Starting phenix.real_space_refine on Sun Jun 15 04:19:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a6l_15210/06_2025/8a6l_15210_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a6l_15210/06_2025/8a6l_15210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a6l_15210/06_2025/8a6l_15210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a6l_15210/06_2025/8a6l_15210.map" model { file = "/net/cci-nas-00/data/ceres_data/8a6l_15210/06_2025/8a6l_15210_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a6l_15210/06_2025/8a6l_15210_trim.cif" } resolution = 3.18 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= 0.003 sd= 0.038 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: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 5531 2.51 5 N 1387 2.21 5 O 1527 1.98 5 H 8495 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16972 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 7066 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain: "B" Number of atoms: 7125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 7125 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 24, 'TRANS': 427} Chain: "C" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2722 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 11, 'TRANS': 161} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 8.27, per 1000 atoms: 0.49 Number of scatterers: 16972 At special positions: 0 Unit cell: (97.818, 89.598, 141.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 1527 8.00 N 1387 7.00 C 5531 6.00 H 8495 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 175 " distance=2.04 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 424 " " NAG A 702 " - " ASN A 506 " " NAG A 703 " - " ASN A 365 " " NAG A 704 " - " ASN A 381 " Time building additional restraints: 4.23 Conformation dependent library (CDL) restraints added in 1.4 seconds 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1978 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 53.8% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 179 through 207 Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.536A pdb=" N THR A 221 " --> pdb=" O TRP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 235 Processing helix chain 'A' and resid 240 through 245 removed outlier: 3.837A pdb=" N LYS A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 286 through 301 Processing helix chain 'A' and resid 323 through 341 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 355 through 371 removed outlier: 3.572A pdb=" N PHE A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 removed outlier: 4.635A pdb=" N SER A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 Processing helix chain 'A' and resid 440 through 445 removed outlier: 4.341A pdb=" N PHE A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 449 through 460 Processing helix chain 'A' and resid 504 through 507 Processing helix chain 'A' and resid 508 through 514 removed outlier: 3.898A pdb=" N GLU A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 533 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.808A pdb=" N HIS A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 588 Processing helix chain 'B' and resid 43 through 54 Processing helix chain 'B' and resid 56 through 70 removed outlier: 3.661A pdb=" N VAL B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) Proline residue: B 62 - end of helix Processing helix chain 'B' and resid 71 through 100 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 129 through 148 Processing helix chain 'B' and resid 157 through 179 removed outlier: 3.535A pdb=" N SER B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 212 removed outlier: 3.794A pdb=" N ALA B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 211 " --> pdb=" O VAL B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 243 removed outlier: 3.557A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.539A pdb=" N VAL B 254 " --> pdb=" O PHE B 250 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 255' Processing helix chain 'B' and resid 260 through 291 Proline residue: B 266 - end of helix removed outlier: 3.752A pdb=" N ILE B 273 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Proline residue: B 274 - end of helix Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 301 through 311 Processing helix chain 'B' and resid 317 through 347 removed outlier: 3.559A pdb=" N ALA B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 379 removed outlier: 3.627A pdb=" N PHE B 370 " --> pdb=" O PRO B 366 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 412 removed outlier: 3.651A pdb=" N LEU B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE B 388 " --> pdb=" O MET B 384 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 394 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.650A pdb=" N ILE B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 468 Proline