Starting phenix.real_space_refine on Thu Jun 19 15:34:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8psx_17864/06_2025/8psx_17864_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psx_17864/06_2025/8psx_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/cci-nas-00/data/ceres_data/8psx_17864/06_2025/8psx_17864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psx_17864/06_2025/8psx_17864.map" model { file = "/net/cci-nas-00/data/ceres_data/8psx_17864/06_2025/8psx_17864_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psx_17864/06_2025/8psx_17864_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. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 15.47, per 1000 atoms: 0.69 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.81 Conformation dependent library (CDL) restraints added in 2.0 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: 10.93 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: 8.63 Time building geometry restraints manager: 6.82 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: 0.00 - 1.95: 40650 1.95 - 3.90: 326 3.90 - 5.85: 15 5.85 - 7.80: 2 7.80 - 9.75: 2 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 2.450 nonbonded pdb="HH22 ARG A 201 " pdb=" O LYS A 263 " model vdw 1.622 2.450 nonbonded pdb="HE22 GLN B 57 " pdb=" OP1 U P 5 " model vdw 1.632 2.450 nonbonded pdb=" OE2 GLU B 148 " pdb=" HE ARG B 155 " model vdw 1.646 2.450 nonbonded pdb=" O LEU C 80 " pdb=" HZ1 LYS C 126 " model vdw 1.654 2.450 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 2.850 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: 0.400 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 71.100 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.100 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:14.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.940 ------------------------------------------------------------------------------- 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 11714 Z= 0.140 Angle : 0.531 13.603 15990 Z= 0.271 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 Details of bonding type rmsd hydrogen bonds : bond 0.13210 ( 494) hydrogen bonds : angle 5.61420 ( 1380) metal coordination : bond 0.00480 ( 12) metal coordination : angle 5.71566 ( 8) covalent geometry : bond 0.00311 (11702) covalent geometry : angle 0.51556 (15982) *********************** 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 to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 18 residues processed: 151 average time/residue: 3.0494 time to fit residues: 494.3362 Evaluate side-chains 143 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.135151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.113275 restraints weight = 45405.097| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.58 r_work: 0.2986 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11714 Z= 0.222 Angle : 0.599 16.252 15990 Z= 0.307 Chirality : 0.041 0.140 1807 Planarity : 0.005 0.072 1934 Dihedral : 11.343 73.483 2045 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.00 % Allowed : 17.91 % 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: 0.46 (0.22), residues: 1352 helix: 1.35 (0.23), residues: 535 sheet: -0.77 (0.36), residues: 154 loop : -0.21 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 77 HIS 0.006 0.001 HIS B 378 PHE 0.016 0.002 PHE B 4 TYR 0.017 0.002 TYR A 403 ARG 0.004 0.001 ARG B 302 Details of bonding type rmsd hydrogen bonds : bond 0.05073 ( 494) hydrogen bonds : angle 4.65699 ( 1380) metal coordination : bond 0.01060 ( 12) metal coordination : angle 7.04998 ( 8) covalent geometry : bond 0.00517 (11702) covalent geometry : angle 0.57789 (15982) *********************** 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 168 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: A 83 GLU cc_start: 0.5166 (OUTLIER) cc_final: 0.4877 (mm-30) REVERT: C 358 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: C 396 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7044 (mt-10) outliers start: 35 outliers final: 19 residues processed: 158 average time/residue: 2.8222 time to fit residues: 482.7979 Evaluate side-chains 146 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.726 ------------------------------------------------------------------------------- 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 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 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 216 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 358 GLU 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 95 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.134934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.112676 restraints weight = 49526.117| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.60 r_work: 0.2979 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11714 Z= 0.205 Angle : 0.582 15.863 15990 Z= 0.298 Chirality : 0.040 0.149 1807 Planarity : 0.005 0.062 1934 Dihedral : 11.243 73.509 2030 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.26 % Allowed : 17.48 % 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: 0.22 (0.22), residues: 1352 helix: 1.18 (0.22), residues: 535 sheet: -0.90 (0.36), residues: 154 loop : -0.37 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 77 HIS 0.006 0.001 HIS B 378 PHE 0.015 0.002 PHE B 4 TYR 0.015 0.002 TYR A 403 ARG 0.004 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 494) hydrogen bonds : angle 4.54718 ( 1380) metal coordination : bond 0.00804 ( 12) metal coordination : angle 6.92063 ( 8) covalent