Starting phenix.real_space_refine on Wed Sep 17 07:06:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iuu_60914/09_2025/9iuu_60914.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iuu_60914/09_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_60914/09_2025/9iuu_60914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iuu_60914/09_2025/9iuu_60914.map" model { file = "/net/cci-nas-00/data/ceres_data/9iuu_60914/09_2025/9iuu_60914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iuu_60914/09_2025/9iuu_60914.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.55, per 1000 atoms: 0.24 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: 0.58 Conformation dependent library (CDL) restraints added in 382.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.16 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: 0.89 Time building geometry restraints manager: 0.76 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: 3.090 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.560 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.160 ------------------------------------------------------------------------------- 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 : 9.53 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG B 498 TYR 0.014 0.001 TYR A 237 PHE 0.022 0.002 PHE A 32 TRP 0.031 0.001 TRP A 163 HIS 0.007 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00643 ( 6700) covalent geometry : angle 0.85185 ( 9107) SS BOND : bond 0.00743 ( 7) SS BOND : angle 1.92410 ( 14) hydrogen bonds : bond 0.15724 ( 311) hydrogen bonds : angle 6.39351 ( 888) metal coordination : bond 0.00040 ( 2) link_NAG-ASN : bond 0.00254 ( 6) link_NAG-ASN : angle 1.60995 ( 18) *********************** 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 : 0.267 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: 0.0794 time to fit residues: 8.4586 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 : 0.251 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.144245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124165 restraints weight = 8713.964| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.80 r_work: 0.3292 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6715 Z= 0.155 Angle : 0.543 5.978 9139 Z= 0.291 Chirality : 0.043 0.196 963 Planarity : 0.004 0.051 1172 Dihedral : 5.764 59.714 993 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.31 % Allowed : 14.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.29), residues: 787 helix: 1.03 (0.26), residues: 381 sheet: -1.32 (0.75), residues: 43 loop : -0.95 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 498 TYR 0.018 0.001 TYR A 41 PHE 0.015 0.001 PHE A 230 TRP 0.010 0.001 TRP B 353 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6700) covalent geometry : angle 0.53677 ( 9107) SS BOND : bond 0.00699 ( 7) SS BOND : angle 1.50386 ( 14) hydrogen bonds : bond 0.05513 ( 311) hydrogen bonds : angle 4.70933 ( 888) metal coordination : bond 0.00057 ( 2) link_NAG-ASN : bond 0.00244 ( 6) link_NAG-ASN : angle 1.55729 ( 18) *********************** 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: 23 poor density : 81 time to evaluate : 0.236 Fit side-chains REVERT: A 35 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: A 163 TRP cc_start: 0.6903 (t60) cc_final: 0.6547 (t60) REVERT: A 313 LYS cc_start: 0.7905 (tttt) cc_final: 0.7677 (ttpt) REVERT: B 400 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8645 (m-10) outliers start: 23 outliers final: 11 residues processed: 97 average time/residue: 0.0682 time to fit residues: 9.5032 Evaluate side-chains 84 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 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 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 71 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 0.0670 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 11 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.146163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126308 restraints weight = 8458.805| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.75 r_work: 0.3399 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6715 Z= 0.117 Angle : 0.504 7.400 9139 Z= 0.266 Chirality : 0.041 0.189 963 Planarity : 0.004 0.050 1172 Dihedral : 5.193 52.126 992 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.17 % Allowed : 15.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.29), residues: 787 helix: 1.25 (0.26), residues: 382 sheet: -1.34 (0.75), residues: 43 loop : -0.86 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.012 0.001 TYR A 41 PHE 0.013 0.001 PHE A 369 TRP 0.010 0.001 TRP A 69 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 6700) covalent geometry : angle 0.49545 ( 9107) SS BOND : bond 0.00762 ( 7) SS BOND : angle 1.76990 ( 14) hydrogen bonds : bond 0.04664 ( 311) hydrogen bonds : angle 4.43669 ( 888) metal coordination : bond 0.00044 ( 2) link_NAG-ASN : bond 0.00249 ( 6) link_NAG-ASN : angle 1.52742 ( 18) *********************** 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 104 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.286 Fit side-chains REVERT: A 35 