Starting phenix.real_space_refine on Sat Jun 14 16:10:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iro_35681/06_2025/8iro_35681_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iro_35681/06_2025/8iro_35681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iro_35681/06_2025/8iro_35681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iro_35681/06_2025/8iro_35681.map" model { file = "/net/cci-nas-00/data/ceres_data/8iro_35681/06_2025/8iro_35681_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iro_35681/06_2025/8iro_35681_trim.cif" } resolution = 2.7 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= 0.007 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 52 5.16 5 C 5300 2.51 5 N 1316 2.21 5 O 1474 1.98 5 H 8208 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16350 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "A" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.83, per 1000 atoms: 0.54 Number of scatterers: 16350 At special positions: 0 Unit cell: (94.461, 108.077, 101.269, 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 52 16.00 O 1474 8.00 N 1316 7.00 C 5300 6.00 H 8208 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 123 " distance=2.04 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 123 " distance=2.04 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 287 " distance=2.03 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 270 " " NAG D 1 " - " ASN B 270 " Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 1.6 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 68.5% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 46 through 61 Processing helix chain 'B' and resid 62 through 74 removed outlier: 4.779A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 117 through 150 Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.952A pdb=" N ALA B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 Processing helix chain 'B' and resid 203 through 209 removed outlier: 3.574A pdb=" N LEU B 207 " --> pdb=" O PHE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 232 removed outlier: 4.400A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 294 through 313 Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 355 removed outlier: 3.906A pdb=" N LYS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 375 removed outlier: 4.341A pdb=" N ASN B 375 " --> pdb=" O SER B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 376 through 405 removed outlier: 3.718A pdb=" N TRP B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 444 through 451 removed outlier: 4.049A pdb=" N GLY B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 480 through 496 Proline residue: B 486 - end of helix Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.659A pdb=" N THR B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 523 Proline residue: B 512 - end of helix removed outlier: 3.771A pdb=" N MET B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 525 through 541 Processing helix chain 'B' and resid 541 through 554 Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 62 through 74 removed outlier: 4.779A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 117 through 150 Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.953A pdb=" N ALA A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.574A pdb=" N LEU A 207 " --> pdb=" O PHE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 232 removed outlier: 4.399A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 294 through 313 Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.907A pdb=" N LYS A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 removed outlier: 4.340A pdb=" N ASN A 375 " --> pdb=" O SER A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 405 removed outlier: 3.717A pdb=" N TRP A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 444 through 451 removed outlier: 4.049A pdb=" N GLY A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 480 through 496 Proline residue: A 486 - end of helix Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.659A pdb=" N THR A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 523 Proline residue: A 512 - end of helix removed outlier: 3.770A pdb=" N MET A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 525 through 541 Processing helix chain 'A' and resid 541 through 554 Processing sheet with id=AA1, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA3, first strand: chain 'B' and resid 241 through 242 Processing sheet with id=AA4, first strand: chain 'B' and resid 274 through 275 removed outlier: 3.692A pdb=" N SER B 274 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 274 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 286 through 287 removed outlier: 3.933A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA8, first strand: chain 'A' and resid 241 through 242 512 hydrogen bonds defined for protein. 