geometry : bond 0.00477 (11702) covalent geometry : angle 0.56104 (15982) *********************** 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 168 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: A 83 GLU cc_start: 0.5149 (OUTLIER) cc_final: 0.4926 (mt-10) REVERT: A 87 GLN cc_start: 0.7356 (tt0) cc_final: 0.6927 (tm-30) REVERT: B 427 ASP cc_start: 0.7820 (t0) cc_final: 0.7259 (t0) REVERT: C 317 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.7109 (ptt180) REVERT: C 396 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7065 (mt-10) outliers start: 38 outliers final: 23 residues processed: 162 average time/residue: 3.0377 time to fit residues: 527.7902 Evaluate side-chains 156 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 1.586 ------------------------------------------------------------------------------- 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 303 LYS 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 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 86 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 120 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 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 300 VAL Chi-restraints excluded: chain C residue 317 ARG Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 396 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 84 optimal weight: 0.0770 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.134347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.111999 restraints weight = 49147.695| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.63 r_work: 0.2973 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11714 Z= 0.156 Angle : 0.537 14.363 15990 Z= 0.275 Chirality : 0.038 0.148 1807 Planarity : 0.004 0.056 1934 Dihedral : 10.951 73.489 2029 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.91 % Allowed : 17.82 % 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: 0.38 (0.22), residues: 1352 helix: 1.35 (0.22), residues: 535 sheet: -0.79 (0.37), residues: 154 loop : -0.32 (0.23), residues: 663 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 0.011 0.001 PHE B 4 TYR 0.014 0.001 TYR A 403 ARG 0.003 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 494) hydrogen bonds : angle 4.39024 ( 1380) metal coordination : bond 0.00643 ( 12) metal coordination : angle 6.17498 ( 8) covalent geometry : bond 0.00360 (11702) covalent geometry : angle 0.51882 (15982) *********************** 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 170 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: A 31 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8367 (m) REVERT: A 83 GLU cc_start: 0.5156 (OUTLIER) cc_final: 0.4929 (mm-30) REVERT: A 87 GLN cc_start: 0.7349 (tt0) cc_final: 0.6898 (tm-30) REVERT: B 427 ASP cc_start: 0.7816 (t0) cc_final: 0.7196 (t0) outliers start: 34 outliers final: 16 residues processed: 161 average time/residue: 3.1677 time to fit residues: 547.1240 Evaluate side-chains 149 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 159 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain B residue 465 LEU 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 86 LEU Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 120 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 224 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 92 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 87 optimal weight: 0.0570 chunk 124 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.136599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.114237 restraints weight = 48732.123| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.60 r_work: 0.3009 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11714 Z= 0.102 Angle : 0.483 12.003 15990 Z= 0.247 Chirality : 0.037 0.148 1807 Planarity : 0.004 0.055 1934 Dihedral : 10.531 73.501 2026 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.23 % Allowed : 18.77 % 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: 0.75 (0.22), residues: 1352 helix: 1.72 (0.23), residues: 535 sheet: -0.64 (0.38), residues: 154 loop : -0.17 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 346 HIS 0.003 0.001 HIS B 174 PHE 0.008 0.001 PHE B 158 TYR 0.011 0.001 TYR A 403 ARG 0.005 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 494) hydrogen bonds : angle 4.14919 ( 1380) metal coordination : bond 0.00435 ( 12) metal coordination : angle 5.02582 ( 8) covalent geometry : bond 0.00236 (11702) covalent geometry : angle 0.47032 (15982) *********************** 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 165 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLN cc_start: 0.7162 (tt0) cc_final: 0.6733 (tm-30) REVERT: B 427 ASP cc_start: 0.7767 (t0) cc_final: 0.7083 (t0) REVERT: C 35 ASP cc_start: 0.7254 (m-30) cc_final: 0.7042 (m-30) outliers start: 26 outliers final: 12 residues processed: 158 average time/residue: 3.1443 time to fit residues: 532.9543 Evaluate side-chains 140 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LYS 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 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 86 LEU 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 216 LYS 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 38 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.135415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.113179 restraints weight = 48639.870| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.60 r_work: 0.2992 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11714 Z= 0.131 Angle : 0.503 11.629 15990 Z= 