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: A 73 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8420 (mt) REVERT: A 129 THR cc_start: 0.8133 (t) cc_final: 0.7909 (t) REVERT: A 163 TRP cc_start: 0.6973 (t60) cc_final: 0.6613 (t60) REVERT: A 435 GLU cc_start: 0.7434 (pt0) cc_final: 0.6907 (mt-10) REVERT: B 400 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.8538 (m-10) outliers start: 22 outliers final: 12 residues processed: 99 average time/residue: 0.0612 time to fit residues: 9.1197 Evaluate side-chains 87 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 487 VAL Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 336 CYS 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 35 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 68 optimal weight: 0.0270 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.146251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.125965 restraints weight = 8522.311| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.81 r_work: 0.3310 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1333 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= 0.117 Angle : 0.494 6.557 9139 Z= 0.261 Chirality : 0.041 0.185 963 Planarity : 0.004 0.050 1172 Dihedral : 4.977 46.288 992 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.29), residues: 787 helix: 1.39 (0.26), residues: 382 sheet: -1.33 (0.73), residues: 43 loop : -0.79 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 498 TYR 0.011 0.001 TYR A 237 PHE 0.013 0.001 PHE A 369 TRP 0.009 0.001 TRP A 69 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6700) covalent geometry : angle 0.48680 ( 9107) SS BOND : bond 0.00677 ( 7) SS BOND : angle 1.45595 ( 14) hydrogen bonds : bond 0.04498 ( 311) hydrogen bonds : angle 4.30613 ( 888) metal coordination : bond 0.00024 ( 2) link_NAG-ASN : bond 0.00247 ( 6) link_NAG-ASN : angle 1.45563 ( 18) *********************** 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 103 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.237 Fit side-chains REVERT: A 35 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: A 73 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8432 (mt) REVERT: A 163 TRP cc_start: 0.6846 (t60) cc_final: 0.6540 (t60) REVERT: A 435 GLU cc_start: 0.7645 (pt0) cc_final: 0.6963 (mt-10) REVERT: B 400 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8599 (m-10) outliers start: 25 outliers final: 17 residues processed: 98 average time/residue: 0.0546 time to fit residues: 8.0112 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 : 0.153 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 0.0270 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 0.0020 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 overall best weight: 0.5848 ------------------------------------------------------------------------------- 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 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.146173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.125950 restraints weight = 8542.186| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.80 r_work: 0.3302 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1451 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= 0.116 Angle : 0.491 5.961 9139 Z= 0.259 Chirality : 0.040 0.184 963 Planarity : 0.004 0.050 1172 Dihedral : 4.680 45.156 989 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.03 % Allowed : 13.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.29), residues: 787 helix: 1.45 (0.26), residues: 383 sheet: -1.23 (0.73), residues: 43 loop : -0.76 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 498 TYR 0.011 0.001 TYR A 237 PHE 0.012 0.001 PHE A 369 TRP 0.008 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 6700) covalent geometry : angle 0.48569 ( 9107) SS BOND : bond 0.00624 ( 7) SS BOND : angle 1.23249 ( 14) hydrogen bonds : bond 0.04359 ( 311) hydrogen bonds : angle 4.26925 ( 888) metal coordination : bond 0.00024 ( 2) link_NAG-ASN : bond 0.00251 ( 6) link_NAG-ASN : angle 1.44828 ( 18) *********************** 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 106 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.245 Fit side-chains REVERT: A 35 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: A 163 TRP cc_start: 0.6815 (t60) cc_final: 0.6484 (t60) REVERT: A 435 GLU cc_start: 0.7642 (pt0) cc_final: 0.6984 (mt-10) REVERT: B 400 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8583 (m-10) outliers start: 28 outliers final: 17 residues processed: 97 average time/residue: 0.0569 time to fit residues: 8.2939 Evaluate side-chains 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 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 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 0.0980 chunk 56 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 0.0770 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS 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 = 0.3738 r_free = 0.3738 target = 0.147838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127774 restraints weight = 8512.337| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.81 r_work: 0.3341 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6715 Z= 0.104 Angle : 0.480 6.355 9139 Z= 0.254 Chirality : 0.040 0.186 963 Planarity : 0.004 0.050 1172 Dihedral : 4.296 40.099 987 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.17 % Allowed : 14.