1452 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: 6.47 Time building geometry restraints manager: 5.49 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: 8204 1.03 - 1.23: 39 1.23 - 1.42: 3387 1.42 - 1.62: 4822 1.62 - 1.82: 84 Bond restraints: 16536 Sorted by residual: bond pdb=" C6 ZEA B 701 " pdb=" N10 ZEA B 701 " ideal model delta sigma weight residual 1.336 1.464 -0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C6 ZEA A 701 " pdb=" N10 ZEA A 701 " ideal model delta sigma weight residual 1.336 1.464 -0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C13 ZEA A 701 " pdb=" C14 ZEA A 701 " ideal model delta sigma weight residual 1.502 1.589 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C13 ZEA B 701 " pdb=" C14 ZEA B 701 " ideal model delta sigma weight residual 1.502 1.588 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.73e+00 ... (remaining 16531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.22: 29910 8.22 - 16.45: 6 16.45 - 24.67: 0 24.67 - 32.90: 0 32.90 - 41.12: 6 Bond angle restraints: 29922 Sorted by residual: angle pdb=" C12 ZEA B 701 " pdb=" C13 ZEA B 701 " pdb=" C15 ZEA B 701 " ideal model delta sigma weight residual 125.58 166.70 -41.12 3.00e+00 1.11e-01 1.88e+02 angle pdb=" C12 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 125.58 166.66 -41.08 3.00e+00 1.11e-01 1.88e+02 angle pdb=" C12 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C14 ZEA A 701 " ideal model delta sigma weight residual 121.92 87.45 34.47 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C12 ZEA B 701 " pdb=" C13 ZEA B 701 " pdb=" C14 ZEA B 701 " ideal model delta sigma weight residual 121.92 87.48 34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C14 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 112.50 79.23 33.27 3.00e+00 1.11e-01 1.23e+02 ... (remaining 29917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.96: 7423 24.96 - 49.93: 328 49.93 - 74.89: 123 74.89 - 99.86: 6 99.86 - 124.82: 2 Dihedral angle restraints: 7882 sinusoidal: 4248 harmonic: 3634 Sorted by residual: dihedral pdb=" CA VAL A 484 " pdb=" C VAL A 484 " pdb=" N GLY A 485 " pdb=" CA GLY A 485 " ideal model delta harmonic sigma weight residual 180.00 141.09 38.91 0 5.00e+00 4.00e-02 6.05e+01 dihedral pdb=" CA VAL B 484 " pdb=" C VAL B 484 " pdb=" N GLY B 485 " pdb=" CA GLY B 485 " ideal model delta harmonic sigma weight residual 180.00 141.10 38.90 0 5.00e+00 4.00e-02 6.05e+01 dihedral pdb=" CA PHE A 332 " pdb=" C PHE A 332 " pdb=" N ARG A 333 " pdb=" CA ARG A 333 " ideal model delta harmonic sigma weight residual 180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 7879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1303 0.097 - 0.194: 49 0.194 - 0.291: 3 0.291 - 0.388: 0 0.388 - 0.486: 1 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 270 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.89 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 270 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR A 250 " pdb=" CA THR A 250 " pdb=" OG1 THR A 250 " pdb=" CG2 THR A 250 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1353 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 270 " -0.091 2.00e-02 2.50e+03 6.88e-02 7.09e+01 pdb=" CG ASN A 270 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 270 " 0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN A 270 " 0.073 2.00e-02 2.50e+03 pdb="HD21 ASN A 270 " 0.045 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO A 487 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO B 487 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.035 5.00e-02 4.00e+02 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 