Starting phenix.real_space_refine on Sat May 10 15:39:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iuu_60914/05_2025/9iuu_60914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iuu_60914/05_2025/9iuu_60914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iuu_60914/05_2025/9iuu_60914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iuu_60914/05_2025/9iuu_60914.map" model { file = "/net/cci-nas-00/data/ceres_data/9iuu_60914/05_2025/9iuu_60914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iuu_60914/05_2025/9iuu_60914.cif" } resolution = 3.29 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= -0.001 sd= 0.050 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 Cl 1 4.86 5 C 4170 2.51 5 N 1072 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6513 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1557 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 13, 'TRANS': 180} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 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 Time building chain proxies: 4.78, per 1000 atoms: 0.73 Number of scatterers: 6513 At special positions: 0 Unit cell: (73.528, 87.264, 116.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 37 16.00 O 1232 8.00 N 1072 7.00 C 4170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 NAG-ASN " NAG A 903 " - " ASN A 546 " " NAG A 904 " - " ASN A 90 " " NAG A 905 " - " ASN A 322 " " NAG A 906 " - " ASN A 53 " " NAG B 601 " - " ASN B 354 " " NAG B 602 " - " ASN B 343 " Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 783.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 57.1% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.229A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 83 removed outlier: 3.564A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.860A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.943A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.593A pdb=" N ASN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.460A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.640A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.687A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.561A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.944A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.595A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.159A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.529A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.693A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.774A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.503A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.117A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.803A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.222A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 311 hydrogen bonds defined for protein. 888 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: 1.68 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1078 1.31 - 1.45: 1981 1.45 - 1.58: 3582 1.58 - 1.72: 1 1.72 - 1.85: 58 Bond restraints: 6700 Sorted by residual: bond pdb=" C LEU A 79 " pdb=" O LEU A 79 " ideal model delta sigma weight residual 1.237 1.368 -0.131 1.19e-02 7.06e+03 1.21e+02 bond pdb=" CA TYR A 83 " pdb=" C TYR A 83 " ideal model delta sigma weight residual 1.524 1.628 -0.104 1.26e-02 6.30e+03 6.86e+01 bond pdb=" C GLU A 75 " pdb=" O GLU A 75 " ideal model delta sigma weight residual 1.237 1.323 -0.087 1.17e-02 7.31e+03 5.49e+01 bond pdb=" N TYR A 83 " pdb=" CA TYR A 83 " ideal model delta sigma weight residual 1.457 1.550 -0.093 1.41e-02 5.03e+03 4.33e+01 bond pdb=" C THR A 78 " pdb=" O THR A 78 " ideal model delta sigma weight residual 1.236 1.306 -0.070 1.18e-02 7.18e+03 3.50e+01 ... (remaining 6695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 8877 2.50 - 5.01: 190 5.01 - 7.51: 36 7.51 - 10.02: 2 10.02 - 12.52: 2 Bond angle restraints: 9107 Sorted by residual: angle pdb=" N GLN A 81 " pdb=" CA GLN A 81 " pdb=" C GLN A 81 " ideal model delta sigma weight residual 111.07 101.98 9.09 1.07e+00 8.73e-01 7.21e+01 angle pdb=" N TYR A 83 " pdb=" CA TYR A 83 " pdb=" C TYR A 83 " ideal model delta sigma weight residual 