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.30), residues: 787 helix: 1.61 (0.26), residues: 382 sheet: -1.25 (0.73), residues: 43 loop : -0.74 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.010 0.001 TYR A 41 PHE 0.011 0.001 PHE A 230 TRP 0.009 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 6700) covalent geometry : angle 0.47268 ( 9107) SS BOND : bond 0.00637 ( 7) SS BOND : angle 1.63350 ( 14) hydrogen bonds : bond 0.04140 ( 311) hydrogen bonds : angle 4.23372 ( 888) metal coordination : bond 0.00019 ( 2) link_NAG-ASN : bond 0.00285 ( 6) link_NAG-ASN : angle 1.40679 ( 18) *********************** 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 102 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.268 Fit side-chains REVERT: A 35 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: A 163 TRP cc_start: 0.6846 (t60) cc_final: 0.6544 (t60) REVERT: A 435 GLU cc_start: 0.7623 (pt0) cc_final: 0.7040 (mt-10) REVERT: A 474 MET cc_start: 0.8240 (mmp) cc_final: 0.8008 (mmp) REVERT: B 400 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8488 (m-10) outliers start: 22 outliers final: 15 residues processed: 96 average time/residue: 0.0612 time to fit residues: 8.7585 Evaluate side-chains 93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.145181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124920 restraints weight = 8468.746| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.80 r_work: 0.3303 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1580 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= 0.137 Angle : 0.515 6.862 9139 Z= 0.271 Chirality : 0.042 0.186 963 Planarity : 0.004 0.049 1172 Dihedral : 4.357 40.106 987 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.29), residues: 787 helix: 1.52 (0.26), residues: 383 sheet: -1.19 (0.74), residues: 43 loop : -0.76 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 355 TYR 0.013 0.001 TYR A 237 PHE 0.014 0.001 PHE A 369 TRP 0.008 0.001 TRP A 165 HIS 0.010 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6700) covalent geometry : angle 0.50862 ( 9107) SS BOND : bond 0.00757 ( 7) SS BOND : angle 1.53488 ( 14) hydrogen bonds : bond 0.04490 ( 311) hydrogen bonds : angle 4.27476 ( 888) metal coordination : bond 0.00012 ( 2) link_NAG-ASN : bond 0.00249 ( 6) link_NAG-ASN : angle 1.48112 ( 18) *********************** 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 99 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.250 Fit side-chains REVERT: A 35 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: A 163 TRP cc_start: 0.6864 (t60) cc_final: 0.6630 (t60) REVERT: A 435 GLU cc_start: 0.7708 (pt0) cc_final: 0.7162 (mt-10) REVERT: A 474 MET cc_start: 0.8282 (mmp) cc_final: 0.7913 (mmp) REVERT: B 400 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8586 (m-10) REVERT: B 428 ASP cc_start: 0.8885 (p0) cc_final: 0.8665 (p0) outliers start: 22 outliers final: 18 residues processed: 94 average time/residue: 0.0585 time to fit residues: 8.2771 Evaluate side-chains 94 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU 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 58 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 23 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3652 r_free = 0.3652 target = 0.140422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117830 restraints weight = 8790.654| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.11 r_work: 0.3307 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1712 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= 0.115 Angle : 0.495 6.370 9139 Z= 0.261 Chirality : 0.041 0.188 963 Planarity : 0.004 0.049 1172 Dihedral : 4.256 40.122 987 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.74 % Allowed : 14.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.29), residues: 787 helix: 1.60 (0.26), residues: 382 sheet: -1.24 (0.74), residues: 43 loop : -0.75 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 219 TYR 0.014 0.001 TYR A 202 PHE 0.012 0.001 PHE A 369 TRP 0.008 0.001 TRP A 165 HIS 0.007 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6700) covalent geometry : angle 0.48850 ( 9107) SS BOND : bond 0.00671 ( 7) SS BOND : angle 1.35000 ( 14) hydrogen bonds : bond 0.04270 ( 311) hydrogen bonds : angle 4.22618 ( 888) metal coordination : bond 0.00018 ( 2) link_NAG-ASN : bond 0.00261 ( 6) link_NAG-ASN : angle 1.44174 ( 18) *********************** 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 102 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.280 Fit side-chains REVERT: A 163 TRP cc_start: 0.6793 (t60) cc_final: 0.6553 (t60) REVERT: A 474 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7846 (mmp) REVERT: B 400 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8613 (m-10) REVERT: B 428 ASP cc_start: 0.8930 (p0) cc_final: 0.8716 (p0) outliers start: 26 outliers final: 21 residues processed: 93 average time/residue: 0.0593 time to fit residues: 8.3813 Evaluate side-chains 95 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 364 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 474 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.119074 restraints weight = 8781.914| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.11 r_work: 0.3293 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6715 Z= 0.136 Angle : 0.521 6.815 9139 Z= 0.273 Chirality : 0.041 0.187 963 Planarity : 0.004 0.049 1172 Dihedral : 4.102 36.700 984 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.60 % Allowed : 15.