440 2.13 - 2.74: 30686 2.74 - 3.36: 50422 3.36 - 3.98: 64783 3.98 - 4.60: 101898 Nonbonded interactions: 248229 Sorted by model distance: nonbonded pdb="HD22 ASN B 67 " pdb=" OG1 THR B 135 " model vdw 1.507 2.450 nonbonded pdb="HD22 ASN A 67 " pdb=" OG1 THR A 135 " model vdw 1.507 2.450 nonbonded pdb="HH22 ARG B 333 " pdb=" OD1 ASP B 347 " model vdw 1.550 2.450 nonbonded pdb="HH22 ARG A 333 " pdb=" OD1 ASP A 347 " model vdw 1.550 2.450 nonbonded pdb=" O PHE B 419 " pdb=" HG SER B 423 " model vdw 1.553 2.450 ... (remaining 248224 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.320 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 39.990 Find NCS groups from input model: 0.440 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: 0.000 Load rotamer database and sin/cos tables:27.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 : 0.006 0.226 8340 Z= 0.298 Angle : 1.097 41.124 11362 Z= 0.458 Chirality : 0.045 0.486 1356 Planarity : 0.005 0.062 1400 Dihedral : 13.581 124.823 2938 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.26), residues: 1076 helix: 1.28 (0.21), residues: 664 sheet: -4.84 (0.53), residues: 20 loop : -0.47 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.002 0.001 HIS B 350 PHE 0.012 0.002 PHE A 414 TYR 0.013 0.002 TYR B 524 ARG 0.002 0.000 ARG B 333 Details of bonding type rmsd link_NAG-ASN : bond 0.16013 ( 2) link_NAG-ASN : angle 2.88791 ( 6) link_BETA1-4 : bond 0.00442 ( 2) link_BETA1-4 : angle 2.61143 ( 6) hydrogen bonds : bond 0.11821 ( 508) hydrogen bonds : angle 5.30231 ( 1452) SS BOND : bond 0.00413 ( 8) SS BOND : angle 3.15153 ( 16) covalent geometry : bond 0.00595 ( 8328) covalent geometry : angle 1.08826 (11334) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7851 (m-30) cc_final: 0.7624 (m-30) REVERT: B 440 THR cc_start: 0.8584 (p) cc_final: 0.8325 (t) REVERT: A 390 ASP cc_start: 0.7851 (m-30) cc_final: 0.7631 (m-30) REVERT: A 440 THR cc_start: 0.8581 (p) cc_final: 0.8315 (t) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 2.0360 time to fit residues: 200.8126 Evaluate side-chains 75 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.122866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.100565 restraints weight = 25714.238| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.38 r_work: 0.3009 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8340 Z= 0.133 Angle : 1.002 36.533 11362 Z= 0.406 Chirality : 0.039 0.167 1356 Planarity : 0.005 0.061 1400 Dihedral : 8.372 107.358 1236 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.70 % Allowed : 5.59 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1076 helix: 1.50 (0.20), residues: 670 sheet: -4.48 (0.63), residues: 20 loop : -0.62 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.003 0.001 HIS A 360 PHE 0.010 0.001 PHE B 414 TYR 0.009 0.001 TYR B 418 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 2) link_NAG-ASN : angle 1.71963 ( 6) link_BETA1-4 : bond 0.00254 ( 2) link_BETA1-4 : angle 3.18554 ( 6) hydrogen bonds : bond 0.04659 ( 508) hydrogen bonds : angle 4.66678 ( 1452) SS BOND : bond 0.00215 ( 8) SS BOND : angle 1.58416 ( 16) covalent geometry : bond 0.00287 ( 8328) covalent geometry : angle 0.99838 (11334) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7840 (m-30) cc_final: 0.7627 (m-30) REVERT: B 440 THR cc_start: 0.8652 (p) cc_final: 0.8104 (t) REVERT: B 494 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7731 (mtp) REVERT: A 390 ASP cc_start: 0.7835 (m-30) cc_final: 0.7625 (m-30) REVERT: A 440 THR cc_start: 0.8643 (p) cc_final: 0.8090 (t) REVERT: A 494 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7757 (mtp) outliers start: 6 outliers final: 1 residues processed: 85 average time/residue: 2.1869 time to fit residues: 201.0078 Evaluate side-chains 85 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 3.9990 chunk 88 optimal weight: 0.0070 chunk 98 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.8400 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.124683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.102136 restraints weight = 25787.187| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.44 r_work: 0.2975 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8340 Z= 0.121 Angle : 0.987 