109.81 122.20 -12.39 2.21e+00 2.05e-01 3.14e+01 angle pdb=" N GLU A 56 " pdb=" CA GLU A 56 " pdb=" C GLU A 56 " ideal model delta sigma weight residual 113.41 106.67 6.74 1.22e+00 6.72e-01 3.06e+01 angle pdb=" C GLU A 37 " pdb=" N ASP A 38 " pdb=" CA ASP A 38 " ideal model delta sigma weight residual 120.44 113.27 7.17 1.30e+00 5.92e-01 3.04e+01 angle pdb=" N GLU A 35 " pdb=" CA GLU A 35 " pdb=" C GLU A 35 " ideal model delta sigma weight residual 113.23 106.54 6.69 1.24e+00 6.50e-01 2.91e+01 ... (remaining 9102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3482 17.95 - 35.89: 412 35.89 - 53.84: 103 53.84 - 71.78: 18 71.78 - 89.73: 13 Dihedral angle restraints: 4028 sinusoidal: 1704 harmonic: 2324 Sorted by residual: dihedral pdb=" CA PHE B 400 " pdb=" C PHE B 400 " pdb=" N VAL B 401 " pdb=" CA VAL B 401 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 52.42 40.58 1 1.00e+01 1.00e-02 2.31e+01 dihedral pdb=" C ASN A 58 " pdb=" N ASN A 58 " pdb=" CA ASN A 58 " pdb=" CB ASN A 58 " ideal model delta harmonic sigma weight residual -122.60 -132.22 9.62 0 2.50e+00 1.60e-01 1.48e+01 ... (remaining 4025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 733 0.051 - 0.102: 194 0.102 - 0.154: 26 0.154 - 0.205: 8 0.205 - 0.256: 2 Chirality restraints: 963 Sorted by residual: chirality pdb=" CA ASN A 58 " pdb=" N ASN A 58 " pdb=" C ASN A 58 " pdb=" CB ASN A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB THR A 229 " pdb=" CA THR A 229 " pdb=" OG1 THR A 229 " pdb=" CG2 THR A 229 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA TYR B 501 " pdb=" N TYR B 501 " pdb=" C TYR B 501 " pdb=" CB TYR B 501 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 960 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 83 " -0.039 2.00e-02 2.50e+03 7.58e-02 5.74e+01 pdb=" C TYR A 83 " 0.131 2.00e-02 2.50e+03 pdb=" O TYR A 83 " -0.045 2.00e-02 2.50e+03 pdb=" N PRO A 84 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 346 " -0.567 9.50e-02 1.11e+02 2.54e-01 3.94e+01 pdb=" NE ARG B 346 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG B 346 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 346 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 346 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 498 " -0.364 9.50e-02 1.11e+02 1.63e-01 1.64e+01 pdb=" NE ARG B 498 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 498 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 498 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 498 " -0.011 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1573 2.78 - 3.31: 6157 3.31 - 3.84: 11023 3.84 - 4.37: 12725 4.37 - 4.90: 22336 Nonbonded interactions: 53814 Sorted by model distance: nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.254 3.040 nonbonded pdb=" O THR A 129 " pdb=" OG1 THR A 129 " model vdw 2.260 3.040 nonbonded pdb=" O ASN A 103 " pdb=" OG SER A 106 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.268 3.040 nonbonded pdb=" NE2 GLN B 474 " pdb=" O GLY B 476 " model vdw 2.288 3.120 ... (remaining 53809 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.280 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 0.131 6715 Z= 0.423 Angle : 0.857 12.524 9139 Z= 0.547 Chirality : 0.049 0.256 963 Planarity : 0.011 0.254 1172 Dihedral : 16.624 89.727 2515 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.86 % Allowed : 16.98 % Favored : 82.16 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.29), residues: 787 helix: 0.62 (0.26), residues: 379 sheet: -1.49 (0.72), residues: 45 loop : -0.99 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 163 HIS 0.007 0.001 HIS A 34 PHE 0.022 0.002 PHE A 32 TYR 0.014 0.001 TYR A 237 ARG 0.005 0.001 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 6) link_NAG-ASN : angle 1.60995 ( 18) hydrogen bonds : bond 0.15724 ( 311) hydrogen bonds : angle 6.39351 ( 888) metal coordination : bond 0.00040 ( 2) SS BOND : bond 0.00743 ( 7) SS BOND : angle 1.92410 ( 14) covalent geometry : bond 0.00643 ( 6700) covalent geometry : angle 0.85185 ( 9107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.670 Fit side-chains REVERT: A 35 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8115 (mm-30) REVERT: A 313 LYS cc_start: 0.8136 (tttt) cc_final: 0.7892 (ttpt) outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 0.1651 time to fit residues: 17.6190 Evaluate side-chains 73 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain B residue 349 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 60 GLN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126130 restraints weight = 8576.639| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.78 r_work: 0.3322 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6715 Z= 0.130 Angle : 0.521 5.776 9139 Z= 0.279 Chirality : 0.042 0.195 963 Planarity : 0.004 0.051 1172 Dihedral : 5.642 60.385 993 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.17 % Allowed : 14.96 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.29), residues: 787 helix: 1.12 (0.26), residues: 381 sheet: -1.30 (0.75), residues: 43 loop : -0.91 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 69 HIS 0.004 0.001 HIS A 374 PHE 0.013 0.001 PHE A 230 TYR 0.019 0.001 TYR A 41 ARG 0.002 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 6) link_NAG-ASN : angle 1.50237 ( 18) hydrogen bonds : bond 0.05293 ( 311) hydrogen bonds : angle 4.67010 ( 888) metal coordination : bond 0.00042 ( 2) SS BOND : bond 0.00660 ( 7) SS BOND : angle 1.40865 ( 14) covalent geometry : bond 0.00281 ( 6700) covalent geometry : angle 0.51428 ( 9107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.700 Fit side-chains REVERT: A 33 ASN cc_start: 0.8713 (m-40) cc_final: 0.8508 (m-40) REVERT: A 35 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: A 163 TRP cc_start: 0.6892 (t60) cc_final: 0.6500 (t60) REVERT: A 313 LYS cc_start: 0.7891 (tttt) cc_final: 0.7668 (ttpt) REVERT: A 335 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.7105 (m-30) REVERT: B 400 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8576 (m-10) REVERT: B 428 ASP cc_start: 0.8910 (p0) cc_final: 0.8696 (p0) outliers start: 22 outliers final: 12 residues processed: 97 average time/residue: 0.1489 time to fit residues: 20.6917 Evaluate side-chains 88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124392 restraints weight = 8514.414| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.79 r_work: 0.3384 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6715 Z= 0.136 Angle : 0.517 7.820 9139 Z= 0.274 Chirality : 0.042 0.191 963 Planarity : 0.004 0.051 1172 Dihedral : 5.077 51.718 989 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.03 % Allowed : 14.82 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.29), residues: 787 helix: 1.22 (0.26), residues: 381 sheet: -1.36 (0.74), residues: 43 loop : -0.91 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 69 HIS 0.004 0.001 HIS A 374 PHE 0.014 0.001 PHE A 369 TYR 0.013 0.001 TYR A 237 ARG 0.002 0.000 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 6) link_NAG-ASN : angle 1.58666 ( 18) hydrogen bonds : bond 0.04892 ( 311) hydrogen bonds : angle 4.47383 ( 888) metal coordination : bond 0.00030 ( 2) SS BOND : bond 0.00804 ( 7) SS BOND : angle 1.82292 ( 14) covalent geometry : bond 0.00306 ( 6700) covalent geometry : angle 0.50797 ( 9107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.690 Fit side-chains REVERT: A 35 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: A 129 THR cc_start: 0.8121 (t) cc_final: 0.7892 (t) REVERT: A 163 TRP cc_start: 0.6869 (t60) cc_final: 0.6516 (t60) REVERT: A 335 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7224 (m-30) REVERT: A 435 GLU cc_start: 0.7584 (pt0) cc_final: 0.6983 (mt-10) REVERT: B 400 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8615 (m-10) outliers start: 28 outliers final: 16 residues processed: 103 average time/residue: 0.1280 time to fit residues: 19.4895 Evaluate side-chains 92 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 0.0770 chunk 14 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.145537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125258 restraints weight = 8535.762| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.81 r_work: 0.3393 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6715 Z= 0.126 Angle : 0.507 