Starting phenix.real_space_refine on Thu Jun 5 17:11:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iuu_60914/06_2025/9iuu_60914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iuu_60914/06_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_60914/06_2025/9iuu_60914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iuu_60914/06_2025/9iuu_60914.map" model { file = "/net/cci-nas-00/data/ceres_data/9iuu_60914/06_2025/9iuu_60914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iuu_60914/06_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-5710/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: 5.33, per 1000 atoms: 0.82 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: 1.72 Conformation dependent library (CDL) restraints added in 940.7 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: 0.65 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: 1.60 Time building geometry restraints manager: 1.91 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: 2.770 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.530 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.610 ------------------------------------------------------------------------------- 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 : 0.716 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: 0.1717 time to fit residues: 18.2656 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 : 0.646 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126130 restraints weight = 8576.639| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.78 r_work: 0.3398 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.740 Fit side-chains REVERT: A 33 ASN cc_start: 0.8734 (m-40) cc_final: 0.8521 (m-40) REVERT: A 35 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: A 163 TRP cc_start: 0.6987 (t60) cc_final: 0.6604 (t60) REVERT: A 313 LYS cc_start: 0.8013 (tttt) cc_final: 0.7792 (ttpt) REVERT: B 400 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8564 (m-10) REVERT: B 428 ASP cc_start: 0.8909 (p0) cc_final: 0.8694 (p0) outliers start: 22 outliers final: 12 residues processed: 97 average time/residue: 0.1506 time to fit residues: 20.9788 Evaluate side-chains 87 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 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: 0.2980 chunk 31 optimal weight: 0.0010 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.146361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.126371 restraints weight = 8635.379| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.78 r_work: 0.3399 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6715 Z= 0.120 Angle : 0.500 7.307 9139 Z= 0.265 Chirality : 0.041 0.190 963 Planarity : 0.004 0.051 1172 Dihedral : 5.017 52.888 989 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.60 % Allowed : 14.82 % 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: 0.21 (0.29), residues: 787 helix: 1.27 (0.26), residues: 382 sheet: -1.37 (0.74), residues: 43 loop : -0.88 (0.32), residues: 362 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 369 TYR 0.012 0.001 TYR A 41 ARG 0.002 0.000 ARG B 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 6) link_NAG-ASN : angle 1.52369 ( 18) hydrogen bonds : bond 0.04722 ( 311) hydrogen bonds : angle 4.44839 ( 888) metal coordination : bond 0.00029 ( 2) SS BOND : bond 0.00745 ( 7) SS BOND : angle 1.69798 ( 14) covalent geometry : bond 0.00261 ( 6700) covalent geometry : angle 0.49149 ( 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 106 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.808 Fit side-chains REVERT: A 35 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: A 129 THR cc_start: 0.8142 (t) cc_final: 0.7909 (t) REVERT: A 163 TRP cc_start: 0.6969 (t60) cc_final: 0.6609 (t60) REVERT: A 435 GLU cc_start: 0.7451 (pt0) cc_final: 0.6957 (mt-10) REVERT: B 400 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8552 (m-10) outliers start: 25 outliers final: 14 residues processed: 100 average time/residue: 0.1634 time to fit residues: 24.4467 Evaluate side-chains 87 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 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 = 0.3705 r_free = 0.3705 target = 0.145165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124792 restraints weight = 8531.984| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.81 r_work: 0.3376 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6715 Z= 0.134 Angle : 0.507 6.824 9139 Z= 0.269 Chirality : 0.041 0.188 963 Planarity : 0.004 0.050 1172 Dihedral : 4.889 46.607 989 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.31 % Allowed : 15.40 % Favored : 81.29 % 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: 0.26 (0.29), residues: 787 helix: 1.31 (0.26), residues: 382 sheet: -1.36 (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 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 0.00241 ( 6) link_NAG-ASN : angle 1.51448 ( 18) hydrogen bonds : bond 0.04675 ( 311) hydrogen bonds : angle 4.34487 ( 888) metal coordination : bond 0.00041 ( 2) SS BOND : bond 0.00732 ( 7) SS BOND : angle 1.51586 ( 14) covalent geometry : bond 0.00301 ( 6700) covalent geometry : angle 0.50018 ( 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 100 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.747 Fit side-chains REVERT: A 35 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: A 73 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8546 (mt) REVERT: A 163 TRP cc_start: 0.7010 (t60) cc_final: 0.6667 (t60) REVERT: A 435 GLU cc_start: 0.7470 (pt0) cc_final: 0.7002 (mt-10) REVERT: B 400 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8605 (m-10) REVERT: B 428 ASP cc_start: 0.8898 (p0) cc_final: 0.8681 (p0) outliers start: 23 outliers final: 16 residues processed: 96 average time/residue: 0.1736 time to fit residues: 25.0000 Evaluate side-chains 90 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.142065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121664 