residue: B 461 - end of helix removed outlier: 3.787A pdb=" N PHE B 464 " --> pdb=" O VAL B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 492 Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 145 through 159 removed outlier: 3.549A pdb=" N LYS C 149 " --> pdb=" O THR C 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 399 through 402 removed outlier: 6.403A pdb=" N LEU A 376 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N THR A 401 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA A 378 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE A 345 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N GLY A 379 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL A 347 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY A 344 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 306 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR A 225 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU A 224 " --> pdb=" O PHE A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 540 through 544 removed outlier: 4.498A pdb=" N SER A 552 " --> pdb=" O PHE A 544 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEU A 595 " --> pdb=" O ARG A 625 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 593 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575 Processing sheet with id=AA4, first strand: chain 'C' and resid 92 through 94 removed outlier: 6.280A pdb=" N LEU C 137 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG C 36 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE C 135 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N HIS C 118 " --> pdb=" O THR C 113 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N THR C 113 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N MET C 120 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 92 through 94 463 hydrogen bonds defined for protein. 1338 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.09 Time building geometry restraints manager: 5.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 8484 1.04 - 1.24: 1093 1.24 - 1.44: 2651 1.44 - 1.64: 4910 1.64 - 1.84: 49 Bond restraints: 17187 Sorted by residual: bond pdb=" CA LEU B 437 " pdb=" C LEU B 437 " ideal model delta sigma weight residual 1.524 1.504 0.020 1.27e-02 6.20e+03 2.39e+00 bond pdb=" CB VAL A 565 " pdb=" CG2 VAL A 565 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.75e+00 bond pdb=" CG LEU A 375 " pdb=" CD1 LEU A 375 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.55e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.45e+00 bond pdb=" CB GLN A 559 " pdb=" CG GLN A 559 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.43e+00 ... (remaining 17182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 30307 1.50 - 3.01: 738 3.01 - 4.51: 60 4.51 - 6.01: 9 6.01 - 7.52: 2 Bond angle restraints: 31116 Sorted by residual: angle pdb=" CA CYS A 210 " pdb=" CB CYS A 210 " pdb=" SG CYS A 210 " ideal model delta sigma weight residual 114.40 121.92 -7.52 2.30e+00 1.89e-01 1.07e+01 angle pdb=" N GLY A 547 " pdb=" CA GLY A 547 " pdb=" C GLY A 547 " ideal model delta sigma weight residual 112.34 106.03 6.31 2.04e+00 2.40e-01 9.57e+00 angle pdb=" N CYS C 76 " pdb=" CA CYS C 76 " pdb=" C CYS C 76 " ideal model delta sigma weight residual 109.59 105.65 3.94 1.47e+00 4.63e-01 7.18e+00 angle pdb=" N TYR C 32 " pdb=" CA TYR C 32 " pdb=" C TYR C 32 " ideal model delta sigma weight residual 110.42 106.76 3.66 1.55e+00 4.16e-01 5.58e+00 angle pdb=" C ILE B 429 " pdb=" N TYR B 430 " pdb=" CA TYR B 430 " ideal model delta sigma weight residual 120.28 117.13 3.15 1.34e+00 5.57e-01 5.53e+00 ... (remaining 31111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 7575 17.71 - 35.43: 349 35.43 - 53.14: 160 53.14 - 70.86: 63 70.86 - 88.57: 8 Dihedral angle restraints: 8155 sinusoidal: 4412 harmonic: 3743 Sorted by residual: dihedral pdb=" CA GLY A 547 " pdb=" C GLY A 547 " pdb=" N PRO A 548 " pdb=" CA PRO A 548 " ideal model delta harmonic sigma weight residual 180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA VAL B 129 " pdb=" C VAL B 129 " pdb=" N ILE B 130 " pdb=" CA ILE B 130 " ideal model delta harmonic sigma weight residual -180.00 -162.94 -17.06 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB CYS A 210 " pdb=" SG CYS A 210 " pdb=" SG CYS B 154 " pdb=" CB CYS B 154 " ideal model delta sinusoidal sigma weight residual -86.00 -114.16 28.16 1 1.00e+01 1.00e-02 1.14e+01 ... (remaining 8152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1087 0.050 - 0.101: 231 0.101 - 0.151: 33 0.151 - 0.202: 1 0.202 - 0.252: 3 Chirality restraints: 1355 Sorted by residual: chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 506 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 365 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 381 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1352 not shown) Planarity restraints: 