6.623 9139 Z= 0.268 Chirality : 0.041 0.187 963 Planarity : 0.004 0.050 1172 Dihedral : 4.865 46.428 989 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.60 % Allowed : 15.40 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.29), residues: 787 helix: 1.33 (0.26), residues: 382 sheet: -1.37 (0.73), residues: 43 loop : -0.86 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 69 HIS 0.004 0.001 HIS A 34 PHE 0.013 0.001 PHE A 369 TYR 0.012 0.001 TYR A 237 ARG 0.002 0.000 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 6) link_NAG-ASN : angle 1.50377 ( 18) hydrogen bonds : bond 0.04604 ( 311) hydrogen bonds : angle 4.34129 ( 888) metal coordination : bond 0.00038 ( 2) SS BOND : bond 0.00698 ( 7) SS BOND : angle 1.47604 ( 14) covalent geometry : bond 0.00280 ( 6700) covalent geometry : angle 0.49993 ( 9107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.778 Fit side-chains REVERT: A 35 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: A 73 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8499 (mt) REVERT: A 163 TRP cc_start: 0.6951 (t60) cc_final: 0.6683 (t60) REVERT: A 335 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: A 435 GLU cc_start: 0.7521 (pt0) cc_final: 0.6994 (mt-10) REVERT: B 400 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8578 (m-10) REVERT: B 428 ASP cc_start: 0.8957 (p0) cc_final: 0.8755 (p0) outliers start: 25 outliers final: 17 residues processed: 98 average time/residue: 0.1369 time to fit residues: 19.8439 Evaluate side-chains 92 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS B 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124694 restraints weight = 8506.089| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.80 r_work: 0.3290 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6715 Z= 0.130 Angle : 0.507 6.132 9139 Z= 0.267 Chirality : 0.041 0.185 963 Planarity : 0.004 0.050 1172 Dihedral : 4.775 45.527 989 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.32 % Allowed : 14.10 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.29), residues: 787 helix: 1.38 (0.26), residues: 382 sheet: -1.33 (0.74), residues: 43 loop : -0.83 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 PHE 0.013 0.001 PHE A 369 TYR 0.012 0.001 TYR A 237 ARG 0.001 0.000 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 6) link_NAG-ASN : angle 1.51860 ( 18) hydrogen bonds : bond 0.04567 ( 311) hydrogen bonds : angle 4.32322 ( 888) metal coordination : bond 0.00021 ( 2) SS BOND : bond 0.00644 ( 7) SS BOND : angle 1.33712 ( 14) covalent geometry : bond 0.00291 ( 6700) covalent geometry : angle 0.50098 ( 9107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.744 Fit side-chains REVERT: A 35 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: A 163 TRP cc_start: 0.6865 (t60) cc_final: 0.6565 (t60) REVERT: A 335 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.7110 (m-30) REVERT: A 435 GLU cc_start: 0.7618 (pt0) cc_final: 0.7108 (mp0) REVERT: B 400 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8620 (m-10) REVERT: B 428 ASP cc_start: 0.8928 (p0) cc_final: 0.8714 (p0) outliers start: 30 outliers final: 18 residues processed: 100 average time/residue: 0.1322 time to fit residues: 19.5826 Evaluate side-chains 94 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 52 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 60 GLN A 194 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.137902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117420 restraints weight = 8535.924| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.78 r_work: 0.3311 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6715 Z= 0.229 Angle : 0.620 9.554 9139 Z= 0.326 Chirality : 0.046 0.194 963 Planarity : 0.005 0.063 1172 Dihedral : 4.992 43.045 987 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.32 % Allowed : 13.96 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.29), residues: 787 helix: 1.10 (0.25), residues: 381 sheet: -1.31 (0.74), residues: 43 loop : -0.99 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 606 HIS 0.006 0.001 HIS A 241 PHE 0.019 0.002 PHE A 230 TYR 0.019 0.002 TYR A 237 ARG 0.003 0.000 