36.652 11362 Z= 0.391 Chirality : 0.039 0.156 1356 Planarity : 0.004 0.061 1400 Dihedral : 7.705 97.546 1236 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.93 % Allowed : 6.64 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1076 helix: 1.66 (0.20), residues: 670 sheet: -4.45 (0.63), residues: 20 loop : -0.71 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.001 0.001 HIS A 360 PHE 0.010 0.001 PHE B 414 TYR 0.008 0.001 TYR B 418 ARG 0.001 0.000 ARG A 36 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 2) link_NAG-ASN : angle 1.95085 ( 6) link_BETA1-4 : bond 0.00454 ( 2) link_BETA1-4 : angle 3.18117 ( 6) hydrogen bonds : bond 0.04210 ( 508) hydrogen bonds : angle 4.49565 ( 1452) SS BOND : bond 0.00579 ( 8) SS BOND : angle 1.17490 ( 16) covalent geometry : bond 0.00262 ( 8328) covalent geometry : angle 0.98301 (11334) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 CYS cc_start: 0.6452 (OUTLIER) cc_final: 0.6227 (t) REVERT: B 390 ASP cc_start: 0.7822 (m-30) cc_final: 0.7575 (m-30) REVERT: B 440 THR cc_start: 0.8598 (p) cc_final: 0.8027 (t) REVERT: A 123 CYS cc_start: 0.6451 (OUTLIER) cc_final: 0.6232 (t) REVERT: A 390 ASP cc_start: 0.7825 (m-30) cc_final: 0.7591 (m-30) REVERT: A 440 THR cc_start: 0.8615 (p) cc_final: 0.8043 (t) outliers start: 8 outliers final: 1 residues processed: 88 average time/residue: 2.1110 time to fit residues: 200.9568 Evaluate side-chains 84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 319 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** 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 = 0.3363 r_free = 0.3363 target = 0.124294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.101960 restraints weight = 25607.887| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.42 r_work: 0.2973 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8340 Z= 0.140 Angle : 0.995 36.937 11362 Z= 0.396 Chirality : 0.039 0.163 1356 Planarity : 0.005 0.060 1400 Dihedral : 7.185 84.977 1236 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.53 % Favored : 96.28 % Rotamer: Outliers : 1.17 % Allowed : 7.34 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1076 helix: 1.69 (0.20), residues: 670 sheet: -4.38 (0.67), residues: 20 loop : -0.73 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.002 0.001 HIS B 350 PHE 0.010 0.001 PHE A 414 TYR 0.009 0.001 TYR B 388 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 2) link_NAG-ASN : angle 1.74830 ( 6) link_BETA1-4 : bond 0.00362 ( 2) link_BETA1-4 : angle 3.32459 ( 6) hydrogen bonds : bond 0.04252 ( 508) hydrogen bonds : angle 4.39125 ( 1452) SS BOND : bond 0.00191 ( 8) SS BOND : angle 1.95322 ( 16) covalent geometry : bond 0.00318 ( 8328) covalent geometry : angle 0.98971 (11334) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 CYS cc_start: 0.6615 (OUTLIER) cc_final: 0.6339 (t) REVERT: B 390 ASP cc_start: 0.7795 (m-30) cc_final: 0.7546 (m-30) REVERT: B 440 THR cc_start: 0.8607 (p) cc_final: 0.8013 (t) REVERT: B 451 GLU cc_start: 0.8117 (tp30) cc_final: 0.7554 (mp0) REVERT: B 494 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7578 (mtp) REVERT: A 123 CYS cc_start: 0.6543 (OUTLIER) cc_final: 0.6313 (t) REVERT: A 390 ASP cc_start: 0.7799 (m-30) cc_final: 0.7563 (m-30) REVERT: A 440 THR cc_start: 0.8605 (p) cc_final: 0.8009 (t) REVERT: A 494 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7582 (mtp) REVERT: A 548 GLU cc_start: 0.6439 (tt0) cc_final: 0.6213 (tt0) outliers start: 10 outliers final: 4 residues processed: 92 average time/residue: 2.0853 time to fit residues: 207.7698 Evaluate side-chains 92 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** 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 = 0.3328 r_free = 0.3328 target = 0.121648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.099187 restraints weight = 26036.828| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.41 r_work: 0.2972 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8340 Z= 0.196 Angle : 1.021 37.308 11362 Z= 0.414 Chirality : 0.041 0.157 1356 Planarity : 0.005 0.059 1400 Dihedral : 6.489 60.199 1236 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.44 % Favored : 96.38 % Rotamer: Outliers : 1.63 % Allowed : 8.62 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.25), residues: 