2507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 437 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C LEU B 437 " -0.070 2.00e-02 2.50e+03 pdb=" O LEU B 437 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU B 438 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 393 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" C PHE B 393 " 0.048 2.00e-02 2.50e+03 pdb=" O PHE B 393 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE B 394 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 439 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.58e+00 pdb=" C VAL B 439 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL B 439 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE B 440 " -0.015 2.00e-02 2.50e+03 ... (remaining 2504 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 447 2.12 - 2.74: 31670 2.74 - 3.36: 49063 3.36 - 3.98: 62067 3.98 - 4.60: 99955 Nonbonded interactions: 243202 Sorted by model distance: nonbonded pdb=" HG SER A 494 " pdb=" OG SER C 125 " model vdw 1.499 2.450 nonbonded pdb=" O LYS A 300 " pdb=" HG SER A 301 " model vdw 1.543 2.450 nonbonded pdb=" O GLY A 409 " pdb=" HG SER A 410 " model vdw 1.549 2.450 nonbonded pdb=" O LEU B 251 " pdb=" HG1 THR B 255 " model vdw 1.586 2.450 nonbonded pdb=" OD1 ASP A 498 " pdb=" HG1 THR C 136 " model vdw 1.588 2.450 ... (remaining 243197 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.290 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 37.880 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8698 Z= 0.229 Angle : 0.627 7.515 11848 Z= 0.345 Chirality : 0.042 0.252 1355 Planarity : 0.005 0.040 1483 Dihedral : 10.515 88.573 3155 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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 (0.26), residues: 1073 helix: 1.67 (0.22), residues: 516 sheet: -1.25 (0.42), residues: 133 loop : -0.18 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 557 HIS 0.002 0.001 HIS A 619 PHE 0.025 0.002 PHE A 444 TYR 0.014 0.002 TYR A 312 ARG 0.004 0.000 ARG B 162 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 4) link_NAG-ASN : angle 2.05924 ( 12) hydrogen bonds : bond 0.12626 ( 443) hydrogen bonds : angle 6.09323 ( 1338) SS BOND : bond 0.00459 ( 2) SS BOND : angle 4.70440 ( 4) covalent geometry : bond 0.00506 ( 8692) covalent geometry : angle 0.61821 (11832) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 SER cc_start: 0.8923 (p) cc_final: 0.8673 (m) REVERT: B 95 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7224 (tm-30) REVERT: B 406 GLN cc_start: 0.7435 (tt0) cc_final: 0.7122 (tt0) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.5313 time to fit residues: 161.7597 Evaluate side-chains 158 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.163280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121520 restraints weight = 32002.774| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.46 r_work: 0.3056 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8698 Z= 0.153 Angle : 0.566 7.353 11848 Z= 0.293 Chirality : 0.041 0.218 1355 Planarity : 0.004 0.034 1483 Dihedral : 5.338 52.680 1234 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.55 % Allowed : 8.68 % Favored : 90.77 % 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: 0.84 (0.26), residues: 1073 helix: 1.79 (0.23), residues: 535 sheet: -1.25 (0.44), residues: 123 loop : -0.45 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 557 HIS 0.003 0.001 HIS B 358 PHE 0.015 0.001 PHE A 444 TYR 0.010 0.001 TYR B 145 ARG 0.005 0.001 ARG A 226 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 4) link_NAG-ASN : angle 1.67503 ( 12) hydrogen bonds : bond 0.04533 ( 443) hydrogen bonds : angle 4.89673 ( 1338) SS BOND : bond 0.00903 ( 2) SS BOND : angle 4.51748 ( 4) covalent geometry : bond 0.00359 ( 8692) covalent geometry : angle 0.55807 (11832) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 177 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 SER cc_start: 0.9235 (t) cc_final: 0.8884 (p) REVERT: A 315 GLU cc_start: 0.7730 (pm20) cc_final: 0.7518 (pm20) REVERT: A 406 SER cc_start: 0.9226 (p) cc_final: 0.8960 (m) REVERT: B 95 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7407 (tm-30) REVERT: B 406 GLN cc_start: 0.7762 (tt0) cc_final: 0.7521 (tt0) REVERT: C 103 ARG cc_start: 0.7398 (ptt90) cc_final: 0.7053 (mtp-110) REVERT: C 117 GLN cc_start: 0.8668 (pt0) cc_final: 0.8331 (pp30) outliers start: 5 outliers final: 2 residues processed: 179 average time/residue: 0.5154 time to fit residues: 123.1903 Evaluate side-chains 156 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 45 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.162656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119005 restraints weight = 32192.044| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.59 r_work: 0.3037 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8698 Z= 0.127 Angle : 0.521 4.351 11848 Z= 0.267 