Starting phenix.real_space_refine on Sun May 18 00:26:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iro_35681/05_2025/8iro_35681_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iro_35681/05_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_35681/05_2025/8iro_35681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iro_35681/05_2025/8iro_35681.map" model { file = "/net/cci-nas-00/data/ceres_data/8iro_35681/05_2025/8iro_35681_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iro_35681/05_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-5687/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: 7.94, per 1000 atoms: 0.49 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: 4.31 Conformation dependent library (CDL) restraints added in 1.4 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: 1.45 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: 6.56 Time building geometry restraints manager: 5.09 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: 0.840 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: 0.280 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.230 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.040 ------------------------------------------------------------------------------- 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 : 1.159 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: 2.0171 time to fit residues: 199.0487 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 : 1.119 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.127724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.105390 restraints weight = 24755.354| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.44 r_work: 0.3031 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0861 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= 0.133 Angle : 1.003 36.799 11362 Z= 0.406 Chirality : 0.039 0.166 1356 Planarity : 0.005 0.061 1400 Dihedral : 8.404 107.609 1236 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.70 % Allowed : 5.48 % Favored : 93.82 % 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: 1.49 (0.20), residues: 670 sheet: -4.47 (0.63), residues: 20 loop : -0.62 (0.32), 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 0.011 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 0.00596 ( 2) link_NAG-ASN : angle 1.77683 ( 6) link_BETA1-4 : bond 0.00677 ( 2) link_BETA1-4 : angle 3.13298 ( 6) hydrogen bonds : bond 0.04707 ( 508) hydrogen bonds : angle 4.67339 ( 1452) SS BOND : bond 0.00208 ( 8) SS BOND : angle 1.63443 ( 16) covalent geometry : bond 0.00286 ( 8328) covalent geometry : angle 0.99860 (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 : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7810 (m-30) cc_final: 0.7582 (m-30) REVERT: B 440 THR cc_start: 0.8638 (p) cc_final: 0.8098 (t) REVERT: B 494 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7709 (mtp) REVERT: A 390 ASP cc_start: 0.7802 (m-30) cc_final: 0.7597 (m-30) REVERT: A 440 THR cc_start: 0.8651 (p) cc_final: 0.8086 (t) REVERT: A 494 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7704 (mtp) outliers start: 6 outliers final: 0 residues processed: 85 average time/residue: 2.1640 time to fit residues: 198.7687 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 : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 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: 0.8980 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.127506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.105050 restraints weight = 25204.473| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.44 r_work: 0.3032 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8340 Z= 0.129 Angle : 0.990 36.735 11362 Z= 0.394 Chirality : 0.039 0.161 1356 Planarity : 0.004 0.060 1400 Dihedral : 7.740 98.494 1236 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.93 % Allowed : 6.41 % Favored : 92.66 % 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: 1.01 (0.26), residues: 1076 helix: 1.62 (0.20), residues: 670 sheet: -4.43 (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 B 350 PHE 0.010 0.001 PHE B 414 TYR 0.008 0.001 TYR B 388 ARG 0.001 0.000 ARG A 36 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 2) link_NAG-ASN : angle 1.87138 ( 6) link_BETA1-4 : bond 0.00347 ( 2) link_BETA1-4 : angle 3.14991 ( 6) hydrogen bonds : bond 0.04343 ( 508) hydrogen bonds : angle 4.51436 ( 1452) SS BOND : bond 0.00258 ( 8) SS BOND : angle 1.47524 ( 16) covalent geometry : bond 0.00287 ( 8328) covalent geometry : angle 0.98557 (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 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 CYS cc_start: 0.6395 (OUTLIER) cc_final: 0.6187 (t) REVERT: B 390 ASP cc_start: 0.7827 (m-30) cc_final: 0.7580 (m-30) REVERT: B 440 THR cc_start: 0.8607 (p) cc_final: 0.8036 (t) REVERT: A 123 CYS cc_start: 0.6392 (OUTLIER) cc_final: 0.6187 (t) REVERT: A 390 ASP cc_start: 0.7820 (m-30) cc_final: 0.7587 (m-30) REVERT: A 440 THR cc_start: 0.8620 (p) cc_final: 0.8065 (t) outliers start: 8 outliers final: 2 residues processed: 86 average time/residue: 2.2354 time to fit residues: 207.5573 Evaluate side-chains 85 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 