1076 helix: 1.50 (0.20), residues: 670 sheet: -4.42 (0.63), residues: 20 loop : -0.84 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 298 HIS 0.002 0.001 HIS A 360 PHE 0.011 0.002 PHE B 414 TYR 0.010 0.002 TYR B 388 ARG 0.002 0.000 ARG A 36 Details of bonding type rmsd link_NAG-ASN : bond 0.00591 ( 2) link_NAG-ASN : angle 1.90102 ( 6) link_BETA1-4 : bond 0.00260 ( 2) link_BETA1-4 : angle 4.06924 ( 6) hydrogen bonds : bond 0.04682 ( 508) hydrogen bonds : angle 4.42848 ( 1452) SS BOND : bond 0.00271 ( 8) SS BOND : angle 1.92058 ( 16) covalent geometry : bond 0.00461 ( 8328) covalent geometry : angle 1.01476 (11334) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 CYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6379 (t) REVERT: B 390 ASP cc_start: 0.7803 (m-30) cc_final: 0.7590 (m-30) REVERT: B 440 THR cc_start: 0.8668 (p) cc_final: 0.8020 (t) REVERT: B 451 GLU cc_start: 0.8147 (tp30) cc_final: 0.7560 (mp0) REVERT: B 494 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7558 (mtp) REVERT: A 123 CYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6381 (t) REVERT: A 390 ASP cc_start: 0.7808 (m-30) cc_final: 0.7594 (m-30) REVERT: A 440 THR cc_start: 0.8650 (p) cc_final: 0.8013 (t) REVERT: A 494 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7568 (mtp) outliers start: 14 outliers final: 4 residues processed: 86 average time/residue: 2.1059 time to fit residues: 195.6958 Evaluate side-chains 84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** 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 = 0.3377 r_free = 0.3377 target = 0.125321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.103028 restraints weight = 25213.857| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.44 r_work: 0.2964 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8340 Z= 0.146 Angle : 0.995 37.266 11362 Z= 0.397 Chirality : 0.039 0.160 1356 Planarity : 0.005 0.060 1400 Dihedral : 5.570 39.228 1236 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.09 % Favored : 95.72 % Rotamer: Outliers : 1.28 % Allowed : 9.67 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.99 (0.26), residues: 1076 helix: 1.63 (0.20), residues: 670 sheet: -4.53 (0.61), residues: 20 loop : -0.76 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.002 0.001 HIS A 360 PHE 0.011 0.001 PHE A 414 TYR 0.009 0.001 TYR B 388 ARG 0.002 0.000 ARG B 333 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 2) link_NAG-ASN : angle 2.12638 ( 6) link_BETA1-4 : bond 0.00227 ( 2) link_BETA1-4 : angle 4.52208 ( 6) hydrogen bonds : bond 0.04210 ( 508) hydrogen bonds : angle 4.34686 ( 1452) SS BOND : bond 0.00261 ( 8) SS BOND : angle 1.80978 ( 16) covalent geometry : bond 0.00336 ( 8328) covalent geometry : angle 0.98718 (11334) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 CYS cc_start: 0.6738 (OUTLIER) cc_final: 0.6433 (t) REVERT: B 390 ASP cc_start: 0.7807 (m-30) cc_final: 0.7560 (m-30) REVERT: B 440 THR cc_start: 0.8663 (p) cc_final: 0.8023 (t) REVERT: B 494 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7512 (mtp) REVERT: A 123 CYS cc_start: 0.6716 (OUTLIER) cc_final: 0.6418 (t) REVERT: A 390 ASP cc_start: 0.7813 (m-30) cc_final: 0.7570 (m-30) REVERT: A 440 THR cc_start: 0.8643 (p) cc_final: 0.7999 (t) REVERT: A 494 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7518 (mtp) outliers start: 11 outliers final: 1 residues processed: 86 average time/residue: 2.1364 time to fit residues: 198.4095 Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 19 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.125111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.102792 restraints weight = 25280.426| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.48 r_work: 0.2985 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8340 Z= 0.142 Angle : 0.991 37.211 11362 Z= 0.395 Chirality : 0.039 0.170 1356 Planarity : 0.005 0.060 1400 Dihedral : 5.411 39.633 1236 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.09 % Favored : 95.72 % Rotamer: Outliers : 1.05 % Allowed : 10.26 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.03 (0.26), residues: 1076 helix: 1.64 (0.20), residues: 670 sheet: -4.40 (0.67), residues: 20 loop : -0.72 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 482 HIS 