restraints weight = 8485.950| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.78 r_work: 0.3339 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6715 Z= 0.180 Angle : 0.560 6.861 9139 Z= 0.294 Chirality : 0.043 0.188 963 Planarity : 0.004 0.050 1172 Dihedral : 4.998 46.158 989 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.03 % Allowed : 14.24 % 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: 0.14 (0.29), residues: 787 helix: 1.21 (0.25), residues: 382 sheet: -1.26 (0.74), residues: 43 loop : -0.93 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 353 HIS 0.004 0.001 HIS A 374 PHE 0.017 0.001 PHE A 369 TYR 0.016 0.001 TYR A 237 ARG 0.002 0.000 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 6) link_NAG-ASN : angle 1.70413 ( 18) hydrogen bonds : bond 0.05064 ( 311) hydrogen bonds : angle 4.43594 ( 888) metal coordination : bond 0.00028 ( 2) SS BOND : bond 0.00761 ( 7) SS BOND : angle 1.54802 ( 14) covalent geometry : bond 0.00421 ( 6700) covalent geometry : angle 0.55226 ( 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 104 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.917 Fit side-chains REVERT: A 35 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: A 73 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8619 (mt) REVERT: A 163 TRP cc_start: 0.6975 (t60) cc_final: 0.6750 (t60) REVERT: B 400 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8687 (m-10) outliers start: 28 outliers final: 16 residues processed: 98 average time/residue: 0.2322 time to fit residues: 34.0903 Evaluate side-chains 91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 52 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 64 optimal weight: 0.0050 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.143642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.122308 restraints weight = 8555.825| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.95 r_work: 0.3348 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1469 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= 0.129 Angle : 0.518 7.655 9139 Z= 0.273 Chirality : 0.042 0.189 963 Planarity : 0.004 0.049 1172 Dihedral : 4.800 44.755 989 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.60 % Allowed : 14.39 % Favored : 82.01 % 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: 0.28 (0.29), residues: 787 helix: 1.36 (0.25), residues: 382 sheet: -1.35 (0.74), residues: 43 loop : -0.88 (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 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 0.00249 ( 6) link_NAG-ASN : angle 1.59417 ( 18) hydrogen bonds : bond 0.04589 ( 311) hydrogen bonds : angle 4.35968 ( 888) metal coordination : bond 0.00030 ( 2) SS BOND : bond 0.00772 ( 7) SS BOND : angle 1.90024 ( 14) covalent geometry : bond 0.00289 ( 6700) covalent geometry : angle 0.50911 ( 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 104 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 1.266 Fit side-chains REVERT: A 35 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: A 163 TRP cc_start: 0.6849 (t60) cc_final: 0.6574 (t60) REVERT: A 435 GLU cc_start: 0.7805 (pt0) cc_final: 0.7210 (mp0) REVERT: B 400 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8616 (m-10) outliers start: 25 outliers final: 18 residues processed: 98 average time/residue: 0.1421 time to fit residues: 21.3119 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 : 0.689 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.0010 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 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 = 0.3698 r_free = 0.3698 target = 0.144112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122825 restraints weight = 8594.324| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.96 r_work: 0.3286 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6715 Z= 0.128 Angle : 0.520 6.938 9139 Z= 0.274 Chirality : 0.042 0.187 963 Planarity : 0.004 0.049 1172 Dihedral : 4.457 42.113 987 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.74 % Allowed : 14.10 % Favored : 82.16 % 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: 0.34 (0.29), residues: 787 helix: 1.39 (0.25), residues: 383 sheet: -1.32 (0.74), residues: 43 loop : -0.84 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.00252 ( 6) link_NAG-ASN : angle 1.53704 ( 18) hydrogen bonds : bond 0.04568 ( 311) hydrogen bonds : angle 4.33386 ( 888) metal coordination : bond 0.00013 ( 2) SS BOND : bond 0.00754 ( 7) SS BOND : angle 1.56171 ( 14) covalent geometry : bond 0.00287 ( 6700) covalent geometry : angle 0.51227 ( 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 102 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.711 Fit side-chains REVERT: A 35 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: A 163 TRP cc_start: 0.6846 (t60) cc_final: 0.6598 (t60) REVERT: B 400 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8630 (m-10) outliers start: 26 outliers final: 19 residues processed: 96 average time/residue: 0.1382 time to fit residues: 19.9481 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 : 0.707 ------------------------------------------------------------------------------- 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 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 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 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: 4.