319 MET 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: 0.6980 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 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: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.125949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.103668 restraints weight = 25439.592| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.43 r_work: 0.3032 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1181 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 : 0.986 36.934 11362 Z= 0.390 Chirality : 0.039 0.167 1356 Planarity : 0.004 0.060 1400 Dihedral : 7.075 85.022 1236 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.93 % Allowed : 7.46 % Favored : 91.61 % 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: 1.13 (0.26), residues: 1076 helix: 1.74 (0.20), residues: 670 sheet: -4.43 (0.66), 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 289 PHE 0.010 0.001 PHE A 414 TYR 0.008 0.001 TYR B 388 ARG 0.002 0.000 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 2) link_NAG-ASN : angle 1.76797 ( 6) link_BETA1-4 : bond 0.00357 ( 2) link_BETA1-4 : angle 3.29089 ( 6) hydrogen bonds : bond 0.04065 ( 508) hydrogen bonds : angle 4.36902 ( 1452) SS BOND : bond 0.00213 ( 8) SS BOND : angle 1.87780 ( 16) covalent geometry : bond 0.00267 ( 8328) covalent geometry : angle 0.98137 (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 94 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7808 (m-30) cc_final: 0.7548 (m-30) REVERT: B 440 THR cc_start: 0.8599 (p) cc_final: 0.8004 (t) REVERT: B 494 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7644 (mtp) REVERT: A 390 ASP cc_start: 0.7811 (m-30) cc_final: 0.7570 (m-30) REVERT: A 440 THR cc_start: 0.8601 (p) cc_final: 0.8013 (t) REVERT: A 494 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7660 (mtp) REVERT: A 548 GLU cc_start: 0.6369 (tt0) cc_final: 0.6138 (tt0) outliers start: 8 outliers final: 0 residues processed: 90 average time/residue: 2.1187 time to fit residues: 205.8034 Evaluate side-chains 85 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 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: 0.9980 chunk 96 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.124204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.102214 restraints weight = 25468.211| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.35 r_work: 0.2952 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8340 Z= 0.177 Angle : 1.013 37.299 11362 Z= 0.408 Chirality : 0.040 0.161 1356 Planarity : 0.005 0.060 1400 Dihedral : 6.550 66.109 1236 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.16 % Favored : 96.65 % Rotamer: Outliers : 1.17 % Allowed : 8.39 % Favored : 90.44 % 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: 0.94 (0.25), residues: 1076 helix: 1.57 (0.20), residues: 670 sheet: -4.31 (0.69), residues: 20 loop : -0.76 (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 A 414 TYR 0.009 0.002 TYR B 388 ARG 0.002 0.000 ARG B 36 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 2) link_NAG-ASN : angle 1.84362 ( 6) link_BETA1-4 : bond 0.00223 ( 2) link_BETA1-4 : angle 3.85639 ( 6) hydrogen bonds : bond 0.04494 ( 508) hydrogen bonds : angle 4.37996 ( 1452) SS BOND : bond 0.00621 ( 8) SS BOND : angle 1.61674 ( 16) covalent geometry : bond 0.00408 ( 8328) covalent geometry : angle 1.00800 (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 95 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7791 (m-30) cc_final: 0.7554 (m-30) REVERT: B 440 THR cc_start: 0.8667 (p) cc_final: 0.8044 (t) REVERT: B 451 GLU cc_start: 0.8147 (tp30) cc_final: 0.7583 (mp0) REVERT: B 494 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7576 (mtp) REVERT: A 390 ASP cc_start: 0.7800 (m-30) cc_final: 0.7564 (m-30) REVERT: A 440 THR cc_start: 0.8654 (p) cc_final: 0.8044 (t) REVERT: A 494 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7593 (mtp) outliers start: 10 outliers final: 6 residues processed: 91 average time/residue: 2.1002 time to fit residues: 206.3452 Evaluate side-chains 89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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: 2.9990 chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.124297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.101393 restraints weight = 25595.502| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.44 r_work: 0.2965 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8340 Z= 0.123 Angle : 0.991 37.095 11362 Z= 0.392 Chirality : 0.038 0.164 1356 Planarity : 0.004 0.059 1400 Dihedral : 5.604 38.196 1236 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.53 % Favored : 96.28 % Rotamer: Outliers : 1.40 % Allowed : 9.44 % Favored : 89.16 % 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: 1.15 (0.26), residues: 1076 helix: 1.74 (0.20), residues: 670 sheet: -4.46 (0.64), residues: 20 loop : -0.66 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 298 HIS 0.001 0.001 HIS A 360 PHE 0.010 0.001 PHE A 414 TYR 0.008 0.001 TYR B 388 ARG 0.001 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 2) link_NAG-ASN : angle 2.01336 ( 6) link_BETA1-4 : bond 0.00158 ( 