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 6) link_NAG-ASN : angle 1.89980 ( 18) hydrogen bonds : bond 0.05510 ( 311) hydrogen bonds : angle 4.55600 ( 888) metal coordination : bond 0.00029 ( 2) SS BOND : bond 0.01094 ( 7) SS BOND : angle 2.23789 ( 14) covalent geometry : bond 0.00539 ( 6700) covalent geometry : angle 0.60888 ( 9107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.783 Fit side-chains REVERT: A 35 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: A 435 GLU cc_start: 0.7602 (pt0) cc_final: 0.7164 (mt-10) REVERT: B 400 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8726 (m-10) outliers start: 30 outliers final: 21 residues processed: 102 average time/residue: 0.1295 time to fit residues: 19.7478 Evaluate side-chains 90 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117418 restraints weight = 8709.915| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.13 r_work: 0.3290 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6715 Z= 0.114 Angle : 0.510 6.845 9139 Z= 0.270 Chirality : 0.041 0.192 963 Planarity : 0.004 0.049 1172 Dihedral : 4.509 42.834 987 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.59 % Allowed : 15.54 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.29), residues: 787 helix: 1.33 (0.25), residues: 383 sheet: -1.40 (0.74), residues: 43 loop : -0.89 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 69 HIS 0.004 0.001 HIS A 374 PHE 0.011 0.001 PHE A 369 TYR 0.010 0.001 TYR A 41 ARG 0.001 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 6) link_NAG-ASN : angle 1.58338 ( 18) hydrogen bonds : bond 0.04435 ( 311) hydrogen bonds : angle 4.36027 ( 888) metal coordination : bond 0.00034 ( 2) SS BOND : bond 0.00737 ( 7) SS BOND : angle 1.57494 ( 14) covalent geometry : bond 0.00243 ( 6700) covalent geometry : angle 0.50249 ( 9107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.711 Fit side-chains REVERT: A 297 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7529 (mmt) REVERT: A 435 GLU cc_start: 0.7837 (pt0) cc_final: 0.7190 (mp0) REVERT: B 400 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8610 (m-10) outliers start: 18 outliers final: 14 residues processed: 88 average time/residue: 0.1329 time to fit residues: 17.3581 Evaluate side-chains 86 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 31 optimal weight: 0.0000 chunk 46 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110513 restraints weight = 8848.426| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.11 r_work: 0.3209 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 6715 Z= 0.229 Angle : 0.621 8.819 9139 Z= 0.327 Chirality : 0.045 0.195 963 Planarity : 0.005 0.056 1172 Dihedral : 4.672 40.410 984 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.31 % Allowed : 15.97 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.29), residues: 787 helix: 1.14 (0.25), residues: 382 sheet: -1.39 (0.74), residues: 43 loop : -1.03 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 353 HIS 0.011 0.002 HIS A 34 PHE 0.019 0.002 PHE A 230 TYR 0.018 0.002 TYR A 237 ARG 0.003 0.000 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 6) link_NAG-ASN : angle 1.86646 ( 18) hydrogen bonds : bond 0.05365 ( 311) hydrogen bonds : angle 4.54332 ( 888) metal coordination : bond 0.00024 ( 2) SS BOND : bond 0.00944 ( 7) SS BOND : angle 1.85097 ( 14) covalent geometry : bond 0.00544 ( 6700) covalent geometry : angle 0.61223 ( 9107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.756 Fit side-chains REVERT: A 297 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7552 (mmt) REVERT: A 435 GLU cc_start: 0.7874 (pt0) cc_final: 0.7173 (mt-10) REVERT: B 400 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8813 (m-10) outliers start: 23 outliers final: 19 residues processed: 88 average time/residue: 0.1434 time to fit residues: 18.7056 Evaluate side-chains 89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.144155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123346 restraints weight = 8651.923| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.88 r_work: 0.3326 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6715 Z= 0.125 Angle : 