0.258 Chirality : 0.037 0.149 1807 Planarity : 0.004 0.054 1934 Dihedral : 10.380 73.426 2019 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.97 % Allowed : 18.94 % 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: 0.72 (0.22), residues: 1352 helix: 1.69 (0.23), residues: 534 sheet: -0.72 (0.38), residues: 156 loop : -0.15 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 209 HIS 0.004 0.001 HIS B 378 PHE 0.010 0.001 PHE B 4 TYR 0.013 0.001 TYR A 403 ARG 0.003 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 494) hydrogen bonds : angle 4.17885 ( 1380) metal coordination : bond 0.00548 ( 12) metal coordination : angle 5.00595 ( 8) covalent geometry : bond 0.00304 (11702) covalent geometry : angle 0.49090 (15982) *********************** 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 160 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8365 (m) REVERT: A 83 GLU cc_start: 0.5088 (OUTLIER) cc_final: 0.4852 (mm-30) REVERT: A 87 GLN cc_start: 0.7171 (tt0) cc_final: 0.6713 (tm-30) REVERT: B 427 ASP cc_start: 0.7773 (t0) cc_final: 0.7069 (t0) REVERT: C 35 ASP cc_start: 0.7281 (m-30) cc_final: 0.7055 (m-30) outliers start: 23 outliers final: 16 residues processed: 155 average time/residue: 3.1361 time to fit residues: 519.8312 Evaluate side-chains 150 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 303 LYS 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 444 ASP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 89 GLU 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 216 LYS Chi-restraints excluded: chain C residue 224 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 102 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.135818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.113477 restraints weight = 50202.936| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.63 r_work: 0.3016 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11714 Z= 0.118 Angle : 0.490 10.826 15990 Z= 0.251 Chirality : 0.037 0.149 1807 Planarity : 0.004 0.052 1934 Dihedral : 10.290 73.462 2019 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.06 % Allowed : 19.02 % Favored : 78.92 % 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: 0.79 (0.23), residues: 1352 helix: 1.77 (0.23), residues: 534 sheet: -0.68 (0.39), residues: 156 loop : -0.13 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 346 HIS 0.004 0.001 HIS B 174 PHE 0.009 0.001 PHE C 175 TYR 0.012 0.001 TYR A 403 ARG 0.004 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 494) hydrogen bonds : angle 4.11628 ( 1380) metal coordination : bond 0.00472 ( 12) metal coordination : angle 4.62757 ( 8) covalent geometry : bond 0.00274 (11702) covalent geometry : angle 0.47947 (15982) *********************** 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 161 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8374 (m) REVERT: A 87 GLN cc_start: 0.7216 (tt0) cc_final: 0.6758 (tm-30) REVERT: B 427 ASP cc_start: 0.7758 (t0) cc_final: 0.7045 (t0) REVERT: C 358 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6734 (mp0) REVERT: C 396 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7110 (mt-10) outliers start: 24 outliers final: 18 residues processed: 156 average time/residue: 3.1405 time to fit residues: 529.2128 Evaluate side-chains 151 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 303 LYS 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 465 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 89 GLU 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 216 LYS Chi-restraints excluded: chain C residue 224 GLU 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 57 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.135546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.112855 restraints weight = 55201.859| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.70 r_work: 0.2965 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11714 Z= 0.171 Angle : 0.534 11.645 15990 Z= 0.275 Chirality : 0.039 0.149 1807 Planarity : 0.005 0.053 1934 Dihedral : 10.501 73.376 2018 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.14 % Allowed : 18.85 % 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: 0.57 (0.22), residues: 1352 helix: 1.52 (0.23), residues: 534 sheet: -0.77 (0.38), residues: 156 loop : -0.20 (0.23), residues: 662 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 A 141 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 494) hydrogen bonds : angle 4.27912 ( 1380) metal coordination : bond 0.00730 ( 12) metal coordination : angle 5.16769 ( 8) covalent geometry : bond 0.00399 (11702) covalent geometry : angle 0.52118 (15982) *********************** 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 153 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8367 (m) REVERT: A 83 GLU cc_start: 0.5123 (OUTLIER) cc_final: 0.4890 (mm-30) REVERT: A 87 GLN cc_start: 0.7284 (tt0) cc_final: 0.6777 (tm-30) REVERT: B 84 ARG cc_start: 0.6485 (mtm110) cc_final: 0.6190 (mtm180) REVERT: B 427 ASP cc_start: 0.7777 (t0) cc_final: 0.7086 (t0) REVERT: C 358 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6553 (mp0) REVERT: C 396 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7162 (mt-10) outliers start: 25 outliers final: 18 residues processed: 149 average time/residue: 2.9841 time to fit residues: 477.6698 Evaluate side-chains 151 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 303 LYS 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 465 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 89 GLU 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 