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** 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 = 0.3642 r_free = 0.3642 target = 0.139441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.118246 restraints weight = 8650.057| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.91 r_work: 0.3221 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6715 Z= 0.226 Angle : 0.613 8.702 9139 Z= 0.322 Chirality : 0.045 0.193 963 Planarity : 0.005 0.059 1172 Dihedral : 4.851 42.088 987 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.45 % Allowed : 15.68 % 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: 0.05 (0.29), residues: 787 helix: 1.16 (0.25), residues: 382 sheet: -1.32 (0.74), residues: 43 loop : -1.01 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 353 HIS 0.010 0.001 HIS A 34 PHE 0.018 0.002 PHE A 230 TYR 0.018 0.002 TYR A 237 ARG 0.005 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 6) link_NAG-ASN : angle 1.84411 ( 18) hydrogen bonds : bond 0.05331 ( 311) hydrogen bonds : angle 4.50940 ( 888) metal coordination : bond 0.00028 ( 2) SS BOND : bond 0.00924 ( 7) SS BOND : angle 1.82350 ( 14) covalent geometry : bond 0.00534 ( 6700) covalent geometry : angle 0.60442 ( 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 99 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.760 Fit side-chains REVERT: A 297 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7541 (mmt) REVERT: A 435 GLU cc_start: 0.7798 (pt0) cc_final: 0.7167 (mt-10) REVERT: B 400 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8772 (m-10) outliers start: 24 outliers final: 20 residues processed: 93 average time/residue: 0.1546 time to fit residues: 20.9531 Evaluate side-chains 94 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.139707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117408 restraints weight = 8762.620| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.07 r_work: 0.3260 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6715 Z= 0.129 Angle : 0.537 7.001 9139 Z= 0.282 Chirality : 0.042 0.195 963 Planarity : 0.004 0.049 1172 Dihedral : 4.335 38.359 984 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.17 % Allowed : 15.97 % 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: 0.23 (0.29), residues: 787 helix: 1.35 (0.25), residues: 382 sheet: -1.39 (0.75), residues: 43 loop : -0.95 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 353 HIS 0.008 0.001 HIS A 34 PHE 0.012 0.001 PHE A 230 TYR 0.015 0.001 TYR A 202 ARG 0.003 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 6) link_NAG-ASN : angle 1.64615 ( 18) hydrogen bonds : bond 0.04579 ( 311) hydrogen bonds : angle 4.43549 ( 888) metal coordination : bond 0.00043 ( 2) SS BOND : bond 0.00718 ( 7) SS BOND : angle 1.46119 ( 14) covalent geometry : bond 0.00287 ( 6700) covalent geometry : angle 0.52992 ( 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 97 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 5.579 Fit side-chains REVERT: A 297 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7546 (mmt) REVERT: A 435 GLU cc_start: 0.7847 (pt0) cc_final: 0.7207 (mp0) REVERT: B 400 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8687 (m-10) outliers start: 22 outliers final: 19 residues processed: 90 average time/residue: 0.1977 time to fit residues: 26.8898 Evaluate side-chains 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 418 ILE 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: 0.8980 chunk 2 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.137155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114381 restraints weight = 8920.190| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.14 r_work: 0.3271 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6715 Z= 0.135 Angle : 0.540 7.012 9139 Z= 0.285 Chirality : 0.042 0.189 963 Planarity : 0.004 0.049 1172 Dihedral : 4.282 37.936 984 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.17 % Allowed : 15.97 % 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: 0.31 (0.29), residues: 787 helix: 1.40 (0.25), residues: 383 sheet: -1.30 (0.76), residues: 43 loop : -0.90 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 353 HIS 0.009 0.001 HIS A 34 PHE 0.014 0.001 PHE A 230 TYR 0.012 0.001 TYR A 237 ARG 0.002 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 6) link_NAG-ASN : angle 1.58193 ( 18) hydrogen bonds : bond 0.04543 ( 311) hydrogen bonds : angle 4.44261 ( 888) metal coordination : bond 0.00029 ( 2) SS BOND : bond 0.00723 ( 7) SS BOND : angle 1.41587 ( 14) covalent geometry : bond 0.00305 ( 6700) covalent geometry : angle 0.53383 ( 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 95 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.882 Fit side-chains REVERT: A 297 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7579 (mmt) REVERT: B 400 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8666 (m-10) outliers start: 22 outliers final: 19 residues processed: 89 average time/residue: 0.2292 time to fit residues: 30.3474 Evaluate side-chains 91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 2.075 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 71 optimal weight: 0.0270 chunk 2 optimal weight: 0.7980 overall best weight: 0.7442 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.144009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122876 restraints weight = 8719.683| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.94 r_work: 0.3292 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6715 Z= 0.132 Angle : 0.540 6.752 9139 Z= 0.284 Chirality : 0.042 0.192 963 Planarity : 0.004 0.049 1172 Dihedral : 4.226 36.983 984 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.31 % Allowed : 15.83 % 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: 0.32 (0.29), residues: 787 helix: 1.43 (0.26), residues: 384 sheet: -1.29 (0.76), residues: 43 loop : -0.93 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 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 0.00238 ( 6) link_NAG-ASN : angle 1.56138 ( 18) hydrogen bonds : bond 0.04510 ( 311) hydrogen bonds : angle 4.43174 ( 888) metal coordination : bond 0.00023 ( 2) SS BOND : bond 0.00697 ( 7) SS BOND : angle 1.36978 ( 14) covalent geometry : bond 0.00299 ( 6700) covalent geometry : angle 0.53365 ( 9107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4193.66 seconds wall clock time: 76 minutes 39.15 seconds (4599.15 seconds total)