0.002 0.001 HIS A 350 PHE 0.011 0.001 PHE A 414 TYR 0.009 0.001 TYR B 388 ARG 0.001 0.000 ARG A 36 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 2) link_NAG-ASN : angle 2.25057 ( 6) link_BETA1-4 : bond 0.00019 ( 2) link_BETA1-4 : angle 4.04741 ( 6) hydrogen bonds : bond 0.04197 ( 508) hydrogen bonds : angle 4.31957 ( 1452) SS BOND : bond 0.00258 ( 8) SS BOND : angle 1.83065 ( 16) covalent geometry : bond 0.00323 ( 8328) covalent geometry : angle 0.98368 (11334) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 CYS cc_start: 0.6734 (OUTLIER) cc_final: 0.6398 (t) REVERT: B 390 ASP cc_start: 0.7820 (m-30) cc_final: 0.7589 (m-30) REVERT: B 440 THR cc_start: 0.8651 (p) cc_final: 0.8000 (t) REVERT: B 494 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7430 (mtp) REVERT: A 123 CYS cc_start: 0.6773 (OUTLIER) cc_final: 0.6454 (t) REVERT: A 390 ASP cc_start: 0.7804 (m-30) cc_final: 0.7576 (m-30) REVERT: A 440 THR cc_start: 0.8648 (p) cc_final: 0.7995 (t) REVERT: A 494 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7494 (mtp) outliers start: 9 outliers final: 3 residues processed: 88 average time/residue: 2.1896 time to fit residues: 208.8832 Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** 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 = 0.3367 r_free = 0.3367 target = 0.124645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.102348 restraints weight = 25584.290| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.43 r_work: 0.2972 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8340 Z= 0.134 Angle : 0.984 37.127 11362 Z= 0.391 Chirality : 0.039 0.180 1356 Planarity : 0.005 0.060 1400 Dihedral : 5.302 39.592 1236 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.18 % Favored : 95.63 % Rotamer: Outliers : 1.05 % Allowed : 10.72 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.08 (0.26), residues: 1076 helix: 1.68 (0.20), residues: 670 sheet: -4.44 (0.66), residues: 20 loop : -0.68 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 482 HIS 0.001 0.001 HIS B 350 PHE 0.011 0.001 PHE A 414 TYR 0.008 0.001 TYR B 388 ARG 0.001 0.000 ARG B 333 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 2) link_NAG-ASN : angle 2.16458 ( 6) link_BETA1-4 : bond 0.00099 ( 2) link_BETA1-4 : angle 3.64299 ( 6) hydrogen bonds : bond 0.04094 ( 508) hydrogen bonds : angle 4.28629 ( 1452) SS BOND : bond 0.00252 ( 8) SS BOND : angle 1.82080 ( 16) covalent geometry : bond 0.00303 ( 8328) covalent geometry : angle 0.97793 (11334) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 CYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6408 (t) REVERT: B 390 ASP cc_start: 0.7814 (m-30) cc_final: 0.7598 (m-30) REVERT: A 123 CYS cc_start: 0.6765 (OUTLIER) cc_final: 0.6392 (t) REVERT: A 390 ASP cc_start: 0.7816 (m-30) cc_final: 0.7581 (m-30) REVERT: A 440 THR cc_start: 0.8633 (p) cc_final: 0.7975 (t) outliers start: 9 outliers final: 4 residues processed: 88 average time/residue: 2.0851 time to fit residues: 198.5832 Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 319 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** 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 = 0.3390 r_free = 0.3390 target = 0.126550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.104320 restraints weight = 25411.088| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.45 r_work: 0.2998 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8340 Z= 0.111 Angle : 0.974 36.987 11362 Z= 0.384 Chirality : 0.038 0.186 1356 Planarity : 0.004 0.058 1400 Dihedral : 5.183 38.166 1236 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.90 % Favored : 95.91 % Rotamer: Outliers : 0.35 % Allowed : 11.54 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.24 (0.26), residues: 1076 helix: 1.80 (0.20), residues: 670 sheet: -4.34 (0.71), residues: 20 loop : -0.62 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.001 0.000 HIS A 364 PHE 0.010 0.001 PHE B 414 TYR 0.009 0.001 TYR A 418 ARG 0.001 0.000 ARG A 333 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 2) link_NAG-ASN : angle 2.03793 ( 6) link_BETA1-4 : bond 0.00223 ( 2) link_BETA1-4 : angle 3.35347 ( 6) hydrogen bonds : bond 0.03845 ( 508) hydrogen bonds : angle 4.21891 ( 1452) SS BOND : bond 0.00235 ( 8) SS BOND : angle 1.77000 ( 