2) link_BETA1-4 : angle 4.46104 ( 6) hydrogen bonds : bond 0.04019 ( 508) hydrogen bonds : angle 4.29027 ( 1452) SS BOND : bond 0.00636 ( 8) SS BOND : angle 1.62460 ( 16) covalent geometry : bond 0.00269 ( 8328) covalent geometry : angle 0.98388 (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 95 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 1.091 Fit side-chains REVERT: B 390 ASP cc_start: 0.7774 (m-30) cc_final: 0.7531 (m-30) REVERT: B 440 THR cc_start: 0.8604 (p) cc_final: 0.7968 (t) REVERT: B 494 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7474 (mtp) REVERT: B 548 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.6336 (tt0) REVERT: A 390 ASP cc_start: 0.7780 (m-30) cc_final: 0.7546 (m-30) REVERT: A 440 THR cc_start: 0.8593 (p) cc_final: 0.7945 (t) REVERT: A 494 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7515 (mtp) outliers start: 12 outliers final: 2 residues processed: 89 average time/residue: 2.1183 time to fit residues: 203.1471 Evaluate side-chains 84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain A residue 81 SER 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: 0.9990 chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.124182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.101263 restraints weight = 25488.857| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.44 r_work: 0.2987 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1376 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= 0.127 Angle : 0.983 37.039 11362 Z= 0.389 Chirality : 0.039 0.174 1356 Planarity : 0.004 0.058 1400 Dihedral : 5.368 38.375 1236 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.72 % Favored : 96.10 % Rotamer: Outliers : 1.05 % Allowed : 9.91 % 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: 1.19 (0.26), residues: 1076 helix: 1.76 (0.20), residues: 670 sheet: -4.24 (0.73), residues: 20 loop : -0.62 (0.31), 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 350 PHE 0.010 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 0.00477 ( 2) link_NAG-ASN : angle 2.26460 ( 6) link_BETA1-4 : bond 0.00058 ( 2) link_BETA1-4 : angle 4.13851 ( 6) hydrogen bonds : bond 0.04020 ( 508) hydrogen bonds : angle 4.25595 ( 1452) SS BOND : bond 0.00418 ( 8) SS BOND : angle 1.22430 ( 16) covalent geometry : bond 0.00285 ( 8328) covalent geometry : angle 0.97754 (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 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 1.119 Fit side-chains REVERT: B 390 ASP cc_start: 0.7807 (m-30) cc_final: 0.7582 (m-30) REVERT: B 494 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7433 (mtp) REVERT: B 548 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6365 (tt0) REVERT: A 390 ASP cc_start: 0.7801 (m-30) cc_final: 0.7584 (m-30) REVERT: A 494 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7463 (mtp) REVERT: A 548 GLU cc_start: 0.6575 (tt0) cc_final: 0.6313 (tt0) outliers start: 9 outliers final: 2 residues processed: 87 average time/residue: 2.0510 time to fit residues: 193.3944 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 : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain A residue 81 SER 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: 4.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.127735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.105401 restraints weight = 24868.461| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.50 r_work: 0.2977 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1450 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= 0.131 Angle : 0.982 37.087 11362 Z= 0.390 Chirality : 0.039 0.182 1356 Planarity : 0.004 0.059 1400 Dihedral : 5.293 38.326 1236 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.00 % Favored : 95.82 % Rotamer: Outliers : 1.40 % Allowed : 9.67 % Favored : 88.93 % 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: 1.20 (0.26), residues: 1076 helix: 1.76 (0.20), residues: 670 sheet: -4.33 (0.70), residues: 20 loop : -0.59 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 482 HIS 0.002 0.001 HIS B 350 PHE 0.010 0.001 PHE A 414 TYR 0.008 0.001 TYR B 418 ARG 0.001 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 2) link_NAG-ASN : angle 2.17259 ( 6) link_BETA1-4 : bond 0.00109 ( 2) link_BETA1-4 : angle 3.68372 ( 6) hydrogen bonds : bond 0.04032 ( 508) hydrogen bonds : angle 4.25048 ( 1452) SS BOND : bond 0.00469 ( 8) SS BOND : angle 1.25919 ( 16) covalent geometry : bond 0.00295 ( 8328) covalent geometry : angle 0.97729 (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 95 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7761 (m-30) cc_final: 0.7555 (m-30) REVERT: B 494 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7327 (mtp) REVERT: B 548 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6355 (tt0) REVERT: A 390 ASP cc_start: 0.7763 (m-30) cc_final: 0.7562 (m-30) REVERT: A 494 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7348 (mtp) REVERT: A 548 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6330 (tt0) outliers start: 12 outliers final: 4 residues processed: 87 average time/residue: 2.0816 time to fit residues: 196.0772 Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 