Chirality : 0.040 0.302 1355 Planarity : 0.004 0.047 1483 Dihedral : 5.144 48.786 1234 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.77 % Allowed : 10.22 % Favored : 89.01 % 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: 0.87 (0.26), residues: 1073 helix: 1.92 (0.23), residues: 536 sheet: -1.27 (0.45), residues: 124 loop : -0.59 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 124 HIS 0.002 0.000 HIS B 358 PHE 0.012 0.001 PHE B 398 TYR 0.008 0.001 TYR A 312 ARG 0.008 0.001 ARG C 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 4) link_NAG-ASN : angle 1.74175 ( 12) hydrogen bonds : bond 0.04041 ( 443) hydrogen bonds : angle 4.61100 ( 1338) SS BOND : bond 0.00122 ( 2) SS BOND : angle 2.53233 ( 4) covalent geometry : bond 0.00297 ( 8692) covalent geometry : angle 0.51621 (11832) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 162 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 SER cc_start: 0.9214 (t) cc_final: 0.8873 (p) REVERT: A 406 SER cc_start: 0.9250 (p) cc_final: 0.8960 (m) REVERT: B 95 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7347 (tm-30) REVERT: B 406 GLN cc_start: 0.7768 (tt0) cc_final: 0.7472 (tt0) REVERT: C 117 GLN cc_start: 0.8637 (pt0) cc_final: 0.8373 (pp30) outliers start: 7 outliers final: 5 residues processed: 165 average time/residue: 0.5529 time to fit residues: 124.5454 Evaluate side-chains 160 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 155 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 75 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.157714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.113796 restraints weight = 32291.011| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.54 r_work: 0.2943 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 8698 Z= 0.333 Angle : 0.632 5.100 11848 Z= 0.329 Chirality : 0.045 0.230 1355 Planarity : 0.004 0.028 1483 Dihedral : 5.370 49.702 1234 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.21 % Allowed : 10.33 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1073 helix: 1.56 (0.22), residues: 537 sheet: -1.50 (0.43), residues: 127 loop : -0.77 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 218 HIS 0.004 0.001 HIS A 619 PHE 0.017 0.002 PHE A 541 TYR 0.010 0.002 TYR A 312 ARG 0.007 0.001 ARG A 226 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 4) link_NAG-ASN : angle 2.19100 ( 12) hydrogen bonds : bond 0.04883 ( 443) hydrogen bonds : angle 4.80471 ( 1338) SS BOND : bond 0.00495 ( 2) SS BOND : angle 2.62069 ( 4) covalent geometry : bond 0.00799 ( 8692) covalent geometry : angle 0.62716 (11832) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 SER cc_start: 0.9309 (t) cc_final: 0.8957 (p) REVERT: A 399 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8588 (mp) REVERT: B 95 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7355 (tm-30) REVERT: C 117 GLN cc_start: 0.8701 (pt0) cc_final: 0.8318 (pp30) outliers start: 11 outliers final: 6 residues processed: 156 average time/residue: 0.5087 time to fit residues: 105.9947 Evaluate side-chains 153 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain C residue 24 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 105 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 62 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.162262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118624 restraints weight = 32357.616| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.57 r_work: 0.3041 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8698 Z= 0.116 Angle : 0.519 4.995 11848 Z= 0.266 Chirality : 0.040 0.224 1355 Planarity : 0.004 0.028 1483 Dihedral : 4.790 46.618 1234 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.99 % Allowed : 11.21 % Favored : 87.80 % 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 (0.26), residues: 1073 helix: 1.92 (0.23), residues: 533 sheet: -1.21 (0.45), residues: 123 loop : -0.73 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.002 0.000 HIS B 358 PHE 0.010 0.001 PHE B 398 TYR 0.009 0.001 TYR A 312 ARG 0.003 0.000 ARG A 209 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 4) link_NAG-ASN : angle 1.69090 ( 12) hydrogen bonds : bond 0.03857 ( 443) hydrogen bonds : angle 4.43636 ( 1338) SS BOND : bond 0.00105 ( 2) SS BOND : angle 1.76520 ( 4) covalent geometry : bond 0.00270 ( 8692) covalent geometry : angle 0.51560 (11832) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 SER cc_start: 0.9236 (t) cc_final: 0.8918 (p) REVERT: B 84 PHE cc_start: 0.8337 (t80) cc_final: 0.7964 (t80) REVERT: B 95 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7480 (tm-30) REVERT: C 117 GLN cc_start: 0.8636 (pt0) cc_final: 0.8346 (pp30) outliers start: 9 outliers final: 7 residues processed: 157 average time/residue: 0.4859 time to fit residues: 103.0085 Evaluate side-chains 154 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 65 optimal weight: 0.1980 chunk 