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.29), residues: 787 helix: 1.55 (0.26), residues: 383 sheet: -1.22 (0.74), residues: 43 loop : -0.75 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.014 0.001 TYR A 237 PHE 0.013 0.001 PHE A 369 TRP 0.008 0.001 TRP A 165 HIS 0.007 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6700) covalent geometry : angle 0.51470 ( 9107) SS BOND : bond 0.00712 ( 7) SS BOND : angle 1.38724 ( 14) hydrogen bonds : bond 0.04425 ( 311) hydrogen bonds : angle 4.31651 ( 888) metal coordination : bond 0.00018 ( 2) link_NAG-ASN : bond 0.00234 ( 6) link_NAG-ASN : angle 1.49667 ( 18) *********************** 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 100 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.268 Fit side-chains REVERT: A 435 GLU cc_start: 0.7879 (pt0) cc_final: 0.7193 (mt-10) REVERT: A 474 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7823 (mmp) REVERT: B 400 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8638 (m-10) REVERT: B 428 ASP cc_start: 0.8918 (p0) cc_final: 0.8715 (p0) outliers start: 25 outliers final: 20 residues processed: 91 average time/residue: 0.0592 time to fit residues: 8.1542 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 : 0.247 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 364 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 474 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 73 optimal weight: 0.0770 chunk 75 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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** A 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.120153 restraints weight = 8622.804| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.08 r_work: 0.3335 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1795 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= 0.114 Angle : 0.508 6.103 9139 Z= 0.267 Chirality : 0.041 0.188 963 Planarity : 0.004 0.049 1172 Dihedral : 4.019 35.910 984 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.17 % Allowed : 15.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.30), residues: 787 helix: 1.59 (0.26), residues: 384 sheet: -1.19 (0.74), residues: 43 loop : -0.74 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 582 TYR 0.014 0.001 TYR A 202 PHE 0.012 0.001 PHE A 230 TRP 0.008 0.001 TRP A 165 HIS 0.007 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 6700) covalent geometry : angle 0.50242 ( 9107) SS BOND : bond 0.00632 ( 7) SS BOND : angle 1.25939 ( 14) hydrogen bonds : bond 0.04238 ( 311) hydrogen bonds : angle 4.34064 ( 888) metal coordination : bond 0.00024 ( 2) link_NAG-ASN : bond 0.00256 ( 6) link_NAG-ASN : angle 1.42962 ( 18) ********************** 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 96 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.284 Fit side-chains REVERT: A 435 GLU cc_start: 0.7814 (pt0) cc_final: 0.7164 (mt-10) REVERT: A 474 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7856 (mmp) REVERT: B 400 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8610 (m-10) outliers start: 22 outliers final: 19 residues processed: 87 average time/residue: 0.0597 time to fit residues: 7.8277 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 : 0.258 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 474 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 67 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- 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 = 0.144577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122571 restraints weight = 8605.100| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.06 r_work: 0.3366 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6715 Z= 0.123 Angle : 0.513 6.254 9139 Z= 0.270 Chirality : 0.041 0.188 963 Planarity : 0.004 0.049 1172 Dihedral : 4.024 36.010 984 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.30), residues: 787 helix: 1.62 (0.26), residues: 384 sheet: -1.18 (0.74), residues: 43 loop : -0.75 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.012 0.001 TYR A 237 PHE 0.013 0.001 PHE A 369 TRP 0.030 0.001 TRP A 163 HIS 0.008 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6700) covalent geometry : angle 0.50773 ( 9107) SS BOND : bond 0.00652 ( 7) SS BOND : angle 1.27657 ( 14) hydrogen bonds : bond 0.04312 ( 311) hydrogen bonds : angle 4.31953 ( 888) metal coordination : bond 0.00017 ( 2) link_NAG-ASN : bond 0.00244 ( 6) link_NAG-ASN : angle 1.43203 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1748.50 seconds wall clock time: 30 minutes 48.16 seconds (1848.16 seconds total)