548 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3358 r_free = 0.3358 target = 0.123611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.101227 restraints weight = 25755.354| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.41 r_work: 0.2998 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8340 Z= 0.152 Angle : 0.997 37.220 11362 Z= 0.400 Chirality : 0.039 0.182 1356 Planarity : 0.005 0.059 1400 Dihedral : 5.332 39.208 1236 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.72 % Favored : 96.10 % Rotamer: Outliers : 1.17 % Allowed : 10.02 % Favored : 88.81 % 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: 1.14 (0.26), residues: 1076 helix: 1.66 (0.20), residues: 670 sheet: -4.31 (0.70), residues: 20 loop : -0.53 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 298 HIS 0.002 0.001 HIS B 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 0.00465 ( 2) link_NAG-ASN : angle 2.08703 ( 6) link_BETA1-4 : bond 0.00205 ( 2) link_BETA1-4 : angle 3.57016 ( 6) hydrogen bonds : bond 0.04218 ( 508) hydrogen bonds : angle 4.27031 ( 1452) SS BOND : bond 0.00717 ( 8) SS BOND : angle 1.80989 ( 16) covalent geometry : bond 0.00348 ( 8328) covalent geometry : angle 0.99112 (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 89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7823 (m-30) cc_final: 0.7609 (m-30) REVERT: B 548 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6414 (tt0) REVERT: A 390 ASP cc_start: 0.7835 (m-30) cc_final: 0.7626 (m-30) REVERT: A 548 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6410 (tt0) outliers start: 10 outliers final: 4 residues processed: 83 average time/residue: 2.1745 time to fit residues: 194.2912 Evaluate side-chains 84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 548 GLU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 548 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 89 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 53 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.129945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.108095 restraints weight = 24714.547| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.45 r_work: 0.3044 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8340 Z= 0.101 Angle : 0.974 36.844 11362 Z= 0.384 Chirality : 0.038 0.189 1356 Planarity : 0.004 0.057 1400 Dihedral : 5.154 39.652 1236 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.18 % Favored : 95.63 % Rotamer: Outliers : 0.35 % Allowed : 10.96 % 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: 1.39 (0.26), residues: 1076 helix: 1.87 (0.20), residues: 670 sheet: -4.27 (0.73), residues: 20 loop : -0.45 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.001 0.000 HIS A 364 PHE 0.010 0.001 PHE A 414 TYR 0.013 0.001 TYR A 418 ARG 0.001 0.000 ARG B 333 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 2) link_NAG-ASN : angle 2.02456 ( 6) link_BETA1-4 : bond 0.00230 ( 2) link_BETA1-4 : angle 3.27490 ( 6) hydrogen bonds : bond 0.03716 ( 508) hydrogen bonds : angle 4.18776 ( 1452) SS BOND : bond 0.00608 ( 8) SS BOND : angle 1.19481 ( 16) covalent geometry : bond 0.00217 ( 8328) covalent geometry : angle 0.97027 (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 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 1.137 Fit side-chains REVERT: B 390 ASP cc_start: 0.7807 (m-30) cc_final: 0.7583 (m-30) REVERT: B 548 GLU cc_start: 0.6708 (tt0) cc_final: 0.6463 (tt0) REVERT: A 390 ASP cc_start: 0.7820 (m-30) cc_final: 0.7602 (m-30) REVERT: A 548 GLU cc_start: 0.6732 (tt0) cc_final: 0.6450 (tt0) outliers start: 3 outliers final: 0 residues processed: 88 average time/residue: 2.1185 time to fit residues: 201.4366 Evaluate side-chains 80 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 53 optimal weight: 0.2980 chunk 43 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.125491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.102963 restraints weight = 25555.599| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.44 r_work: 0.3056 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1675 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= 0.104 Angle : 0.973 36.812 11362 Z= 0.382 Chirality : 0.038 0.183 1356 Planarity : 0.004 0.056 1400 Dihedral : 5.122 41.673 1236 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.09 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 11.77 % 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: 1.52 (0.26), residues: 1076 helix: 1.95 (0.20), residues: 668 sheet: -4.16 (0.76), residues: 20 loop : -0.32 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.001 0.001 HIS A 364 PHE 0.009 0.001 PHE A 414 TYR 0.013 0.001 TYR A 418 ARG 0.001 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 2) link_NAG-ASN : angle 1.89799 ( 6) link_BETA1-4 : bond 0.00184 ( 2) link_BETA1-4 : angle 3.11685 ( 6) hydrogen bonds : bond 0.03730 ( 508) hydrogen bonds : angle 4.15460 ( 1452) SS BOND : bond 0.00578 ( 8) SS BOND : angle 1.14510 ( 16) covalent geometry : bond 0.00225 ( 8328) covalent geometry : angle 0.96913 (11334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9402.97 seconds wall clock time: 161 minutes 36.29 seconds (9696.29 seconds total)