERT: C 115 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7182 (mm-30) REVERT: C 199 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6187 (tptt) REVERT: C 358 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6365 (mp0) outliers start: 22 outliers final: 16 residues processed: 152 average time/residue: 3.0273 time to fit residues: 497.3886 Evaluate side-chains 149 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 411 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11702 Z= 0.221 Angle : 0.492 4.624 15982 Z= 0.258 Chirality : 0.038 0.151 1807 Planarity : 0.004 0.049 1934 Dihedral : 10.491 73.419 2021 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.63 % Allowed : 19.88 % Favored : 78.49 % 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: 0.80 (0.23), residues: 1352 helix: 1.68 (0.23), residues: 534 sheet: -0.66 (0.38), residues: 152 loop : -0.04 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 77 HIS 0.005 0.001 HIS B 378 PHE 0.013 0.001 PHE B 4 TYR 0.012 0.001 TYR A 403 ARG 0.006 0.000 ARG A 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 427 ASP cc_start: 0.7766 (t0) cc_final: 0.7149 (t0) REVERT: C 115 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6628 (mp0) REVERT: C 358 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6334 (mp0) outliers start: 19 outliers final: 17 residues processed: 143 average time/residue: 3.0432 time to fit residues: 467.1478 Evaluate side-chains 146 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 39 ARG Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 411 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.137752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.114927 restraints weight = 55609.532| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.71 r_work: 0.3004 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11702 Z= 0.172 Angle : 0.470 4.482 15982 Z= 0.245 Chirality : 0.037 0.150 1807 Planarity : 0.004 0.066 1934 Dihedral : 10.378 73.456 2021 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.71 % Allowed : 19.71 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.23), residues: 1352 helix: 1.82 (0.23), residues: 534 sheet: -0.63 (0.39), residues: 151 loop : 0.05 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 209 HIS 0.004 0.001 HIS C 276 PHE 0.008 0.001 PHE C 44 TYR 0.011 0.001 TYR A 403 ARG 0.009 0.000 ARG A 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8874.58 seconds wall clock time: 153 minutes 18.28 seconds (9198.28 seconds total)