23 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.161995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118224 restraints weight = 32397.250| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.56 r_work: 0.2999 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8698 Z= 0.116 Angle : 0.505 4.220 11848 Z= 0.258 Chirality : 0.039 0.213 1355 Planarity : 0.003 0.028 1483 Dihedral : 4.530 44.669 1234 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.10 % Allowed : 11.76 % Favored : 87.14 % 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: 0.97 (0.26), residues: 1073 helix: 2.09 (0.23), residues: 532 sheet: -1.23 (0.45), residues: 128 loop : -0.61 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 174 HIS 0.002 0.000 HIS B 358 PHE 0.014 0.001 PHE B 398 TYR 0.008 0.001 TYR B 385 ARG 0.007 0.000 ARG B 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 4) link_NAG-ASN : angle 1.55480 ( 12) hydrogen bonds : bond 0.03587 ( 443) hydrogen bonds : angle 4.29775 ( 1338) SS BOND : bond 0.00150 ( 2) SS BOND : angle 2.40571 ( 4) covalent geometry : bond 0.00272 ( 8692) covalent geometry : angle 0.50077 (11832) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 SER cc_start: 0.9209 (t) cc_final: 0.8875 (p) REVERT: A 406 SER cc_start: 0.9258 (p) cc_final: 0.8886 (m) REVERT: B 84 PHE cc_start: 0.8336 (t80) cc_final: 0.7993 (t80) REVERT: B 95 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7532 (tm-30) REVERT: B 227 GLN cc_start: 0.7832 (tp40) cc_final: 0.7628 (tp-100) REVERT: C 117 GLN cc_start: 0.8634 (pt0) cc_final: 0.8331 (pp30) outliers start: 10 outliers final: 8 residues processed: 157 average time/residue: 0.6404 time to fit residues: 133.2636 Evaluate side-chains 155 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.162292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118790 restraints weight = 32037.112| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.52 r_work: 0.3024 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8698 Z= 0.135 Angle : 0.511 4.609 11848 Z= 0.261 Chirality : 0.039 0.211 1355 Planarity : 0.004 0.032 1483 Dihedral : 4.527 44.646 1234 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.88 % Allowed : 12.42 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1073 helix: 2.06 (0.23), residues: 533 sheet: -1.19 (0.45), residues: 128 loop : -0.58 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.002 0.001 HIS A 538 PHE 0.010 0.001 PHE B 398 TYR 0.009 0.001 TYR B 390 ARG 0.005 0.000 ARG A 429 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 4) link_NAG-ASN : angle 1.56993 ( 12) hydrogen bonds : bond 0.03602 ( 443) hydrogen bonds : angle 4.27991 ( 1338) SS BOND : bond 0.00269 ( 2) SS BOND : angle 2.58414 ( 4) covalent geometry : bond 0.00322 ( 8692) covalent geometry : angle 0.50687 (11832) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 SER cc_start: 0.9218 (t) cc_final: 0.8878 (p) REVERT: A 406 SER cc_start: 0.9252 (p) cc_final: 0.8887 (m) REVERT: B 84 PHE cc_start: 0.8343 (t80) cc_final: 0.7986 (t80) REVERT: B 95 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7537 (tm-30) REVERT: B 227 GLN cc_start: 0.7840 (tp40) cc_final: 0.7633 (tp-100) REVERT: C 117 GLN cc_start: 0.8652 (pt0) cc_final: 0.8349 (pp30) outliers start: 8 outliers final: 7 residues processed: 156 average time/residue: 0.5117 time to fit residues: 108.0931 Evaluate side-chains 154 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.162064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118420 restraints weight = 32185.170| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.54 r_work: 0.2979 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8698 Z= 0.161 Angle : 0.523 4.400 11848 Z= 0.267 Chirality : 0.040 0.266 1355 Planarity : 0.004 0.029 1483 Dihedral : 4.702 45.561 1234 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.99 % Allowed : 12.20 % Favored : 86.81 % 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: 0.94 (0.26), residues: 1073 helix: 2.02 (0.23), residues: 536 sheet: -1.17 (0.43), residues: 134 loop : -0.61 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 318 HIS 0.003 0.001 HIS B 358 PHE 0.011 0.001 PHE B 398 TYR 0.006 0.001 TYR B 385 ARG 0.006 0.001 ARG A 429 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 4) link_NAG-ASN : angle 1.97692 ( 12) hydrogen bonds : bond 0.03698 ( 443) hydrogen bonds : angle 4.29340 ( 1338) SS BOND : bond 0.00143 ( 2) SS BOND : angle 2.48588 ( 4) covalent geometry : bond 0.00386 ( 8692) covalent geometry : angle 0.51794 (11832) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 SER cc_start: 0.9243 (t) cc_final: 0.8898 (p) REVERT: B 95 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7542 (tm-30) REVERT: C 117 GLN cc_start: 0.8656 (pt0) cc_final: 0.8328 (pp30) outliers start: 9 outliers final: 8 residues processed: 152 average time/residue: 0.5071 time to fit residues: 104.1109 Evaluate