16) covalent geometry : bond 0.00245 ( 8328) covalent geometry : angle 0.96912 (11334) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 CYS cc_start: 0.6729 (OUTLIER) cc_final: 0.6380 (t) REVERT: B 390 ASP cc_start: 0.7785 (m-30) cc_final: 0.7568 (m-30) REVERT: B 548 GLU cc_start: 0.6654 (tt0) cc_final: 0.6397 (tt0) REVERT: A 123 CYS cc_start: 0.6795 (OUTLIER) cc_final: 0.6472 (t) REVERT: A 390 ASP cc_start: 0.7795 (m-30) cc_final: 0.7594 (m-30) REVERT: A 548 GLU cc_start: 0.6574 (tt0) cc_final: 0.6326 (tt0) outliers start: 3 outliers final: 0 residues processed: 86 average time/residue: 2.1377 time to fit residues: 198.9631 Evaluate side-chains 83 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain A residue 123 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** 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 = 0.3406 r_free = 0.3406 target = 0.127633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.105572 restraints weight = 24992.550| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.49 r_work: 0.3042 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8340 Z= 0.117 Angle : 0.976 36.938 11362 Z= 0.385 Chirality : 0.038 0.181 1356 Planarity : 0.004 0.058 1400 Dihedral : 5.172 38.804 1236 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.72 % Favored : 96.10 % Rotamer: Outliers : 0.70 % Allowed : 11.31 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.30 (0.26), residues: 1076 helix: 1.83 (0.20), residues: 670 sheet: -4.28 (0.72), residues: 20 loop : -0.55 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.001 0.001 HIS B 350 PHE 0.010 0.001 PHE B 414 TYR 0.011 0.001 TYR A 418 ARG 0.001 0.000 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 2) link_NAG-ASN : angle 1.93729 ( 6) link_BETA1-4 : bond 0.00250 ( 2) link_BETA1-4 : angle 3.22103 ( 6) hydrogen bonds : bond 0.03893 ( 508) hydrogen bonds : angle 4.19603 ( 1452) SS BOND : bond 0.00226 ( 8) SS BOND : angle 1.81617 ( 16) covalent geometry : bond 0.00262 ( 8328) covalent geometry : angle 0.97070 (11334) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 CYS cc_start: 0.6717 (OUTLIER) cc_final: 0.6405 (t) REVERT: B 390 ASP cc_start: 0.7791 (m-30) cc_final: 0.7577 (m-30) REVERT: B 494 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7206 (mpp) REVERT: B 548 GLU cc_start: 0.6648 (tt0) cc_final: 0.6393 (tt0) REVERT: A 123 CYS cc_start: 0.6696 (OUTLIER) cc_final: 0.6389 (t) REVERT: A 390 ASP cc_start: 0.7811 (m-30) cc_final: 0.7598 (m-30) REVERT: A 494 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7213 (mpp) REVERT: A 548 GLU cc_start: 0.6573 (tt0) cc_final: 0.6329 (tt0) outliers start: 6 outliers final: 1 residues processed: 86 average time/residue: 2.0946 time to fit residues: 194.6793 Evaluate side-chains 85 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.1980 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** 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 = 0.3386 r_free = 0.3386 target = 0.126515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.104521 restraints weight = 25816.810| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.45 r_work: 0.3059 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8340 Z= 0.102 Angle : 0.967 36.827 11362 Z= 0.378 Chirality : 0.038 0.181 1356 Planarity : 0.004 0.057 1400 Dihedral : 5.075 40.661 1236 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.09 % Favored : 95.72 % Rotamer: Outliers : 0.58 % Allowed : 11.31 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.49 (0.26), residues: 1076 helix: 1.97 (0.20), residues: 668 sheet: -4.25 (0.73), residues: 20 loop : -0.43 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.001 0.000 HIS A 364 PHE 0.009 0.001 PHE B 414 TYR 0.012 0.001 TYR A 418 ARG 0.001 0.000 ARG B 333 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 2) link_NAG-ASN : angle 1.82978 ( 6) link_BETA1-4 : bond 0.00246 ( 2) link_BETA1-4 : angle 3.03896 ( 6) hydrogen bonds : bond 0.03663 ( 508) hydrogen bonds : angle 4.13681 ( 1452) SS BOND : bond 0.00222 ( 8) SS BOND : angle 1.74835 ( 16) covalent geometry : bond 0.00221 ( 8328) covalent geometry : angle 0.96260 (11334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9666.91 seconds wall clock time: 164 minutes 31.00 seconds (9871.00 seconds total)