0.530 6.754 9139 Z= 0.280 Chirality : 0.042 0.195 963 Planarity : 0.004 0.049 1172 Dihedral : 4.305 37.835 984 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.02 % Allowed : 16.12 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.29), residues: 787 helix: 1.35 (0.25), residues: 383 sheet: -1.39 (0.75), residues: 43 loop : -0.89 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 353 HIS 0.008 0.001 HIS A 34 PHE 0.013 0.001 PHE A 230 TYR 0.014 0.001 TYR A 202 ARG 0.002 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 6) link_NAG-ASN : angle 1.61370 ( 18) hydrogen bonds : bond 0.04516 ( 311) hydrogen bonds : angle 4.38695 ( 888) metal coordination : bond 0.00045 ( 2) SS BOND : bond 0.00698 ( 7) SS BOND : angle 1.44578 ( 14) covalent geometry : bond 0.00279 ( 6700) covalent geometry : angle 0.52333 ( 9107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.729 Fit side-chains REVERT: A 297 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7488 (mmt) REVERT: A 435 GLU cc_start: 0.7782 (pt0) cc_final: 0.7204 (mp0) REVERT: B 400 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8669 (m-10) outliers start: 21 outliers final: 18 residues processed: 89 average time/residue: 0.1400 time to fit residues: 18.1235 Evaluate side-chains 92 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 76 optimal weight: 0.4980 chunk 74 optimal weight: 0.0010 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.142377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.120091 restraints weight = 8788.986| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.11 r_work: 0.3321 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6715 Z= 0.109 Angle : 0.499 5.695 9139 Z= 0.264 Chirality : 0.041 0.193 963 Planarity : 0.004 0.049 1172 Dihedral : 3.981 33.922 984 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.30 % Allowed : 16.83 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.29), residues: 787 helix: 1.57 (0.26), residues: 384 sheet: -1.20 (0.77), residues: 43 loop : -0.85 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 69 HIS 0.007 0.001 HIS A 34 PHE 0.012 0.001 PHE A 230 TYR 0.010 0.001 TYR A 41 ARG 0.001 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 6) link_NAG-ASN : angle 1.41767 ( 18) hydrogen bonds : bond 0.04128 ( 311) hydrogen bonds : angle 4.31599 ( 888) metal coordination : bond 0.00055 ( 2) SS BOND : bond 0.00614 ( 7) SS BOND : angle 1.25084 ( 14) covalent geometry : bond 0.00234 ( 6700) covalent geometry : angle 0.49339 ( 9107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.802 Fit side-chains REVERT: A 297 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7421 (mmt) REVERT: B 400 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8503 (m-10) outliers start: 16 outliers final: 12 residues processed: 87 average time/residue: 0.1361 time to fit residues: 17.5364 Evaluate side-chains 88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 71 optimal weight: 0.0570 chunk 2 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123525 restraints weight = 8732.760| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.07 r_work: 0.3342 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6715 Z= 0.121 Angle : 0.516 6.007 9139 Z= 0.274 Chirality : 0.041 0.189 963 Planarity : 0.004 0.049 1172 Dihedral : 4.019 34.289 984 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.59 % Allowed : 16.83 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.30), residues: 787 helix: 1.54 (0.26), residues: 385 sheet: -1.19 (0.76), residues: 43 loop : -0.79 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 163 HIS 0.008 0.001 HIS A 34 PHE 0.013 0.001 PHE A 369 TYR 0.014 0.001 TYR A 202 ARG 0.001 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 6) link_NAG-ASN : angle 1.43056 ( 18) hydrogen bonds : bond 0.04287 ( 311) hydrogen bonds : angle 4.35977 ( 888) metal coordination : bond 0.00008 ( 2) SS BOND : bond 0.00643 ( 7) SS BOND : angle 1.27403 ( 14) covalent geometry : bond 0.00269 ( 6700) covalent geometry : angle 0.51030 ( 9107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3434.63 seconds wall clock time: 60 minutes 20.59 seconds (3620.59 seconds total)