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 127 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 103 optimal weight: 0.4980 chunk 120 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 130 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.137070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.115203 restraints weight = 48311.365| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.58 r_work: 0.3012 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11714 Z= 0.117 Angle : 0.507 14.684 15990 Z= 0.255 Chirality : 0.037 0.149 1807 Planarity : 0.004 0.068 1934 Dihedral : 10.305 73.478 2018 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.89 % Allowed : 19.19 % Favored : 78.92 % 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: 0.74 (0.22), residues: 1352 helix: 1.70 (0.23), residues: 534 sheet: -0.73 (0.39), residues: 156 loop : -0.13 (0.23), residues: 662 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 0.012 0.001 TYR A 403 ARG 0.010 0.000 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 494) hydrogen bonds : angle 4.15087 ( 1380) metal coordination : bond 0.00408 ( 12) metal coordination : angle 6.84054 ( 8) covalent geometry : bond 0.00272 (11702) covalent geometry : angle 0.48345 (15982) *********************** 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 152 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8385 (m) REVERT: A 87 GLN cc_start: 0.7220 (tt0) cc_final: 0.6753 (tm-30) REVERT: B 84 ARG cc_start: 0.6416 (mtm110) cc_final: 0.6145 (mtm180) REVERT: B 427 ASP cc_start: 0.7709 (t0) cc_final: 0.7015 (t0) REVERT: C 358 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6457 (mp0) REVERT: C 396 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7085 (mt-10) outliers start: 22 outliers final: 16 residues processed: 148 average time/residue: 3.0495 time to fit residues: 484.3835 Evaluate side-chains 148 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 303 LYS 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 465 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 86 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 81 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.134996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.112522 restraints weight = 54084.015| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.67 r_work: 0.2964 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11714 Z= 0.187 Angle : 0.561 15.106 15990 Z= 0.285 Chirality : 0.039 0.150 1807 Planarity : 0.005 0.074 1934 Dihedral : 10.595 73.382 2018 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.80 % Allowed : 19.37 % Favored : 78.83 % 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 (0.22), residues: 1352 helix: 1.44 (0.23), residues: 533 sheet: -0.84 (0.38), residues: 156 loop : -0.25 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 77 HIS 0.007 0.001 HIS B 378 PHE 0.016 0.002 PHE B 4 TYR 0.015 0.002 TYR A 403 ARG 0.010 0.000 ARG C 20 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 494) hydrogen bonds : angle 4.32702 ( 1380) metal coordination : bond 0.00781 ( 12) metal coordination : angle 7.32783 ( 8) covalent geometry : bond 0.00436 (11702) covalent geometry : angle 0.53716 (15982) ********************** 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 153 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.795 Fit side-chains revert: symmetry clash REVERT: A 31 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8373 (m) REVERT: A 87 GLN cc_start: 0.7234 (tt0) cc_final: 0.6716 (tm-30) REVERT: B 84 ARG cc_start: 0.6438 (mtm110) cc_final: 0.6166 (mtm180) REVERT: B 427 ASP cc_start: 0.7785 (t0) cc_final: 0.7104 (t0) REVERT: C 35 ASP cc_start: 0.7340 (m-30) cc_final: 0.7139 (m-30) REVERT: C 358 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6306 (mp0) REVERT: C 396 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7094 (mt-10) outliers start: 21 outliers final: 16 residues processed: 149 average time/residue: 3.1060 time to fit residues: 497.0866 Evaluate side-chains 153 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR 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 465 LEU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 89 GLU 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 300 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 67 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.135696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.112993 restraints weight = 53895.163| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.70 r_work: 0.2997 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11714 Z= 0.130 Angle : 0.519 14.337 15990 Z= 0.262 Chirality : 0.038 0.149 1807 Planarity : 0.005 0.073 1934 Dihedral : 10.413 73.448 2018 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.54 % Allowed : 19.54 % Favored : 78.92 % 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: 0.64 (0.22), residues: 1352 helix: 1.58 (0.23), residues: 534 sheet: -0.71 (0.39), residues: 154 loop : -0.18 (0.23), residues: 664 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 0.009 0.001 PHE C 44 TYR 0.013 0.001 TYR A 403 ARG 0.009 0.000 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 494) hydrogen bonds : angle 4.21856 ( 1380) metal coordination : bond 0.00508 ( 12) metal coordination : angle 6.62232 ( 8) covalent geometry : bond 0.00302 (11702) covalent geometry : angle 0.49707 (15982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15729.26 seconds wall clock time: 266 minutes 39.73 seconds (15999.73 seconds total)