side-chains 152 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 4 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.164503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123905 restraints weight = 32100.877| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.38 r_work: 0.3034 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8698 Z= 0.128 Angle : 0.506 4.591 11848 Z= 0.258 Chirality : 0.039 0.220 1355 Planarity : 0.004 0.028 1483 Dihedral : 4.557 45.249 1234 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.99 % Allowed : 12.31 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.26), residues: 1073 helix: 2.13 (0.23), residues: 532 sheet: -1.17 (0.43), residues: 134 loop : -0.56 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 190 HIS 0.001 0.000 HIS A 236 PHE 0.013 0.001 PHE B 398 TYR 0.007 0.001 TYR B 385 ARG 0.006 0.000 ARG B 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 4) link_NAG-ASN : angle 1.75674 ( 12) hydrogen bonds : bond 0.03535 ( 443) hydrogen bonds : angle 4.23166 ( 1338) SS BOND : bond 0.00135 ( 2) SS BOND : angle 2.21232 ( 4) covalent geometry : bond 0.00306 ( 8692) covalent geometry : angle 0.50116 (11832) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 SER cc_start: 0.9207 (t) cc_final: 0.8869 (p) REVERT: A 406 SER cc_start: 0.9252 (p) cc_final: 0.8880 (m) REVERT: B 84 PHE cc_start: 0.8357 (t80) cc_final: 0.8032 (t80) REVERT: B 95 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7560 (tm-30) REVERT: B 447 VAL cc_start: 0.7707 (t) cc_final: 0.7426 (m) REVERT: C 117 GLN cc_start: 0.8646 (pt0) cc_final: 0.8354 (pp30) outliers start: 9 outliers final: 8 residues processed: 149 average time/residue: 0.4993 time to fit residues: 103.1556 Evaluate side-chains 148 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 77 optimal weight: 0.0970 chunk 45 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 chunk 87 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.164923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.127380 restraints weight = 31979.914| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.30 r_work: 0.3103 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8698 Z= 0.115 Angle : 0.499 4.312 11848 Z= 0.255 Chirality : 0.039 0.211 1355 Planarity : 0.004 0.073 1483 Dihedral : 4.457 44.161 1234 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.88 % Allowed : 12.64 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1073 helix: 2.16 (0.23), residues: 532 sheet: -1.14 (0.44), residues: 130 loop : -0.57 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 190 HIS 0.001 0.000 HIS B 358 PHE 0.014 0.001 PHE B 398 TYR 0.007 0.001 TYR B 385 ARG 0.009 0.001 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 4) link_NAG-ASN : angle 1.67147 ( 12) hydrogen bonds : bond 0.03387 ( 443) hydrogen bonds : angle 4.16106 ( 1338) SS BOND : bond 0.00067 ( 2) SS BOND : angle 2.08422 ( 4) covalent geometry : bond 0.00274 ( 8692) covalent geometry : angle 0.49531 (11832) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 SER cc_start: 0.9167 (t) cc_final: 0.8859 (p) REVERT: A 279 GLN cc_start: 0.8539 (mt0) cc_final: 0.8316 (mt0) REVERT: A 406 SER cc_start: 0.9185 (p) cc_final: 0.8859 (m) REVERT: B 84 PHE cc_start: 0.8321 (t80) cc_final: 0.7991 (t80) REVERT: B 95 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7567 (tm-30) REVERT: C 117 GLN cc_start: 0.8637 (pt0) cc_final: 0.8395 (pp30) outliers start: 8 outliers final: 8 residues processed: 155 average time/residue: 0.5098 time to fit residues: 112.5702 Evaluate side-chains 155 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 455 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 70 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.163681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122898 restraints weight = 31919.302| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.36 r_work: 0.2991 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8698 Z= 0.162 Angle : 0.520 4.216 11848 Z= 0.268 Chirality : 0.040 0.211 1355 Planarity : 0.004 0.057 1483 Dihedral : 4.562 45.023 1234 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.99 % Allowed : 12.64 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1073 helix: 2.13 (0.23), residues: 532 sheet: -1.17 (0.44), residues: 132 loop : -0.60 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 190 HIS 0.002 0.001 HIS A 538 PHE 0.016 0.001 PHE A 544 TYR 0.009 0.001 TYR B 390 ARG 0.007 0.001 ARG A 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 4) link_NAG-ASN : angle 1.80278 ( 12) hydrogen bonds : bond 0.03636 ( 443) hydrogen bonds : angle 4.22847 ( 1338) SS BOND : bond 0.00158 ( 2) SS BOND : angle 2.19997 ( 4) covalent geometry : bond 0.00392 ( 8692) covalent geometry : angle 0.51582 (11832) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11788.02 seconds wall clock time: 207 minutes 30.29 seconds (12450.29 seconds total)